Flawfinder version 2.0.10, (C) 2001-2019 David A. Wheeler.
Number of rules (primarily dangerous function names) in C/C++ ruleset: 223
Examining data/genometools-1.6.1+ds/src/mgth/mg_outputwriter.h
Examining data/genometools-1.6.1+ds/src/mgth/mg_combinedscore.c
Examining data/genometools-1.6.1+ds/src/mgth/mg_codon.c
Examining data/genometools-1.6.1+ds/src/mgth/mg_combinedscore.h
Examining data/genometools-1.6.1+ds/src/mgth/mg_xmlparser.c
Examining data/genometools-1.6.1+ds/src/mgth/mg_xmlparser.h
Examining data/genometools-1.6.1+ds/src/mgth/mg_computepath.h
Examining data/genometools-1.6.1+ds/src/mgth/mg_outputwriter.c
Examining data/genometools-1.6.1+ds/src/mgth/metagenomethreader.c
Examining data/genometools-1.6.1+ds/src/mgth/mg_compute_gene_prediction.h
Examining data/genometools-1.6.1+ds/src/mgth/mg_reverse.c
Examining data/genometools-1.6.1+ds/src/mgth/mg_reverse.h
Examining data/genometools-1.6.1+ds/src/mgth/mg_codon.h
Examining data/genometools-1.6.1+ds/src/mgth/mg_computepath.c
Examining data/genometools-1.6.1+ds/src/mgth/mg_compute_gene_prediction.c
Examining data/genometools-1.6.1+ds/src/mgth/metagenomethreader.h
Examining data/genometools-1.6.1+ds/src/gtr.h
Examining data/genometools-1.6.1+ds/src/gtt.c
Examining data/genometools-1.6.1+ds/src/interactive.h
Examining data/genometools-1.6.1+ds/src/examples/custom_stream.c
Examining data/genometools-1.6.1+ds/src/examples/sketch_parsed_with_ordering.c
Examining data/genometools-1.6.1+ds/src/examples/gff3sort.c
Examining data/genometools-1.6.1+ds/src/examples/gtkviewer.c
Examining data/genometools-1.6.1+ds/src/examples/noop.c
Examining data/genometools-1.6.1+ds/src/examples/gff3validator.c
Examining data/genometools-1.6.1+ds/src/examples/sketch_parsed_with_ctrack.c
Examining data/genometools-1.6.1+ds/src/examples/sketch_parsed.c
Examining data/genometools-1.6.1+ds/src/examples/sketch_constructed.c
Examining data/genometools-1.6.1+ds/src/gtr.c
Examining data/genometools-1.6.1+ds/src/tools/gt_paircmp.h
Examining data/genometools-1.6.1+ds/src/tools/gt_show_seedext.h
Examining data/genometools-1.6.1+ds/src/tools/gt_uniq.h
Examining data/genometools-1.6.1+ds/src/tools/gt_seqmutate.h
Examining data/genometools-1.6.1+ds/src/tools/gt_mmapandread.c
Examining data/genometools-1.6.1+ds/src/tools/gt_extracttarget.h
Examining data/genometools-1.6.1+ds/src/tools/gt_readreads.h
Examining data/genometools-1.6.1+ds/src/tools/gt_featureindex.h
Examining data/genometools-1.6.1+ds/src/tools/gt_encseq_bitextract.c
Examining data/genometools-1.6.1+ds/src/tools/gt_trieins.c
Examining data/genometools-1.6.1+ds/src/tools/gt_seqcorrect.h
Examining data/genometools-1.6.1+ds/src/tools/gt_seqorder.c
Examining data/genometools-1.6.1+ds/src/tools/gt_seqmutate.c
Examining data/genometools-1.6.1+ds/src/tools/gt_uniq.c
Examining data/genometools-1.6.1+ds/src/tools/gt_packedindex_mkctxmap.c
Examining data/genometools-1.6.1+ds/src/tools/gt_readjoiner_assembly.c
Examining data/genometools-1.6.1+ds/src/tools/gt_mgth.c
Examining data/genometools-1.6.1+ds/src/tools/gt_magicmatch.h
Examining data/genometools-1.6.1+ds/src/tools/gt_readjoiner_cnttest.h
Examining data/genometools-1.6.1+ds/src/tools/gt_encseq_sample.c
Examining data/genometools-1.6.1+ds/src/tools/gt_encseq_encode.c
Examining data/genometools-1.6.1+ds/src/tools/gt_readjoiner_cgraph.h
Examining data/genometools-1.6.1+ds/src/tools/gt_readjoiner_graph.c
Examining data/genometools-1.6.1+ds/src/tools/gt_patternmatch.h
Examining data/genometools-1.6.1+ds/src/tools/gt_condenseq_hmmsearch.c
Examining data/genometools-1.6.1+ds/src/tools/gt_sfxmap.c
Examining data/genometools-1.6.1+ds/src/tools/gt_bed_to_gff3.h
Examining data/genometools-1.6.1+ds/src/tools/gt_magicmatch.c
Examining data/genometools-1.6.1+ds/src/tools/gt_dev.h
Examining data/genometools-1.6.1+ds/src/tools/gt_packedindex.c
Examining data/genometools-1.6.1+ds/src/tools/gt_readreads.c
Examining data/genometools-1.6.1+ds/src/tools/gt_readjoiner_asqg.c
Examining data/genometools-1.6.1+ds/src/tools/gt_sfxmap.h
Examining data/genometools-1.6.1+ds/src/tools/gt_seq.h
Examining data/genometools-1.6.1+ds/src/tools/gt_select.c
Examining data/genometools-1.6.1+ds/src/tools/gt_gtf_to_gff3.h
Examining data/genometools-1.6.1+ds/src/tools/gt_splicesiteinfo.c
Examining data/genometools-1.6.1+ds/src/tools/gt_regioncov.c
Examining data/genometools-1.6.1+ds/src/tools/gt_compreads.c
Examining data/genometools-1.6.1+ds/src/tools/gt_id_to_md5.c
Examining data/genometools-1.6.1+ds/src/tools/gt_sain.c
Examining data/genometools-1.6.1+ds/src/tools/gt_gtf_to_gff3.c
Examining data/genometools-1.6.1+ds/src/tools/gt_tallymer.c
Examining data/genometools-1.6.1+ds/src/tools/gt_shulen.c
Examining data/genometools-1.6.1+ds/src/tools/gt_splitfasta.h
Examining data/genometools-1.6.1+ds/src/tools/gt_condenseq_blast.h
Examining data/genometools-1.6.1+ds/src/tools/gt_shredder.h
Examining data/genometools-1.6.1+ds/src/tools/gt_guessprot.c
Examining data/genometools-1.6.1+ds/src/tools/gt_speck.c
Examining data/genometools-1.6.1+ds/src/tools/gt_seqlensort.c
Examining data/genometools-1.6.1+ds/src/tools/gt_packedindex_trsuftab.h
Examining data/genometools-1.6.1+ds/src/tools/gt_encseq_check.c
Examining data/genometools-1.6.1+ds/src/tools/gt_script_filter.c
Examining data/genometools-1.6.1+ds/src/tools/gt_compressedbits.c
Examining data/genometools-1.6.1+ds/src/tools/gt_condenseq_extract.c
Examining data/genometools-1.6.1+ds/src/tools/gt_eval.c
Examining data/genometools-1.6.1+ds/src/tools/gt_script_filter.h
Examining data/genometools-1.6.1+ds/src/tools/gt_consensus_sa.h
Examining data/genometools-1.6.1+ds/src/tools/gt_extracttarget.c
Examining data/genometools-1.6.1+ds/src/tools/gt_convertseq.c
Examining data/genometools-1.6.1+ds/src/tools/gt_fingerprint.c
Examining data/genometools-1.6.1+ds/src/tools/gt_compreads_refdecompress.c
Examining data/genometools-1.6.1+ds/src/tools/gt_sequniq.h
Examining data/genometools-1.6.1+ds/src/tools/gt_readjoiner_spmtest.c
Examining data/genometools-1.6.1+ds/src/tools/gt_seqlensort.h
Examining data/genometools-1.6.1+ds/src/tools/gt_seqtranslate.h
Examining data/genometools-1.6.1+ds/src/tools/gt_md5_to_id.h
Examining data/genometools-1.6.1+ds/src/tools/gt_encseq_info.h
Examining data/genometools-1.6.1+ds/src/tools/gt_seqstat.c
Examining data/genometools-1.6.1+ds/src/tools/gt_featureindex.c
Examining data/genometools-1.6.1+ds/src/tools/gt_clean.h
Examining data/genometools-1.6.1+ds/src/tools/gt_seqids.h
Examining data/genometools-1.6.1+ds/src/tools/gt_readjoiner_gfa.h
Examining data/genometools-1.6.1+ds/src/tools/gt_skproto.h
Examining data/genometools-1.6.1+ds/src/tools/gt_gff3validator.h
Examining data/genometools-1.6.1+ds/src/tools/gt_select.h
Examining data/genometools-1.6.1+ds/src/tools/gt_dev.c
Examining data/genometools-1.6.1+ds/src/tools/gt_fingerprint.h
Examining data/genometools-1.6.1+ds/src/tools/gt_encseq_decode.c
Examining data/genometools-1.6.1+ds/src/tools/gt_encseq2spm.h
Examining data/genometools-1.6.1+ds/src/tools/gt_chain2dim.h
Examining data/genometools-1.6.1+ds/src/tools/gt_stat.c
Examining data/genometools-1.6.1+ds/src/tools/gt_readjoiner_gfa.c
Examining data/genometools-1.6.1+ds/src/tools/gt_sam_interface.c
Examining data/genometools-1.6.1+ds/src/tools/gt_tagerator.h
Examining data/genometools-1.6.1+ds/src/tools/gt_encseq.h
Examining data/genometools-1.6.1+ds/src/tools/gt_mkfeatureindex.c
Examining data/genometools-1.6.1+ds/src/tools/gt_chseqids.c
Examining data/genometools-1.6.1+ds/src/tools/gt_mgth.h
Examining data/genometools-1.6.1+ds/src/tools/gt_extractseq.h
Examining data/genometools-1.6.1+ds/src/tools/gt_dot.c
Examining data/genometools-1.6.1+ds/src/tools/gt_suffixerator.h
Examining data/genometools-1.6.1+ds/src/tools/gt_sortbench.c
Examining data/genometools-1.6.1+ds/src/tools/gt_template.h
Examining data/genometools-1.6.1+ds/src/tools/gt_skproto.c
Examining data/genometools-1.6.1+ds/src/tools/gt_merge.c
Examining data/genometools-1.6.1+ds/src/tools/gt_extractseq.c
Examining data/genometools-1.6.1+ds/src/tools/gt_readjoiner_correct.c
Examining data/genometools-1.6.1+ds/src/tools/gt_condenseq.h
Examining data/genometools-1.6.1+ds/src/tools/gt_compreads_decompress.h
Examining data/genometools-1.6.1+ds/src/tools/gt_compreads_compress.c
Examining data/genometools-1.6.1+ds/src/tools/gt_inlineseq_split.h
Examining data/genometools-1.6.1+ds/src/tools/gt_regioncov.h
Examining data/genometools-1.6.1+ds/src/tools/gt_snpper.h
Examining data/genometools-1.6.1+ds/src/tools/gt_seqtransform.h
Examining data/genometools-1.6.1+ds/src/tools/gt_fastq_sample.h
Examining data/genometools-1.6.1+ds/src/tools/gt_packedindex_trsuftab.c
Examining data/genometools-1.6.1+ds/src/tools/gt_readjoiner.h
Examining data/genometools-1.6.1+ds/src/tools/gt_idxlocali.c
Examining data/genometools-1.6.1+ds/src/tools/gt_parsexrf.c
Examining data/genometools-1.6.1+ds/src/tools/gt_gff3validator.c
Examining data/genometools-1.6.1+ds/src/tools/gt_compressedbits.h
Examining data/genometools-1.6.1+ds/src/tools/gt_congruence.h
Examining data/genometools-1.6.1+ds/src/tools/gt_encseq_md5.c
Examining data/genometools-1.6.1+ds/src/tools/gt_condenseq.c
Examining data/genometools-1.6.1+ds/src/tools/gt_csa.c
Examining data/genometools-1.6.1+ds/src/tools/gt_splitfasta.c
Examining data/genometools-1.6.1+ds/src/tools/gt_inlineseq_add.h
Examining data/genometools-1.6.1+ds/src/tools/gt_inlineseq_split.c
Examining data/genometools-1.6.1+ds/src/tools/gt_wtree_bench.h
Examining data/genometools-1.6.1+ds/src/tools/gt_tallymer.h
Examining data/genometools-1.6.1+ds/src/tools/gt_condenseq_extract.h
Examining data/genometools-1.6.1+ds/src/tools/gt_packedindex_chk_search.h
Examining data/genometools-1.6.1+ds/src/tools/gt_compreads_refdecompress.h
Examining data/genometools-1.6.1+ds/src/tools/gt_snpper.c
Examining data/genometools-1.6.1+ds/src/tools/gt_compreads_refcompress.h
Examining data/genometools-1.6.1+ds/src/tools/gt_id_to_md5.h
Examining data/genometools-1.6.1+ds/src/tools/gt_orffinder.h
Examining data/genometools-1.6.1+ds/src/tools/gt_kmer_database.c
Examining data/genometools-1.6.1+ds/src/tools/gt_tagerator.c
Examining data/genometools-1.6.1+ds/src/tools/gt_dupfeat.h
Examining data/genometools-1.6.1+ds/src/tools/gt_wtree_bench.c
Examining data/genometools-1.6.1+ds/src/tools/gt_readjoiner_prefilter.c
Examining data/genometools-1.6.1+ds/src/tools/gt_condenseq_info.c
Examining data/genometools-1.6.1+ds/src/tools/gt_cds.h
Examining data/genometools-1.6.1+ds/src/tools/gt_interfeat.c
Examining data/genometools-1.6.1+ds/src/tools/gt_extractfeat.c
Examining data/genometools-1.6.1+ds/src/tools/gt_condenseq_info.h
Examining data/genometools-1.6.1+ds/src/tools/gt_condenseq_compress.h
Examining data/genometools-1.6.1+ds/src/tools/gt_encseq_md5.h
Examining data/genometools-1.6.1+ds/src/tools/gt_seqtransform.c
Examining data/genometools-1.6.1+ds/src/tools/gt_readjoiner_asqg.h
Examining data/genometools-1.6.1+ds/src/tools/gt_wtree.c
Examining data/genometools-1.6.1+ds/src/tools/gt_sam_interface.h
Examining data/genometools-1.6.1+ds/src/tools/gt_matchtool.c
Examining data/genometools-1.6.1+ds/src/tools/gt_seqfilter.c
Examining data/genometools-1.6.1+ds/src/tools/gt_readjoiner_cgraph.c
Examining data/genometools-1.6.1+ds/src/tools/gt_mmapandread.h
Examining data/genometools-1.6.1+ds/src/tools/gt_genomediff.h
Examining data/genometools-1.6.1+ds/src/tools/gt_extractfeat.h
Examining data/genometools-1.6.1+ds/src/tools/gt_gff3.c
Examining data/genometools-1.6.1+ds/src/tools/gt_encseq_bitextract.h
Examining data/genometools-1.6.1+ds/src/tools/gt_seqcorrect.c
Examining data/genometools-1.6.1+ds/src/tools/gt_seqids.c
Examining data/genometools-1.6.1+ds/src/tools/gt_tir.h
Examining data/genometools-1.6.1+ds/src/tools/gt_packedindex_mkctxmap.h
Examining data/genometools-1.6.1+ds/src/tools/gt_parsexrf.h
Examining data/genometools-1.6.1+ds/src/tools/gt_compreads.h
Examining data/genometools-1.6.1+ds/src/tools/gt_compreads_refcompress.c
Examining data/genometools-1.6.1+ds/src/tools/gt_convertseq.h
Examining data/genometools-1.6.1+ds/src/tools/gt_linspace_align.h
Examining data/genometools-1.6.1+ds/src/tools/gt_condenseq_search.h
Examining data/genometools-1.6.1+ds/src/tools/gt_encseq.c
Examining data/genometools-1.6.1+ds/src/tools/gt_csa.h
Examining data/genometools-1.6.1+ds/src/tools/gt_merge.h
Examining data/genometools-1.6.1+ds/src/tools/gt_mergefeat.c
Examining data/genometools-1.6.1+ds/src/tools/gt_seqfilter.h
Examining data/genometools-1.6.1+ds/src/tools/gt_md5_to_id.c
Examining data/genometools-1.6.1+ds/src/tools/gt_gdiffcalc.c
Examining data/genometools-1.6.1+ds/src/tools/gt_readjoiner_correct.h
Examining data/genometools-1.6.1+ds/src/tools/gt_cds.c
Examining data/genometools-1.6.1+ds/src/tools/gt_loccheck.h
Examining data/genometools-1.6.1+ds/src/tools/gt_suffixerator.c
Examining data/genometools-1.6.1+ds/src/tools/gt_encseq_encode.h
Examining data/genometools-1.6.1+ds/src/tools/gt_fastq_sample.c
Examining data/genometools-1.6.1+ds/src/tools/gt_orffinder.c
Examining data/genometools-1.6.1+ds/src/tools/gt_template.c
Examining data/genometools-1.6.1+ds/src/tools/gt_inlineseq_add.c
Examining data/genometools-1.6.1+ds/src/tools/gt_gff3_to_gtf.c
Examining data/genometools-1.6.1+ds/src/tools/gt_readjoiner_overlap.h
Examining data/genometools-1.6.1+ds/src/tools/gt_interfeat.h
Examining data/genometools-1.6.1+ds/src/tools/gt_encseq_decode.h
Examining data/genometools-1.6.1+ds/src/tools/gt_encseq_bench.h
Examining data/genometools-1.6.1+ds/src/tools/gt_encseq_info.c
Examining data/genometools-1.6.1+ds/src/tools/gt_repfind.h
Examining data/genometools-1.6.1+ds/src/tools/gt_readjoiner_cnttest.c
Examining data/genometools-1.6.1+ds/src/tools/gt_seq.c
Examining data/genometools-1.6.1+ds/src/tools/gt_compreads_decompress.c
Examining data/genometools-1.6.1+ds/src/tools/gt_compreads_compress.h
Examining data/genometools-1.6.1+ds/src/tools/gt_stat.h
Examining data/genometools-1.6.1+ds/src/tools/gt_mkfmindex.h
Examining data/genometools-1.6.1+ds/src/tools/gt_show_seedext.c
Examining data/genometools-1.6.1+ds/src/tools/gt_loccheck.c
Examining data/genometools-1.6.1+ds/src/tools/gt_readjoiner_prefilter.h
Examining data/genometools-1.6.1+ds/src/tools/gt_patternmatch.c
Examining data/genometools-1.6.1+ds/src/tools/gt_kmer_database.h
Examining data/genometools-1.6.1+ds/src/tools/gt_chain2dim.c
Examining data/genometools-1.6.1+ds/src/tools/gt_seqorder.h
Examining data/genometools-1.6.1+ds/src/tools/gt_sain.h
Examining data/genometools-1.6.1+ds/src/tools/gt_splicesiteinfo.h
Examining data/genometools-1.6.1+ds/src/tools/gt_tir.c
Examining data/genometools-1.6.1+ds/src/tools/gt_mergefeat.h
Examining data/genometools-1.6.1+ds/src/tools/gt_condenseq_search.c
Examining data/genometools-1.6.1+ds/src/tools/gt_readjoiner_graph.h
Examining data/genometools-1.6.1+ds/src/tools/gt_trieins.h
Examining data/genometools-1.6.1+ds/src/tools/gt_gdiffcalc.h
Examining data/genometools-1.6.1+ds/src/tools/gt_bed_to_gff3.c
Examining data/genometools-1.6.1+ds/src/tools/gt_encseq_sample.h
Examining data/genometools-1.6.1+ds/src/tools/gt_dupfeat.c
Examining data/genometools-1.6.1+ds/src/tools/gt_readjoiner_assembly.h
Examining data/genometools-1.6.1+ds/src/tools/gt_dot.h
Examining data/genometools-1.6.1+ds/src/tools/gt_readjoiner_spmtest.h
Examining data/genometools-1.6.1+ds/src/tools/gt_matchtool.h
Examining data/genometools-1.6.1+ds/src/tools/gt_uniquesub.h
Examining data/genometools-1.6.1+ds/src/tools/gt_hop.c
Examining data/genometools-1.6.1+ds/src/tools/gt_prebwt.h
Examining data/genometools-1.6.1+ds/src/tools/gt_seqstat.h
Examining data/genometools-1.6.1+ds/src/tools/gt_gff3.h
Examining data/genometools-1.6.1+ds/src/tools/gt_matstat.c
Examining data/genometools-1.6.1+ds/src/tools/gt_shulen.h
Examining data/genometools-1.6.1+ds/src/tools/gt_sortbench.h
Examining data/genometools-1.6.1+ds/src/tools/gt_wtree.h
Examining data/genometools-1.6.1+ds/src/tools/gt_encseq_check.h
Examining data/genometools-1.6.1+ds/src/tools/gt_readjoiner_overlap.c
Examining data/genometools-1.6.1+ds/src/tools/gt_packedindex.h
Examining data/genometools-1.6.1+ds/src/tools/gt_simreads.c
Examining data/genometools-1.6.1+ds/src/tools/gt_eval.h
Examining data/genometools-1.6.1+ds/src/tools/gt_guessprot.h
Examining data/genometools-1.6.1+ds/src/tools/gt_gff3_to_gtf.h
Examining data/genometools-1.6.1+ds/src/tools/gt_congruence.c
Examining data/genometools-1.6.1+ds/src/tools/gt_condenseq_hmmsearch.h
Examining data/genometools-1.6.1+ds/src/tools/gt_condenseq_compress.c
Examining data/genometools-1.6.1+ds/src/tools/gt_mkfmindex.c
Examining data/genometools-1.6.1+ds/src/tools/gt_packedindex_chk_integrity.h
Examining data/genometools-1.6.1+ds/src/tools/gt_clean.c
Examining data/genometools-1.6.1+ds/src/tools/gt_shredder.c
Examining data/genometools-1.6.1+ds/src/tools/gt_genomediff.c
Examining data/genometools-1.6.1+ds/src/tools/gt_condenseq_blast.c
Examining data/genometools-1.6.1+ds/src/tools/gt_speck.h
Examining data/genometools-1.6.1+ds/src/tools/gt_packedindex_chk_integrity.c
Examining data/genometools-1.6.1+ds/src/tools/gt_prebwt.c
Examining data/genometools-1.6.1+ds/src/tools/gt_consensus_sa.c
Examining data/genometools-1.6.1+ds/src/tools/gt_mkfeatureindex.h
Examining data/genometools-1.6.1+ds/src/tools/gt_linspace_align.c
Examining data/genometools-1.6.1+ds/src/tools/gt_mergeesa.h
Examining data/genometools-1.6.1+ds/src/tools/gt_hop.h
Examining data/genometools-1.6.1+ds/src/tools/gt_simreads.h
Examining data/genometools-1.6.1+ds/src/tools/gt_encseq2spm.c
Examining data/genometools-1.6.1+ds/src/tools/gt_idxlocali.h
Examining data/genometools-1.6.1+ds/src/tools/gt_seqtranslate.c
Examining data/genometools-1.6.1+ds/src/tools/gt_repfind.c
Examining data/genometools-1.6.1+ds/src/tools/gt_seed_extend.h
Examining data/genometools-1.6.1+ds/src/tools/gt_matstat.h
Examining data/genometools-1.6.1+ds/src/tools/gt_paircmp.c
Examining data/genometools-1.6.1+ds/src/tools/gt_sequniq.c
Examining data/genometools-1.6.1+ds/src/tools/gt_packedindex_chk_search.c
Examining data/genometools-1.6.1+ds/src/tools/gt_readjoiner.c
Examining data/genometools-1.6.1+ds/src/tools/gt_mergeesa.c
Examining data/genometools-1.6.1+ds/src/tools/gt_seed_extend.c
Examining data/genometools-1.6.1+ds/src/tools/gt_chseqids.h
Examining data/genometools-1.6.1+ds/src/tools/gt_encseq_bench.c
Examining data/genometools-1.6.1+ds/src/ltr/ltrharvest_tabout_visitor.h
Examining data/genometools-1.6.1+ds/src/ltr/ltrdigest_pbs_visitor.h
Examining data/genometools-1.6.1+ds/src/ltr/gt_ltrdigest.c
Examining data/genometools-1.6.1+ds/src/ltr/ltrdigest_pdom_visitor.h
Examining data/genometools-1.6.1+ds/src/ltr/ltrdigest_pbs_visitor.c
Examining data/genometools-1.6.1+ds/src/ltr/ltrdigest_pdom_visitor.c
Examining data/genometools-1.6.1+ds/src/ltr/ltrharvest_tabout_stream.c
Examining data/genometools-1.6.1+ds/src/ltr/gt_ltrclustering.h
Examining data/genometools-1.6.1+ds/src/ltr/ltr_refseq_match_stream.h
Examining data/genometools-1.6.1+ds/src/ltr/ltr_input_check_visitor.h
Examining data/genometools-1.6.1+ds/src/ltr/ltrharvest_tabout_visitor.c
Examining data/genometools-1.6.1+ds/src/ltr/ltrharvest_stream.c
Examining data/genometools-1.6.1+ds/src/ltr/ltr_four_char_motif.h
Examining data/genometools-1.6.1+ds/src/ltr/ltr_orf_annotator_stream_api.h
Examining data/genometools-1.6.1+ds/src/ltr/gt_ltrharvest.h
Examining data/genometools-1.6.1+ds/src/ltr/gt_ltrharvest.c
Examining data/genometools-1.6.1+ds/src/ltr/ltrharvest_stream.h
Examining data/genometools-1.6.1+ds/src/ltr/ltrdigest_ppt_visitor.h
Examining data/genometools-1.6.1+ds/src/ltr/ltr_orf_annotator_stream.c
Examining data/genometools-1.6.1+ds/src/ltr/ltrdigest_def.h
Examining data/genometools-1.6.1+ds/src/ltr/ltrharvest_fasta_out_visitor.c
Examining data/genometools-1.6.1+ds/src/ltr/ltr_cluster_prepare_seq_visitor.c
Examining data/genometools-1.6.1+ds/src/ltr/ltr_input_check_visitor.c
Examining data/genometools-1.6.1+ds/src/ltr/ltrdigest_strand_assign_visitor.c
Examining data/genometools-1.6.1+ds/src/ltr/ltrharvest_fasta_out_visitor.h
Examining data/genometools-1.6.1+ds/src/ltr/ltrharvest_fasta_out_stream.c
Examining data/genometools-1.6.1+ds/src/ltr/pdom_model_set.c
Examining data/genometools-1.6.1+ds/src/ltr/ltrharvest_fasta_out_stream.h
Examining data/genometools-1.6.1+ds/src/ltr/gt_ltrclustering.c
Examining data/genometools-1.6.1+ds/src/ltr/ltr_classify_stream.c
Examining data/genometools-1.6.1+ds/src/ltr/ltrdigest_file_out_stream.h
Examining data/genometools-1.6.1+ds/src/ltr/ltr_classify_stream_api.h
Examining data/genometools-1.6.1+ds/src/ltr/ltr_cluster_stream_api.h
Examining data/genometools-1.6.1+ds/src/ltr/ltr_cluster_stream.h
Examining data/genometools-1.6.1+ds/src/ltr/ltr_cluster_prepare_seq_visitor.h
Examining data/genometools-1.6.1+ds/src/ltr/pdom_model_set.h
Examining data/genometools-1.6.1+ds/src/ltr/ltrharvest_tabout_stream.h
Examining data/genometools-1.6.1+ds/src/ltr/ltr_four_char_motif.c
Examining data/genometools-1.6.1+ds/src/ltr/ltrdigest_ppt_visitor.c
Examining data/genometools-1.6.1+ds/src/ltr/ltr_refseq_match_stream_api.h
Examining data/genometools-1.6.1+ds/src/ltr/ltr_refseq_match_stream.c
Examining data/genometools-1.6.1+ds/src/ltr/ltr_cluster_stream.c
Examining data/genometools-1.6.1+ds/src/ltr/ltrdigest_strand_assign_visitor.h
Examining data/genometools-1.6.1+ds/src/ltr/ltr_classify_stream.h
Examining data/genometools-1.6.1+ds/src/ltr/gt_ltrdigest.h
Examining data/genometools-1.6.1+ds/src/ltr/ltrdigest_file_out_stream.c
Examining data/genometools-1.6.1+ds/src/gtt.h
Examining data/genometools-1.6.1+ds/src/memcpy.c
Examining data/genometools-1.6.1+ds/src/match/mssufpat.c
Examining data/genometools-1.6.1+ds/src/match/test-mappedstr.h
Examining data/genometools-1.6.1+ds/src/match/rdj-ovlfind-bf.c
Examining data/genometools-1.6.1+ds/src/match/specialrank.c
Examining data/genometools-1.6.1+ds/src/match/sfx-suffixgetset.c
Examining data/genometools-1.6.1+ds/src/match/esa-mmsearch.c
Examining data/genometools-1.6.1+ds/src/match/randomcodes-tab.c
Examining data/genometools-1.6.1+ds/src/match/randomcodes.c
Examining data/genometools-1.6.1+ds/src/match/rdj-strgraph-edges-single-bitpack-def.h
Examining data/genometools-1.6.1+ds/src/match/sfx-outprj.h
Examining data/genometools-1.6.1+ds/src/match/esa-scanprj.h
Examining data/genometools-1.6.1+ds/src/match/esa-scanprj.c
Examining data/genometools-1.6.1+ds/src/match/rdj-spmfind.c
Examining data/genometools-1.6.1+ds/src/match/rdj-contigpaths.c
Examining data/genometools-1.6.1+ds/src/match/spmsuftab.h
Examining data/genometools-1.6.1+ds/src/match/spaced-seeds.h
Examining data/genometools-1.6.1+ds/src/match/eis-headerid.h
Examining data/genometools-1.6.1+ds/src/match/hlk-version.c
Examining data/genometools-1.6.1+ds/src/match/rdj-contfinder.h
Examining data/genometools-1.6.1+ds/src/match/test-pairwise.c
Examining data/genometools-1.6.1+ds/src/match/reads_libraries_table.c
Examining data/genometools-1.6.1+ds/src/match/rdj-spmfind.h
Examining data/genometools-1.6.1+ds/src/match/eis-seqranges.c
Examining data/genometools-1.6.1+ds/src/match/seqnumrelpos.h
Examining data/genometools-1.6.1+ds/src/match/eis-encidxseq-siop.h
Examining data/genometools-1.6.1+ds/src/match/rdj-contfind-bottomup.h
Examining data/genometools-1.6.1+ds/src/match/eis-suffixarray-interface-priv.h
Examining data/genometools-1.6.1+ds/src/match/fmi-locate.c
Examining data/genometools-1.6.1+ds/src/match/xdrop.c
Examining data/genometools-1.6.1+ds/src/match/fmi-sufbwtstream.c
Examining data/genometools-1.6.1+ds/src/match/greedyfwdmat.h
Examining data/genometools-1.6.1+ds/src/match/kmer2string.c
Examining data/genometools-1.6.1+ds/src/match/encseq2offset.h
Examining data/genometools-1.6.1+ds/src/match/rdj-version.c
Examining data/genometools-1.6.1+ds/src/match/esa-splititv.h
Examining data/genometools-1.6.1+ds/src/match/eis-bwtseq-context-priv.h
Examining data/genometools-1.6.1+ds/src/match/eis-encidxseq-param.h
Examining data/genometools-1.6.1+ds/src/match/eis-seqblocktranslate.h
Examining data/genometools-1.6.1+ds/src/match/eis-bwtseq-construct.h
Examining data/genometools-1.6.1+ds/src/match/firstcodes-cache.c
Examining data/genometools-1.6.1+ds/src/match/rdj-ensure-output.h
Examining data/genometools-1.6.1+ds/src/match/rdj-twobitenc-editor.h
Examining data/genometools-1.6.1+ds/src/match/tyr-map.h
Examining data/genometools-1.6.1+ds/src/match/pckbucket.c
Examining data/genometools-1.6.1+ds/src/match/sfx-mappedstr.c
Examining data/genometools-1.6.1+ds/src/match/fmi-sufbwtstream.h
Examining data/genometools-1.6.1+ds/src/match/gfa_writer.c
Examining data/genometools-1.6.1+ds/src/match/fmi-save.c
Examining data/genometools-1.6.1+ds/src/match/sfx-apfxlen.h
Examining data/genometools-1.6.1+ds/src/match/shu-dfs.h
Examining data/genometools-1.6.1+ds/src/match/firstcodes-accum.c
Examining data/genometools-1.6.1+ds/src/match/querymatch-align.c
Examining data/genometools-1.6.1+ds/src/match/randomcodes-correct.c
Examining data/genometools-1.6.1+ds/src/match/ft-polish.c
Examining data/genometools-1.6.1+ds/src/match/rdj-strgraph-edges-bitpack-def.h
Examining data/genometools-1.6.1+ds/src/match/marksubstring.c
Examining data/genometools-1.6.1+ds/src/match/diagbandseed.c
Examining data/genometools-1.6.1+ds/src/match/esa-map.c
Examining data/genometools-1.6.1+ds/src/match/karlin_altschul_stat.h
Examining data/genometools-1.6.1+ds/src/match/querymatch-align.h
Examining data/genometools-1.6.1+ds/src/match/fmi-map.h
Examining data/genometools-1.6.1+ds/src/match/rdj-strgraph-edges-bitfield-def.h
Examining data/genometools-1.6.1+ds/src/match/ft-eoplist.c
Examining data/genometools-1.6.1+ds/src/match/seed_extend_parts.h
Examining data/genometools-1.6.1+ds/src/match/firstcodes-spacelog.h
Examining data/genometools-1.6.1+ds/src/match/firstcodes-spacelog.c
Examining data/genometools-1.6.1+ds/src/match/revcompl.c
Examining data/genometools-1.6.1+ds/src/match/declare-readfunc.h
Examining data/genometools-1.6.1+ds/src/match/bcktab.h
Examining data/genometools-1.6.1+ds/src/match/echoseq.c
Examining data/genometools-1.6.1+ds/src/match/eis-bwtseq-context-param.c
Examining data/genometools-1.6.1+ds/src/match/genomediff_opt.h
Examining data/genometools-1.6.1+ds/src/match/test-pairwise.h
Examining data/genometools-1.6.1+ds/src/match/emimergeesa.h
Examining data/genometools-1.6.1+ds/src/match/sfx-suftaborder.h
Examining data/genometools-1.6.1+ds/src/match/esa_lcpintervals_visitor.c
Examining data/genometools-1.6.1+ds/src/match/esa-fileend.h
Examining data/genometools-1.6.1+ds/src/match/idxlocali.c
Examining data/genometools-1.6.1+ds/src/match/test-mtrieins.c
Examining data/genometools-1.6.1+ds/src/match/esa-dfs.c
Examining data/genometools-1.6.1+ds/src/match/mssufpat.h
Examining data/genometools-1.6.1+ds/src/match/ft-trimstat.h
Examining data/genometools-1.6.1+ds/src/match/rdj-ovlfind-kmp.h
Examining data/genometools-1.6.1+ds/src/match/tyr-map.c
Examining data/genometools-1.6.1+ds/src/match/triangular_def.h
Examining data/genometools-1.6.1+ds/src/match/eis-bwtseq-extinfo.c
Examining data/genometools-1.6.1+ds/src/match/sfx-lwcheck.c
Examining data/genometools-1.6.1+ds/src/match/tyr-mkindex.c
Examining data/genometools-1.6.1+ds/src/match/eis-sequencemultiread.h
Examining data/genometools-1.6.1+ds/src/match/esa-spmitvs.c
Examining data/genometools-1.6.1+ds/src/match/eis-bwtseq-construct.c
Examining data/genometools-1.6.1+ds/src/match/firstcodes-cache.h
Examining data/genometools-1.6.1+ds/src/match/tyr-search.h
Examining data/genometools-1.6.1+ds/src/match/dist-short.c
Examining data/genometools-1.6.1+ds/src/match/esa-spmsk.c
Examining data/genometools-1.6.1+ds/src/match/substriter.h
Examining data/genometools-1.6.1+ds/src/match/shu-encseq-gc.h
Examining data/genometools-1.6.1+ds/src/match/revcompl.h
Examining data/genometools-1.6.1+ds/src/match/enum-patt.c
Examining data/genometools-1.6.1+ds/src/match/sfx-copysort.h
Examining data/genometools-1.6.1+ds/src/match/rdj-spmlist.h
Examining data/genometools-1.6.1+ds/src/match/pckbucket.h
Examining data/genometools-1.6.1+ds/src/match/esa-shulen.c
Examining data/genometools-1.6.1+ds/src/match/sfx-suftaborder.c
Examining data/genometools-1.6.1+ds/src/match/hlk-version.h
Examining data/genometools-1.6.1+ds/src/match/radixsort_str.h
Examining data/genometools-1.6.1+ds/src/match/ft-front-generation.c
Examining data/genometools-1.6.1+ds/src/match/rectangle-store.c
Examining data/genometools-1.6.1+ds/src/match/cutendpfx.c
Examining data/genometools-1.6.1+ds/src/match/esa-mmsearch.h
Examining data/genometools-1.6.1+ds/src/match/sfx-suffixer.c
Examining data/genometools-1.6.1+ds/src/match/esa-spmsk.h
Examining data/genometools-1.6.1+ds/src/match/dist-short.h
Examining data/genometools-1.6.1+ds/src/match/twobits2kmers.h
Examining data/genometools-1.6.1+ds/src/match/chainofin.c
Examining data/genometools-1.6.1+ds/src/match/myersapm.h
Examining data/genometools-1.6.1+ds/src/match/greedyedist.h
Examining data/genometools-1.6.1+ds/src/match/firstcodes.c
Examining data/genometools-1.6.1+ds/src/match/rdj-strgraph-counts-char-def.h
Examining data/genometools-1.6.1+ds/src/match/firstcodes-buf.h
Examining data/genometools-1.6.1+ds/src/match/iter-window.h
Examining data/genometools-1.6.1+ds/src/match/index_options.c
Examining data/genometools-1.6.1+ds/src/match/esa-minunique.h
Examining data/genometools-1.6.1+ds/src/match/seed-extend.c
Examining data/genometools-1.6.1+ds/src/match/tyr-occratio.h
Examining data/genometools-1.6.1+ds/src/match/eis-mrangealphabet.c
Examining data/genometools-1.6.1+ds/src/match/idxlocalidp.c
Examining data/genometools-1.6.1+ds/src/match/hashfirstcodes.c
Examining data/genometools-1.6.1+ds/src/match/ft-front-prune.c
Examining data/genometools-1.6.1+ds/src/match/merger-trie.h
Examining data/genometools-1.6.1+ds/src/match/eis-bwtseq-sass.h
Examining data/genometools-1.6.1+ds/src/match/esa-spmitvs.h
Examining data/genometools-1.6.1+ds/src/match/eis-seqranges-priv.h
Examining data/genometools-1.6.1+ds/src/match/eis-bwtseq-siop.h
Examining data/genometools-1.6.1+ds/src/match/randomcodes-insert.h
Examining data/genometools-1.6.1+ds/src/match/seq_or_encseq.h
Examining data/genometools-1.6.1+ds/src/match/pck-count-nodes.h
Examining data/genometools-1.6.1+ds/src/match/rdj-contigs-graph.c
Examining data/genometools-1.6.1+ds/src/match/idxlocali.h
Examining data/genometools-1.6.1+ds/src/match/rdj-ovlfind-kmp.c
Examining data/genometools-1.6.1+ds/src/match/test-mergeesa.c
Examining data/genometools-1.6.1+ds/src/match/eis-bwtseq-context.c
Examining data/genometools-1.6.1+ds/src/match/sfx-maprange.c
Examining data/genometools-1.6.1+ds/src/match/iter-window.c
Examining data/genometools-1.6.1+ds/src/match/procmatch.h
Examining data/genometools-1.6.1+ds/src/match/reads2twobit.h
Examining data/genometools-1.6.1+ds/src/match/squarededist.c
Examining data/genometools-1.6.1+ds/src/match/asqg_writer.c
Examining data/genometools-1.6.1+ds/src/match/fmi-keyval.h
Examining data/genometools-1.6.1+ds/src/match/splititv.h
Examining data/genometools-1.6.1+ds/src/match/fmi-mkindex.c
Examining data/genometools-1.6.1+ds/src/match/esa-maxpairs.h
Examining data/genometools-1.6.1+ds/src/match/idxlocalisw.h
Examining data/genometools-1.6.1+ds/src/match/esa_lcpintervals_visitor.h
Examining data/genometools-1.6.1+ds/src/match/shu-genomediff.c
Examining data/genometools-1.6.1+ds/src/match/hplstore.h
Examining data/genometools-1.6.1+ds/src/match/sfx-enumcodes.h
Examining data/genometools-1.6.1+ds/src/match/rdj-pairwise.c
Examining data/genometools-1.6.1+ds/src/match/esa-splititv-simple.c
Examining data/genometools-1.6.1+ds/src/match/firstcodes-accum.h
Examining data/genometools-1.6.1+ds/src/match/lua_tools.c
Examining data/genometools-1.6.1+ds/src/match/seed-extend-iter.c
Examining data/genometools-1.6.1+ds/src/match/firstcodes-tab.h
Examining data/genometools-1.6.1+ds/src/match/apmeoveridx.h
Examining data/genometools-1.6.1+ds/src/match/eis-specialsrank-priv.h
Examining data/genometools-1.6.1+ds/src/match/echoseq.h
Examining data/genometools-1.6.1+ds/src/match/randomcodes-sfx-partssuf.c
Examining data/genometools-1.6.1+ds/src/match/chain2dim.h
Examining data/genometools-1.6.1+ds/src/match/lcpoverflow.h
Examining data/genometools-1.6.1+ds/src/match/tyr-occratio.c
Examining data/genometools-1.6.1+ds/src/match/esa_spmitvs_visitor.c
Examining data/genometools-1.6.1+ds/src/match/tab-diffcover.h
Examining data/genometools-1.6.1+ds/src/match/shu-encseq-gc.c
Examining data/genometools-1.6.1+ds/src/match/shu-genomediff.h
Examining data/genometools-1.6.1+ds/src/match/seed-extend-params.h
Examining data/genometools-1.6.1+ds/src/match/eis-seqblocktranslate.c
Examining data/genometools-1.6.1+ds/src/match/sfx-radixsort.c
Examining data/genometools-1.6.1+ds/src/match/eis-suffixarray-interface.h
Examining data/genometools-1.6.1+ds/src/match/tagerator.h
Examining data/genometools-1.6.1+ds/src/match/fmi-map.c
Examining data/genometools-1.6.1+ds/src/match/test-maxpairs.h
Examining data/genometools-1.6.1+ds/src/match/randomcodes-hpcorrect.c
Examining data/genometools-1.6.1+ds/src/match/giextract.h
Examining data/genometools-1.6.1+ds/src/match/tyr-mersplit.h
Examining data/genometools-1.6.1+ds/src/match/pckdfs.h
Examining data/genometools-1.6.1+ds/src/match/fmi-save.h
Examining data/genometools-1.6.1+ds/src/match/esa-lcpintervals.h
Examining data/genometools-1.6.1+ds/src/match/eis-blockcomp-param.h
Examining data/genometools-1.6.1+ds/src/match/nullcols.c
Examining data/genometools-1.6.1+ds/src/match/firstcodes-psbuf.h
Examining data/genometools-1.6.1+ds/src/match/rdj-strgraph.h
Examining data/genometools-1.6.1+ds/src/match/eis-seqdatasrc.h
Examining data/genometools-1.6.1+ds/src/match/sarr-def.h
Examining data/genometools-1.6.1+ds/src/match/seqnumrelpos.c
Examining data/genometools-1.6.1+ds/src/match/ft-trimstat.c
Examining data/genometools-1.6.1+ds/src/match/eis-blockcomp.c
Examining data/genometools-1.6.1+ds/src/match/esa-seqread.h
Examining data/genometools-1.6.1+ds/src/match/rdj-contigs-writer.c
Examining data/genometools-1.6.1+ds/src/match/fmi-mapspec.h
Examining data/genometools-1.6.1+ds/src/match/greedyfwdmat.c
Examining data/genometools-1.6.1+ds/src/match/rdj-strgraph-vertices-common-def.h
Examining data/genometools-1.6.1+ds/src/match/eis-sequencemultiread.c
Examining data/genometools-1.6.1+ds/src/match/firstcodes-insert.h
Examining data/genometools-1.6.1+ds/src/match/sfx-bentsedg.h
Examining data/genometools-1.6.1+ds/src/match/xdrop.h
Examining data/genometools-1.6.1+ds/src/match/queue-inline.h
Examining data/genometools-1.6.1+ds/src/match/radixsort_str.c
Examining data/genometools-1.6.1+ds/src/match/firstcodes-scan.c
Examining data/genometools-1.6.1+ds/src/match/rdj-pairwise.h
Examining data/genometools-1.6.1+ds/src/match/eis-sa-common-priv.h
Examining data/genometools-1.6.1+ds/src/match/initbasepower.c
Examining data/genometools-1.6.1+ds/src/match/absdfstrans-def.h
Examining data/genometools-1.6.1+ds/src/match/stamp.h
Examining data/genometools-1.6.1+ds/src/match/hashfirstcodes.h
Examining data/genometools-1.6.1+ds/src/match/cgr_spacedseed.h
Examining data/genometools-1.6.1+ds/src/match/absdfstrans-imp.h
Examining data/genometools-1.6.1+ds/src/match/sfx-shortreadsort.h
Examining data/genometools-1.6.1+ds/src/match/tyr-basic.h
Examining data/genometools-1.6.1+ds/src/match/esa-minunique.c
Examining data/genometools-1.6.1+ds/src/match/firstcodes-psbuf.c
Examining data/genometools-1.6.1+ds/src/match/asqg_writer.h
Examining data/genometools-1.6.1+ds/src/match/firstcodes-tab.c
Examining data/genometools-1.6.1+ds/src/match/rdj-contigpaths.h
Examining data/genometools-1.6.1+ds/src/match/querymatch-display.h
Examining data/genometools-1.6.1+ds/src/match/diagband-struct.h
Examining data/genometools-1.6.1+ds/src/match/eis-specialsrank.h
Examining data/genometools-1.6.1+ds/src/match/sfx-lcpvalues.h
Examining data/genometools-1.6.1+ds/src/match/esa-seqread.c
Examining data/genometools-1.6.1+ds/src/match/fmi-fwduni.h
Examining data/genometools-1.6.1+ds/src/match/eis-bwtseq-sass.c
Examining data/genometools-1.6.1+ds/src/match/fmi-keyval.c
Examining data/genometools-1.6.1+ds/src/match/sfx-apfxlen.c
Examining data/genometools-1.6.1+ds/src/match/esa_visitor_rep.h
Examining data/genometools-1.6.1+ds/src/match/merger-trie.c
Examining data/genometools-1.6.1+ds/src/match/esa-splititv.c
Examining data/genometools-1.6.1+ds/src/match/twobits2kmers.c
Examining data/genometools-1.6.1+ds/src/match/eis-encidxseq-construct.c
Examining data/genometools-1.6.1+ds/src/match/esa-bottomup.h
Examining data/genometools-1.6.1+ds/src/match/fmindex.h
Examining data/genometools-1.6.1+ds/src/match/eis-bwtseq-context-param.h
Examining data/genometools-1.6.1+ds/src/match/bare-encseq.h
Examining data/genometools-1.6.1+ds/src/match/idx-limdfs.c
Examining data/genometools-1.6.1+ds/src/match/eis-seqranges.h
Examining data/genometools-1.6.1+ds/src/match/eis-encidxseq-param.c
Examining data/genometools-1.6.1+ds/src/match/eis-voiditf.c
Examining data/genometools-1.6.1+ds/src/match/eis-bwtseq.h
Examining data/genometools-1.6.1+ds/src/match/lcpinterval.h
Examining data/genometools-1.6.1+ds/src/match/querymatch.h
Examining data/genometools-1.6.1+ds/src/match/ft-eoplist.h
Examining data/genometools-1.6.1+ds/src/match/esa_visitor.h
Examining data/genometools-1.6.1+ds/src/match/eis-suffixarray-interface-siop.h
Examining data/genometools-1.6.1+ds/src/match/eis-voiditf.h
Examining data/genometools-1.6.1+ds/src/match/esa-bottomup.c
Examining data/genometools-1.6.1+ds/src/match/randomcodes-sfx-partssuf.h
Examining data/genometools-1.6.1+ds/src/match/rdj-filesuf-def.h
Examining data/genometools-1.6.1+ds/src/match/reads_libraries_table.h
Examining data/genometools-1.6.1+ds/src/match/eis-bwtseq.c
Examining data/genometools-1.6.1+ds/src/match/eis-mrangealphabet-priv.h
Examining data/genometools-1.6.1+ds/src/match/ft-front-generation.h
Examining data/genometools-1.6.1+ds/src/match/rdj-contfinder.c
Examining data/genometools-1.6.1+ds/src/match/eis-random-seqaccess.h
Examining data/genometools-1.6.1+ds/src/match/seqabstract.c
Examining data/genometools-1.6.1+ds/src/match/tyr-mkindex.h
Examining data/genometools-1.6.1+ds/src/match/sfx-enumcodes.c
Examining data/genometools-1.6.1+ds/src/match/eis-mrangealphabet-siop.h
Examining data/genometools-1.6.1+ds/src/match/sfx-maprange.h
Examining data/genometools-1.6.1+ds/src/match/eis-encidxseq-construct.h
Examining data/genometools-1.6.1+ds/src/match/randomcodes-find-seldom.h
Examining data/genometools-1.6.1+ds/src/match/hplstore.c
Examining data/genometools-1.6.1+ds/src/match/firstcodes-insert.c
Examining data/genometools-1.6.1+ds/src/match/spaced-seeds.c
Examining data/genometools-1.6.1+ds/src/match/randomcodes-hpcorrect.h
Examining data/genometools-1.6.1+ds/src/match/eis-bwtseq-param.h
Examining data/genometools-1.6.1+ds/src/match/rdj-twobitenc-editor.c
Examining data/genometools-1.6.1+ds/src/match/eis-mrangealphabet.h
Examining data/genometools-1.6.1+ds/src/match/cutendpfx.h
Examining data/genometools-1.6.1+ds/src/match/prsqualint.c
Examining data/genometools-1.6.1+ds/src/match/extend-offset.h
Examining data/genometools-1.6.1+ds/src/match/myersapm.c
Examining data/genometools-1.6.1+ds/src/match/sfx-suffixgetset.h
Examining data/genometools-1.6.1+ds/src/match/initeqsvec.c
Examining data/genometools-1.6.1+ds/src/match/sfx-lcpvalues.c
Examining data/genometools-1.6.1+ds/src/match/spmsuftab.c
Examining data/genometools-1.6.1+ds/src/match/rdj-strgraph-edges-short-def.h
Examining data/genometools-1.6.1+ds/src/match/karlin_altschul_stat.c
Examining data/genometools-1.6.1+ds/src/match/sfx-linlcp.c
Examining data/genometools-1.6.1+ds/src/match/esa-dfs.h
Examining data/genometools-1.6.1+ds/src/match/shu_unitfile.h
Examining data/genometools-1.6.1+ds/src/match/dbs_spaced_seeds.h
Examining data/genometools-1.6.1+ds/src/match/fmi-fwduni.c
Examining data/genometools-1.6.1+ds/src/match/idxlocalidp.h
Examining data/genometools-1.6.1+ds/src/match/turnwheels.c
Examining data/genometools-1.6.1+ds/src/match/sfx-opt.c
Examining data/genometools-1.6.1+ds/src/match/seed-extend.h
Examining data/genometools-1.6.1+ds/src/match/pckdfs.c
Examining data/genometools-1.6.1+ds/src/match/sfx-partssuf.c
Examining data/genometools-1.6.1+ds/src/match/sfx-bltrie.h
Examining data/genometools-1.6.1+ds/src/match/optionargmode.h
Examining data/genometools-1.6.1+ds/src/match/initeqsvec.h
Examining data/genometools-1.6.1+ds/src/match/idx-limdfs.h
Examining data/genometools-1.6.1+ds/src/match/sfx-shortreadsort.c
Examining data/genometools-1.6.1+ds/src/match/index_options.h
Examining data/genometools-1.6.1+ds/src/match/eis-encidxseq.c
Examining data/genometools-1.6.1+ds/src/match/randomcodes-correct.h
Examining data/genometools-1.6.1+ds/src/match/firstcodes.h
Examining data/genometools-1.6.1+ds/src/match/querymatch-display.c
Examining data/genometools-1.6.1+ds/src/match/eis-bitpackseqpos.h
Examining data/genometools-1.6.1+ds/src/match/eis-bwtseq-context-siop.h
Examining data/genometools-1.6.1+ds/src/match/rdj-strgraph-vertices-bitpack-def.h
Examining data/genometools-1.6.1+ds/src/match/rdj-cntlist.h
Examining data/genometools-1.6.1+ds/src/match/sfx-run.h
Examining data/genometools-1.6.1+ds/src/match/test-maxpairs.c
Examining data/genometools-1.6.1+ds/src/match/seed-extend-iter.h
Examining data/genometools-1.6.1+ds/src/match/pck-count-nodes.c
Examining data/genometools-1.6.1+ds/src/match/sfx-opt.h
Examining data/genometools-1.6.1+ds/src/match/querymatch.c
Examining data/genometools-1.6.1+ds/src/match/sfx-linlcp.h
Examining data/genometools-1.6.1+ds/src/match/rdj-ovlfind-dp.c
Examining data/genometools-1.6.1+ds/src/match/eis-suffixerator-interface.c
Examining data/genometools-1.6.1+ds/src/match/rdj-ovlfind-gusfield.c
Examining data/genometools-1.6.1+ds/src/match/randomcodes-tab.h
Examining data/genometools-1.6.1+ds/src/match/substriter.c
Examining data/genometools-1.6.1+ds/src/match/rectangle-store.h
Examining data/genometools-1.6.1+ds/src/match/prsqualint.h
Examining data/genometools-1.6.1+ds/src/match/test-mergeesa.h
Examining data/genometools-1.6.1+ds/src/match/rdj-version.h
Examining data/genometools-1.6.1+ds/src/match/chain2dim.c
Examining data/genometools-1.6.1+ds/src/match/esa-lcpintervals.c
Examining data/genometools-1.6.1+ds/src/match/eis-sa-common.c
Examining data/genometools-1.6.1+ds/src/match/eis-list-do.h
Examining data/genometools-1.6.1+ds/src/match/ft-polish.h
Examining data/genometools-1.6.1+ds/src/match/rdj-strgraph.c
Examining data/genometools-1.6.1+ds/src/match/sfx-copysort.c
Examining data/genometools-1.6.1+ds/src/match/esa-maxpairs.c
Examining data/genometools-1.6.1+ds/src/match/eis-encidxseq-priv.h
Examining data/genometools-1.6.1+ds/src/match/lua_tools.h
Examining data/genometools-1.6.1+ds/src/match/esa-map.h
Examining data/genometools-1.6.1+ds/src/match/randomcodes-find-seldom.c
Examining data/genometools-1.6.1+ds/src/match/dataalign.h
Examining data/genometools-1.6.1+ds/src/match/idxlocalisw.c
Examining data/genometools-1.6.1+ds/src/match/firstcodes-scan.h
Examining data/genometools-1.6.1+ds/src/match/eis-blockcomp-construct.h
Examining data/genometools-1.6.1+ds/src/match/sfx-sain.c
Examining data/genometools-1.6.1+ds/src/match/eis-sa-common.h
Examining data/genometools-1.6.1+ds/src/match/reads2twobit.c
Examining data/genometools-1.6.1+ds/src/match/gfa_writer.h
Examining data/genometools-1.6.1+ds/src/match/cgr_spacedseed.c
Examining data/genometools-1.6.1+ds/src/match/rdj-ovlfind-bf.h
Examining data/genometools-1.6.1+ds/src/match/seqabstract.h
Examining data/genometools-1.6.1+ds/src/match/pssm.c
Examining data/genometools-1.6.1+ds/src/match/squarededist.h
Examining data/genometools-1.6.1+ds/src/match/ft-front-prune.h
Examining data/genometools-1.6.1+ds/src/match/rdj-ovlfind-dp.h
Examining data/genometools-1.6.1+ds/src/match/rdj-revcompl-def.h
Examining data/genometools-1.6.1+ds/src/match/eis-bwtseq-context.h
Examining data/genometools-1.6.1+ds/src/match/eis-encidxseq.h
Examining data/genometools-1.6.1+ds/src/match/eis-suffixarray-interface.c
Examining data/genometools-1.6.1+ds/src/match/randomcodes.h
Examining data/genometools-1.6.1+ds/src/match/sfx-mappedstr.h
Examining data/genometools-1.6.1+ds/src/match/shu-divergence.h
Examining data/genometools-1.6.1+ds/src/match/shu-dfs.c
Examining data/genometools-1.6.1+ds/src/match/enum-patt.h
Examining data/genometools-1.6.1+ds/src/match/rdj-cntlist.c
Examining data/genometools-1.6.1+ds/src/match/qgram2code.h
Examining data/genometools-1.6.1+ds/src/match/shu_unitfile.c
Examining data/genometools-1.6.1+ds/src/match/optionargmode.c
Examining data/genometools-1.6.1+ds/src/match/bare-encseq.c
Examining data/genometools-1.6.1+ds/src/match/sfx-nextchar.h
Examining data/genometools-1.6.1+ds/src/match/rdj-spmlist.c
Examining data/genometools-1.6.1+ds/src/match/intcode-def.h
Examining data/genometools-1.6.1+ds/src/match/tagerator.c
Examining data/genometools-1.6.1+ds/src/match/giextract.c
Examining data/genometools-1.6.1+ds/src/match/rdj-spmproc.c
Examining data/genometools-1.6.1+ds/src/match/sfx-suffixer.h
Examining data/genometools-1.6.1+ds/src/match/diagbandseed.h
Examining data/genometools-1.6.1+ds/src/match/eis-sa-common-siop.h
Examining data/genometools-1.6.1+ds/src/match/rdj-contfind-def.h
Examining data/genometools-1.6.1+ds/src/match/rdj-contig-info.h
Examining data/genometools-1.6.1+ds/src/match/fmi-locate.h
Examining data/genometools-1.6.1+ds/src/match/test-mtrieins.h
Examining data/genometools-1.6.1+ds/src/match/esa-shulen.h
Examining data/genometools-1.6.1+ds/src/match/rdj-strgraph-vmark-def.h
Examining data/genometools-1.6.1+ds/src/match/tyr-show.h
Examining data/genometools-1.6.1+ds/src/match/eis-bwtseq-priv.h
Examining data/genometools-1.6.1+ds/src/match/encseq2offset.c
Examining data/genometools-1.6.1+ds/src/match/sfx-diffcov.h
Examining data/genometools-1.6.1+ds/src/match/sfx-radixsort.h
Examining data/genometools-1.6.1+ds/src/match/rdj-contigs-writer.h
Examining data/genometools-1.6.1+ds/src/match/rdj-contfind-bottomup.c
Examining data/genometools-1.6.1+ds/src/match/esa_spmitvs_visitor.h
Examining data/genometools-1.6.1+ds/src/match/eis-blockcomp-param.c
Examining data/genometools-1.6.1+ds/src/match/dbs_spaced_seeds.c
Examining data/genometools-1.6.1+ds/src/match/greedyedist.c
Examining data/genometools-1.6.1+ds/src/match/rdj-ovlfind-gusfield.h
Examining data/genometools-1.6.1+ds/src/match/esa-merge.c
Examining data/genometools-1.6.1+ds/src/match/esa_visitor.c
Examining data/genometools-1.6.1+ds/src/match/rdj-contigs-graph.h
Examining data/genometools-1.6.1+ds/src/match/seed_extend_parts.c
Examining data/genometools-1.6.1+ds/src/match/eis-specialsrank.c
Examining data/genometools-1.6.1+ds/src/match/tyr-mersplit.c
Examining data/genometools-1.6.1+ds/src/match/tyr-search.c
Examining data/genometools-1.6.1+ds/src/match/bcktab.c
Examining data/genometools-1.6.1+ds/src/match/sfx-lwcheck.h
Examining data/genometools-1.6.1+ds/src/match/sfx-outprj.c
Examining data/genometools-1.6.1+ds/src/match/turnwheels.h
Examining data/genometools-1.6.1+ds/src/match/initbasepower.h
Examining data/genometools-1.6.1+ds/src/match/sfx-partssuf.h
Examining data/genometools-1.6.1+ds/src/match/shu-divergence.c
Examining data/genometools-1.6.1+ds/src/match/rdj-spmproc.h
Examining data/genometools-1.6.1+ds/src/match/sfx-strategy.h
Examining data/genometools-1.6.1+ds/src/match/apmeoveridx.c
Examining data/genometools-1.6.1+ds/src/match/fmi-mapspec.c
Examining data/genometools-1.6.1+ds/src/match/fmi-mkindex.h
Examining data/genometools-1.6.1+ds/src/match/sfx-diffcov.c
Examining data/genometools-1.6.1+ds/src/match/diagband-struct.c
Examining data/genometools-1.6.1+ds/src/match/rdj-errfind.h
Examining data/genometools-1.6.1+ds/src/match/marksubstring.h
Examining data/genometools-1.6.1+ds/src/match/test-mappedstr.c
Examining data/genometools-1.6.1+ds/src/match/randomcodes-insert.c
Examining data/genometools-1.6.1+ds/src/match/kmer2string.h
Examining data/genometools-1.6.1+ds/src/match/eis-bwtseq-extinfo.h
Examining data/genometools-1.6.1+ds/src/match/eis-suffixerator-interface.h
Examining data/genometools-1.6.1+ds/src/match/rdj-errfind.c
Examining data/genometools-1.6.1+ds/src/match/eis-bwtseq-param.c
Examining data/genometools-1.6.1+ds/src/match/rdj-strgraph-vertices-bitfield-def.h
Examining data/genometools-1.6.1+ds/src/match/sfx-bltrie.c
Examining data/genometools-1.6.1+ds/src/match/kmercodes.h
Examining data/genometools-1.6.1+ds/src/match/sfx-bentsedg.c
Examining data/genometools-1.6.1+ds/src/match/sfx-sain.h
Examining data/genometools-1.6.1+ds/src/match/sfx-run.c
Examining data/genometools-1.6.1+ds/src/lualib.c
Examining data/genometools-1.6.1+ds/src/extended/splice_site_info_stream.c
Examining data/genometools-1.6.1+ds/src/extended/gff3_linesorted_out_stream.h
Examining data/genometools-1.6.1+ds/src/extended/seqpos_classifier.h
Examining data/genometools-1.6.1+ds/src/extended/gff3_defines.h
Examining data/genometools-1.6.1+ds/src/extended/match_blast_api.h
Examining data/genometools-1.6.1+ds/src/extended/match_visitor_api.h
Examining data/genometools-1.6.1+ds/src/extended/type_node.c
Examining data/genometools-1.6.1+ds/src/extended/match_blast.c
Examining data/genometools-1.6.1+ds/src/extended/match_iterator.c
Examining data/genometools-1.6.1+ds/src/extended/feature_info.h
Examining data/genometools-1.6.1+ds/src/extended/string_matching.h
Examining data/genometools-1.6.1+ds/src/extended/match_open.c
Examining data/genometools-1.6.1+ds/src/extended/dice_hmm.c
Examining data/genometools-1.6.1+ds/src/extended/rdb_mysql.c
Examining data/genometools-1.6.1+ds/src/extended/csa_stream.c
Examining data/genometools-1.6.1+ds/src/extended/sam_alignment.h
Examining data/genometools-1.6.1+ds/src/extended/region_node.c
Examining data/genometools-1.6.1+ds/src/extended/cds_check_stream.h
Examining data/genometools-1.6.1+ds/src/extended/alignment.c
Examining data/genometools-1.6.1+ds/src/extended/blast_process_call.c
Examining data/genometools-1.6.1+ds/src/extended/meta_node.c
Examining data/genometools-1.6.1+ds/src/extended/feature_out_stream_api.h
Examining data/genometools-1.6.1+ds/src/extended/rdb_visitor_api.h
Examining data/genometools-1.6.1+ds/src/extended/feature_visitor.h
Examining data/genometools-1.6.1+ds/src/extended/golomb.h
Examining data/genometools-1.6.1+ds/src/extended/multi_sanitizer_visitor.h
Examining data/genometools-1.6.1+ds/src/extended/feature_in_stream_api.h
Examining data/genometools-1.6.1+ds/src/extended/maxcoordvalue.c
Examining data/genometools-1.6.1+ds/src/extended/dup_feature_stream_api.h
Examining data/genometools-1.6.1+ds/src/extended/ranked_list.h
Examining data/genometools-1.6.1+ds/src/extended/select_visitor.c
Examining data/genometools-1.6.1+ds/src/extended/select_stream.c
Examining data/genometools-1.6.1+ds/src/extended/mutate.c
Examining data/genometools-1.6.1+ds/src/extended/add_ids_visitor.h
Examining data/genometools-1.6.1+ds/src/extended/dice_hmm.h
Examining data/genometools-1.6.1+ds/src/extended/sampling.c
Examining data/genometools-1.6.1+ds/src/extended/load_stream.c
Examining data/genometools-1.6.1+ds/src/extended/wtree_rep.h
Examining data/genometools-1.6.1+ds/src/extended/intset.c
Examining data/genometools-1.6.1+ds/src/extended/gff3_out_stream_api.h
Examining data/genometools-1.6.1+ds/src/extended/id_to_md5_stream_api.h
Examining data/genometools-1.6.1+ds/src/extended/wtree.h
Examining data/genometools-1.6.1+ds/src/extended/script_wrapper_visitor_api.h
Examining data/genometools-1.6.1+ds/src/extended/transcript_evaluators.h
Examining data/genometools-1.6.1+ds/src/extended/bed_in_stream.h
Examining data/genometools-1.6.1+ds/src/extended/reconstructalignment.h
Examining data/genometools-1.6.1+ds/src/extended/condenseq.h
Examining data/genometools-1.6.1+ds/src/extended/add_ids_visitor.c
Examining data/genometools-1.6.1+ds/src/extended/uniq_stream.c
Examining data/genometools-1.6.1+ds/src/extended/sequence_node.c
Examining data/genometools-1.6.1+ds/src/extended/feature_index_rep.h
Examining data/genometools-1.6.1+ds/src/extended/sspliced_alignment_parsing.h
Examining data/genometools-1.6.1+ds/src/extended/maxcoordvalue.h
Examining data/genometools-1.6.1+ds/src/extended/swalign.h
Examining data/genometools-1.6.1+ds/src/extended/seqpos_classifier.c
Examining data/genometools-1.6.1+ds/src/extended/rbtree.c
Examining data/genometools-1.6.1+ds/src/extended/rdb_visitor.c
Examining data/genometools-1.6.1+ds/src/extended/splice_site_info_visitor.c
Examining data/genometools-1.6.1+ds/src/extended/permute_words.c
Examining data/genometools-1.6.1+ds/src/extended/dup_feature_visitor.h
Examining data/genometools-1.6.1+ds/src/extended/fasta_header_iterator.h
Examining data/genometools-1.6.1+ds/src/extended/uniq_stream_api.h
Examining data/genometools-1.6.1+ds/src/extended/load_stream.h
Examining data/genometools-1.6.1+ds/src/extended/gtdatahelp.h
Examining data/genometools-1.6.1+ds/src/extended/intset_16.h
Examining data/genometools-1.6.1+ds/src/extended/check_boundaries_visitor_api.h
Examining data/genometools-1.6.1+ds/src/extended/match_iterator_sw.c
Examining data/genometools-1.6.1+ds/src/extended/type_checker_builtin.c
Examining data/genometools-1.6.1+ds/src/extended/compressed_bitsequence.c
Examining data/genometools-1.6.1+ds/src/extended/collect_ids_visitor.h
Examining data/genometools-1.6.1+ds/src/extended/tag_value_map.c
Examining data/genometools-1.6.1+ds/src/extended/intset_rep.h
Examining data/genometools-1.6.1+ds/src/extended/match_api.h
Examining data/genometools-1.6.1+ds/src/extended/bed_parser.h
Examining data/genometools-1.6.1+ds/src/extended/uint64hashtable_primes.h
Examining data/genometools-1.6.1+ds/src/extended/stat_stream_api.h
Examining data/genometools-1.6.1+ds/src/extended/clustered_set_uf.c
Examining data/genometools-1.6.1+ds/src/extended/samfile_encseq_mapping.h
Examining data/genometools-1.6.1+ds/src/extended/gff3_in_stream.h
Examining data/genometools-1.6.1+ds/src/extended/rdb_sqlite.c
Examining data/genometools-1.6.1+ds/src/extended/xrf_abbr_entry.h
Examining data/genometools-1.6.1+ds/src/extended/md5set_primes_table.h
Examining data/genometools-1.6.1+ds/src/extended/sequence_node_add_stream.h
Examining data/genometools-1.6.1+ds/src/extended/encdesc.h
Examining data/genometools-1.6.1+ds/src/extended/sampling.h
Examining data/genometools-1.6.1+ds/src/extended/sspliced_alignment_parsing.c
Examining data/genometools-1.6.1+ds/src/extended/csa_variable_strands.h
Examining data/genometools-1.6.1+ds/src/extended/orf_iterator.c
Examining data/genometools-1.6.1+ds/src/extended/cds_visitor.c
Examining data/genometools-1.6.1+ds/src/extended/sort_stream.h
Examining data/genometools-1.6.1+ds/src/extended/feature_node.c
Examining data/genometools-1.6.1+ds/src/extended/stat_stream.c
Examining data/genometools-1.6.1+ds/src/extended/shredder.h
Examining data/genometools-1.6.1+ds/src/extended/type_checker_api.h
Examining data/genometools-1.6.1+ds/src/extended/assembly_stats_calculator.h
Examining data/genometools-1.6.1+ds/src/extended/typecheck_info.h
Examining data/genometools-1.6.1+ds/src/extended/targetbest_select_stream.h
Examining data/genometools-1.6.1+ds/src/extended/obo_stanza.c
Examining data/genometools-1.6.1+ds/src/extended/cstr_iterator.h
Examining data/genometools-1.6.1+ds/src/extended/match_iterator_open.h
Examining data/genometools-1.6.1+ds/src/extended/csa_variable_strands.c
Examining data/genometools-1.6.1+ds/src/extended/stat_visitor.h
Examining data/genometools-1.6.1+ds/src/extended/mapping.h
Examining data/genometools-1.6.1+ds/src/extended/sam_alignment.c
Examining data/genometools-1.6.1+ds/src/extended/dup_feature_visitor.c
Examining data/genometools-1.6.1+ds/src/extended/rdb_rep.h
Examining data/genometools-1.6.1+ds/src/extended/spec_results.h
Examining data/genometools-1.6.1+ds/src/extended/feature_visitor.c
Examining data/genometools-1.6.1+ds/src/extended/splice_site_info_stream_api.h
Examining data/genometools-1.6.1+ds/src/extended/xrf_abbr_entry.c
Examining data/genometools-1.6.1+ds/src/extended/assembly_stats_calculator.c
Examining data/genometools-1.6.1+ds/src/extended/genome_node_rep.h
Examining data/genometools-1.6.1+ds/src/extended/rdb.c
Examining data/genometools-1.6.1+ds/src/extended/linspace_management.c
Examining data/genometools-1.6.1+ds/src/extended/buffer_stream.c
Examining data/genometools-1.6.1+ds/src/extended/match_iterator_blast.c
Examining data/genometools-1.6.1+ds/src/extended/io_function_pointers.h
Examining data/genometools-1.6.1+ds/src/extended/rcr.c
Examining data/genometools-1.6.1+ds/src/extended/coin_hmm.h
Examining data/genometools-1.6.1+ds/src/extended/encdesc_header_io.c
Examining data/genometools-1.6.1+ds/src/extended/hcr.c
Examining data/genometools-1.6.1+ds/src/extended/xrf_abbr_parse_tree.c
Examining data/genometools-1.6.1+ds/src/extended/match_last.c
Examining data/genometools-1.6.1+ds/src/extended/dot_out_stream.c
Examining data/genometools-1.6.1+ds/src/extended/gtf_parser.h
Examining data/genometools-1.6.1+ds/src/extended/xrf_abbr_parse_tree.h
Examining data/genometools-1.6.1+ds/src/extended/bitoutstream.h
Examining data/genometools-1.6.1+ds/src/extended/mapping.c
Examining data/genometools-1.6.1+ds/src/extended/match_open.h
Examining data/genometools-1.6.1+ds/src/extended/match_iterator_last.h
Examining data/genometools-1.6.1+ds/src/extended/select_stream.h
Examining data/genometools-1.6.1+ds/src/extended/chain_api.h
Examining data/genometools-1.6.1+ds/src/extended/bed_parser.c
Examining data/genometools-1.6.1+ds/src/extended/stat_visitor.c
Examining data/genometools-1.6.1+ds/src/extended/regular_seqid.c
Examining data/genometools-1.6.1+ds/src/extended/multieoplist.h
Examining data/genometools-1.6.1+ds/src/extended/condenseq_search_arguments.c
Examining data/genometools-1.6.1+ds/src/extended/gff3_in_stream_api.h
Examining data/genometools-1.6.1+ds/src/extended/sequence_node_api.h
Examining data/genometools-1.6.1+ds/src/extended/sequence_node_out_visitor.h
Examining data/genometools-1.6.1+ds/src/extended/transcript_exons.h
Examining data/genometools-1.6.1+ds/src/extended/transcript_used_exons.c
Examining data/genometools-1.6.1+ds/src/extended/wtree_encseq.c
Examining data/genometools-1.6.1+ds/src/extended/gtf_visitor.h
Examining data/genometools-1.6.1+ds/src/extended/rdb_sqlite_api.h
Examining data/genometools-1.6.1+ds/src/extended/uint64hashtable.h
Examining data/genometools-1.6.1+ds/src/extended/extract_feature_visitor.h
Examining data/genometools-1.6.1+ds/src/extended/union_find.c
Examining data/genometools-1.6.1+ds/src/extended/sam_query_name_iterator.c
Examining data/genometools-1.6.1+ds/src/extended/feature_index_memory.h
Examining data/genometools-1.6.1+ds/src/extended/sspliced_alignment.c
Examining data/genometools-1.6.1+ds/src/extended/feature_node_iterator.c
Examining data/genometools-1.6.1+ds/src/extended/array_out_stream.h
Examining data/genometools-1.6.1+ds/src/extended/visitor_stream.c
Examining data/genometools-1.6.1+ds/src/extended/diagonalbandalign_affinegapcost.c
Examining data/genometools-1.6.1+ds/src/extended/orf_finder_visitor.h
Examining data/genometools-1.6.1+ds/src/extended/hmm.h
Examining data/genometools-1.6.1+ds/src/extended/condenseq_creator.h
Examining data/genometools-1.6.1+ds/src/extended/md5_to_id_stream.c
Examining data/genometools-1.6.1+ds/src/extended/string_matching.c
Examining data/genometools-1.6.1+ds/src/extended/script_filter.c
Examining data/genometools-1.6.1+ds/src/extended/feature_node_observer.h
Examining data/genometools-1.6.1+ds/src/extended/inter_feature_visitor.h
Examining data/genometools-1.6.1+ds/src/extended/sam_alignment_rep.h
Examining data/genometools-1.6.1+ds/src/extended/intset.h
Examining data/genometools-1.6.1+ds/src/extended/transcript_feature_type.h
Examining data/genometools-1.6.1+ds/src/extended/sequence_node_out_stream.h
Examining data/genometools-1.6.1+ds/src/extended/obo_parse_tree.c
Examining data/genometools-1.6.1+ds/src/extended/set_source_visitor.c
Examining data/genometools-1.6.1+ds/src/extended/diagonalbandalign.h
Examining data/genometools-1.6.1+ds/src/extended/add_introns_stream_api.h
Examining data/genometools-1.6.1+ds/src/extended/xrfcheck_info.h
Examining data/genometools-1.6.1+ds/src/extended/type_checker.h
Examining data/genometools-1.6.1+ds/src/extended/chseqids_stream.c
Examining data/genometools-1.6.1+ds/src/extended/type_checker_builtin_api.h
Examining data/genometools-1.6.1+ds/src/extended/script_wrapper_stream.c
Examining data/genometools-1.6.1+ds/src/extended/globalchaining.c
Examining data/genometools-1.6.1+ds/src/extended/md5_to_id_visitor.c
Examining data/genometools-1.6.1+ds/src/extended/sam_query_name_iterator.h
Examining data/genometools-1.6.1+ds/src/extended/kmer_database.h
Examining data/genometools-1.6.1+ds/src/extended/samfile_iterator.c
Examining data/genometools-1.6.1+ds/src/extended/gap_str.h
Examining data/genometools-1.6.1+ds/src/extended/huffcode.h
Examining data/genometools-1.6.1+ds/src/extended/aligned_segment.c
Examining data/genometools-1.6.1+ds/src/extended/feature_node_rep.h
Examining data/genometools-1.6.1+ds/src/extended/node_stream.c
Examining data/genometools-1.6.1+ds/src/extended/tag_value_map_api.h
Examining data/genometools-1.6.1+ds/src/extended/transcript_exons.c
Examining data/genometools-1.6.1+ds/src/extended/regioncov_visitor.h
Examining data/genometools-1.6.1+ds/src/extended/editscript.c
Examining data/genometools-1.6.1+ds/src/extended/select_stream_api.h
Examining data/genometools-1.6.1+ds/src/extended/compressed_bitsequence.h
Examining data/genometools-1.6.1+ds/src/extended/csa_visitor.h
Examining data/genometools-1.6.1+ds/src/extended/feature_node.h
Examining data/genometools-1.6.1+ds/src/extended/script_wrapper_visitor.h
Examining data/genometools-1.6.1+ds/src/extended/match_iterator_last.c
Examining data/genometools-1.6.1+ds/src/extended/region_mapping.h
Examining data/genometools-1.6.1+ds/src/extended/node_visitor.h
Examining data/genometools-1.6.1+ds/src/extended/coin_hmm.c
Examining data/genometools-1.6.1+ds/src/extended/uniq_stream.h
Examining data/genometools-1.6.1+ds/src/extended/match_sw.h
Examining data/genometools-1.6.1+ds/src/extended/match_rep.h
Examining data/genometools-1.6.1+ds/src/extended/gff3_visitor_api.h
Examining data/genometools-1.6.1+ds/src/extended/comment_node_api.h
Examining data/genometools-1.6.1+ds/src/extended/seqid2file_api.h
Examining data/genometools-1.6.1+ds/src/extended/match_last_api.h
Examining data/genometools-1.6.1+ds/src/extended/wtree_encseq.h
Examining data/genometools-1.6.1+ds/src/extended/elias_gamma.h
Examining data/genometools-1.6.1+ds/src/extended/buffer_stream_api.h
Examining data/genometools-1.6.1+ds/src/extended/clustered_set.c
Examining data/genometools-1.6.1+ds/src/extended/dot_out_stream.h
Examining data/genometools-1.6.1+ds/src/extended/md5set.h
Examining data/genometools-1.6.1+ds/src/extended/editscript.h
Examining data/genometools-1.6.1+ds/src/extended/match_iterator_rep.h
Examining data/genometools-1.6.1+ds/src/extended/snp_annotator_visitor.h
Examining data/genometools-1.6.1+ds/src/extended/anno_db_prepared_stmt.h
Examining data/genometools-1.6.1+ds/src/extended/condenseq.c
Examining data/genometools-1.6.1+ds/src/extended/shredder.c
Examining data/genometools-1.6.1+ds/src/extended/extract_feature_sequence.h
Examining data/genometools-1.6.1+ds/src/extended/script_wrapper_visitor.c
Examining data/genometools-1.6.1+ds/src/extended/orf_finder_stream.c
Examining data/genometools-1.6.1+ds/src/extended/md5_to_id_stream_api.h
Examining data/genometools-1.6.1+ds/src/extended/sort_stream_api.h
Examining data/genometools-1.6.1+ds/src/extended/id_to_md5_visitor.h
Examining data/genometools-1.6.1+ds/src/extended/typecheck_info.c
Examining data/genometools-1.6.1+ds/src/extended/evaluator.c
Examining data/genometools-1.6.1+ds/src/extended/array_in_stream.c
Examining data/genometools-1.6.1+ds/src/extended/popcount_tab.c
Examining data/genometools-1.6.1+ds/src/extended/priority_queue.c
Examining data/genometools-1.6.1+ds/src/extended/match_iterator_api.h
Examining data/genometools-1.6.1+ds/src/extended/comment_node.c
Examining data/genometools-1.6.1+ds/src/extended/reverse.c
Examining data/genometools-1.6.1+ds/src/extended/array_out_stream_api.h
Examining data/genometools-1.6.1+ds/src/extended/array_in_stream.h
Examining data/genometools-1.6.1+ds/src/extended/rdb_mysql_api.h
Examining data/genometools-1.6.1+ds/src/extended/multi_sanitizer_visitor.c
Examining data/genometools-1.6.1+ds/src/extended/feature_index_api.h
Examining data/genometools-1.6.1+ds/src/extended/gff3_output.h
Examining data/genometools-1.6.1+ds/src/extended/gff3_numsorted_out_stream.c
Examining data/genometools-1.6.1+ds/src/extended/seqid2seqnum_mapping.c
Examining data/genometools-1.6.1+ds/src/extended/kmer_database.c
Examining data/genometools-1.6.1+ds/src/extended/gtf_out_stream_api.h
Examining data/genometools-1.6.1+ds/src/extended/gff3_in_stream_plain.h
Examining data/genometools-1.6.1+ds/src/extended/gtf_visitor.c
Examining data/genometools-1.6.1+ds/src/extended/cds_visitor_api.h
Examining data/genometools-1.6.1+ds/src/extended/sspliced_alignment.h
Examining data/genometools-1.6.1+ds/src/extended/type_checker_obo.c
Examining data/genometools-1.6.1+ds/src/extended/match_visitor.h
Examining data/genometools-1.6.1+ds/src/extended/reverse_api.h
Examining data/genometools-1.6.1+ds/src/extended/hcr.h
Examining data/genometools-1.6.1+ds/src/extended/check_boundaries_visitor.c
Examining data/genometools-1.6.1+ds/src/extended/feature_node_iterator_api.h
Examining data/genometools-1.6.1+ds/src/extended/hmm.c
Examining data/genometools-1.6.1+ds/src/extended/dot_visitor.h
Examining data/genometools-1.6.1+ds/src/extended/luaserialize.h
Examining data/genometools-1.6.1+ds/src/extended/tidy_region_node_visitor.c
Examining data/genometools-1.6.1+ds/src/extended/luahelper.h
Examining data/genometools-1.6.1+ds/src/extended/csa_splice_form.h
Examining data/genometools-1.6.1+ds/src/extended/feature_stream.c
Examining data/genometools-1.6.1+ds/src/extended/clustered_set_rep.h
Examining data/genometools-1.6.1+ds/src/extended/csa_gene.h
Examining data/genometools-1.6.1+ds/src/extended/aligned_segment.h
Examining data/genometools-1.6.1+ds/src/extended/feature_in_stream.c
Examining data/genometools-1.6.1+ds/src/extended/clustered_set.h
Examining data/genometools-1.6.1+ds/src/extended/gff3_numsorted_out_stream.h
Examining data/genometools-1.6.1+ds/src/extended/genome_node_api.h
Examining data/genometools-1.6.1+ds/src/extended/obo_parse_tree.h
Examining data/genometools-1.6.1+ds/src/extended/script_filter.h
Examining data/genometools-1.6.1+ds/src/extended/spec_results.c
Examining data/genometools-1.6.1+ds/src/extended/sequence_node_add_stream.c
Examining data/genometools-1.6.1+ds/src/extended/type_graph.c
Examining data/genometools-1.6.1+ds/src/extended/encdesc_rep.h
Examining data/genometools-1.6.1+ds/src/extended/gff3_parser.c
Examining data/genometools-1.6.1+ds/src/extended/anno_db_gfflike.c
Examining data/genometools-1.6.1+ds/src/extended/golomb.c
Examining data/genometools-1.6.1+ds/src/extended/consensus_sa_api.h
Examining data/genometools-1.6.1+ds/src/extended/add_ids_stream.h
Examining data/genometools-1.6.1+ds/src/extended/targetbest_select_stream.c
Examining data/genometools-1.6.1+ds/src/extended/stream_evaluator.h
Examining data/genometools-1.6.1+ds/src/extended/gtdatahelp.c
Examining data/genometools-1.6.1+ds/src/extended/gff3_escaping_api.h
Examining data/genometools-1.6.1+ds/src/extended/match_visitor.c
Examining data/genometools-1.6.1+ds/src/extended/alignment.h
Examining data/genometools-1.6.1+ds/src/extended/orf_finder_stream.h
Examining data/genometools-1.6.1+ds/src/extended/squarealign.c
Examining data/genometools-1.6.1+ds/src/extended/affinealign.h
Examining data/genometools-1.6.1+ds/src/extended/encdesc_header_io.h
Examining data/genometools-1.6.1+ds/src/extended/script_wrapper_stream.h
Examining data/genometools-1.6.1+ds/src/extended/tidy_region_node_visitor.h
Examining data/genometools-1.6.1+ds/src/extended/consensus_sa.c
Examining data/genometools-1.6.1+ds/src/extended/match_iterator_open.c
Examining data/genometools-1.6.1+ds/src/extended/gtf_in_stream.c
Examining data/genometools-1.6.1+ds/src/extended/merge_stream_api.h
Examining data/genometools-1.6.1+ds/src/extended/diagonalbandalign_affinegapcost.h
Examining data/genometools-1.6.1+ds/src/extended/feature_index.h
Examining data/genometools-1.6.1+ds/src/extended/eof_node.c
Examining data/genometools-1.6.1+ds/src/extended/stream_evaluator.c
Examining data/genometools-1.6.1+ds/src/extended/region_node_builder.c
Examining data/genometools-1.6.1+ds/src/extended/match_sw_api.h
Examining data/genometools-1.6.1+ds/src/extended/wtree.c
Examining data/genometools-1.6.1+ds/src/extended/xrf_checker_api.h
Examining data/genometools-1.6.1+ds/src/extended/regioncov_visitor.c
Examining data/genometools-1.6.1+ds/src/extended/tidy_region_node_stream.h
Examining data/genometools-1.6.1+ds/src/extended/tir_stream.h
Examining data/genometools-1.6.1+ds/src/extended/linearalign.c
Examining data/genometools-1.6.1+ds/src/extended/tir_stream.c
Examining data/genometools-1.6.1+ds/src/extended/merge_stream.c
Examining data/genometools-1.6.1+ds/src/extended/snp_annotator_stream.h
Examining data/genometools-1.6.1+ds/src/extended/hpol_processor.h
Examining data/genometools-1.6.1+ds/src/extended/md5set.c
Examining data/genometools-1.6.1+ds/src/extended/intset_32.c
Examining data/genometools-1.6.1+ds/src/extended/transcript_counts.c
Examining data/genometools-1.6.1+ds/src/extended/feature_index_memory.c
Examining data/genometools-1.6.1+ds/src/extended/cds_stream.c
Examining data/genometools-1.6.1+ds/src/extended/multieoplist.c
Examining data/genometools-1.6.1+ds/src/extended/tidy_region_node_stream.c
Examining data/genometools-1.6.1+ds/src/extended/id_to_md5_stream.c
Examining data/genometools-1.6.1+ds/src/extended/splice_site_info_visitor.h
Examining data/genometools-1.6.1+ds/src/extended/intset_32.h
Examining data/genometools-1.6.1+ds/src/extended/gff3_visitor.h
Examining data/genometools-1.6.1+ds/src/extended/dot_visitor.c
Examining data/genometools-1.6.1+ds/src/extended/type_checker_obo_api.h
Examining data/genometools-1.6.1+ds/src/extended/anno_db_gfflike_api.h
Examining data/genometools-1.6.1+ds/src/extended/type_node.h
Examining data/genometools-1.6.1+ds/src/extended/visitor_stream_api.h
Examining data/genometools-1.6.1+ds/src/extended/condenseq_creator.c
Examining data/genometools-1.6.1+ds/src/extended/rcr.h
Examining data/genometools-1.6.1+ds/src/extended/splicedseq.c
Examining data/genometools-1.6.1+ds/src/extended/bitinstream.h
Examining data/genometools-1.6.1+ds/src/extended/samfile_encseq_mapping.c
Examining data/genometools-1.6.1+ds/src/extended/mutate.h
Examining data/genometools-1.6.1+ds/src/extended/match_iterator_sw.h
Examining data/genometools-1.6.1+ds/src/extended/encdesc.c
Examining data/genometools-1.6.1+ds/src/extended/merge_stream.h
Examining data/genometools-1.6.1+ds/src/extended/rbtree_api.h
Examining data/genometools-1.6.1+ds/src/extended/snp_annotator_stream.c
Examining data/genometools-1.6.1+ds/src/extended/gff3_output.c
Examining data/genometools-1.6.1+ds/src/extended/affinealign.c
Examining data/genometools-1.6.1+ds/src/extended/feature_stream_api.h
Examining data/genometools-1.6.1+ds/src/extended/orf_iterator_api.h
Examining data/genometools-1.6.1+ds/src/extended/condenseq_search_arguments.h
Examining data/genometools-1.6.1+ds/src/extended/merge_feature_stream.c
Examining data/genometools-1.6.1+ds/src/extended/clustered_set_uf.h
Examining data/genometools-1.6.1+ds/src/extended/meta_node_api.h
Examining data/genometools-1.6.1+ds/src/extended/gff3_parser_api.h
Examining data/genometools-1.6.1+ds/src/extended/chseqids_stream.h
Examining data/genometools-1.6.1+ds/src/extended/luahelper.c
Examining data/genometools-1.6.1+ds/src/extended/orphanage.h
Examining data/genometools-1.6.1+ds/src/extended/hpol_processor.c
Examining data/genometools-1.6.1+ds/src/extended/extract_feature_sequence.c
Examining data/genometools-1.6.1+ds/src/extended/sequence_node_out_stream.c
Examining data/genometools-1.6.1+ds/src/extended/sort_stream.c
Examining data/genometools-1.6.1+ds/src/extended/csa_splice_form.c
Examining data/genometools-1.6.1+ds/src/extended/feature_index.c
Examining data/genometools-1.6.1+ds/src/extended/cds_stream_api.h
Examining data/genometools-1.6.1+ds/src/extended/genome_node.c
Examining data/genometools-1.6.1+ds/src/extended/collect_ids_visitor.c
Examining data/genometools-1.6.1+ds/src/extended/xrfcheck_info.c
Examining data/genometools-1.6.1+ds/src/extended/elias_gamma.c
Examining data/genometools-1.6.1+ds/src/extended/feature_info.c
Examining data/genometools-1.6.1+ds/src/extended/rmq.c
Examining data/genometools-1.6.1+ds/src/extended/uint64hashtable.c
Examining data/genometools-1.6.1+ds/src/extended/match_iterator_blast.h
Examining data/genometools-1.6.1+ds/src/extended/gff3_escaping.c
Examining data/genometools-1.6.1+ds/src/extended/orf_finder_visitor.c
Examining data/genometools-1.6.1+ds/src/extended/array_in_stream_api.h
Examining data/genometools-1.6.1+ds/src/extended/swalign.c
Examining data/genometools-1.6.1+ds/src/extended/merge_feature_visitor.h
Examining data/genometools-1.6.1+ds/src/extended/type_checker_rep.h
Examining data/genometools-1.6.1+ds/src/extended/feature_in_stream.h
Examining data/genometools-1.6.1+ds/src/extended/splicedseq.h
Examining data/genometools-1.6.1+ds/src/extended/feature_node_observer.c
Examining data/genometools-1.6.1+ds/src/extended/genome_node.h
Examining data/genometools-1.6.1+ds/src/extended/chain.c
Examining data/genometools-1.6.1+ds/src/extended/merge_feature_visitor.c
Examining data/genometools-1.6.1+ds/src/extended/anno_db_schema.c
Examining data/genometools-1.6.1+ds/src/extended/select_visitor.h
Examining data/genometools-1.6.1+ds/src/extended/xrf_checker.c
Examining data/genometools-1.6.1+ds/src/extended/csa_gene.c
Examining data/genometools-1.6.1+ds/src/extended/cstr_iterator_rep.h
Examining data/genometools-1.6.1+ds/src/extended/samfile_iterator.h
Examining data/genometools-1.6.1+ds/src/extended/transcript_used_exons.h
Examining data/genometools-1.6.1+ds/src/extended/id_to_md5_visitor.c
Examining data/genometools-1.6.1+ds/src/extended/type_graph.h
Examining data/genometools-1.6.1+ds/src/extended/set_source_visitor_api.h
Examining data/genometools-1.6.1+ds/src/extended/region_node_api.h
Examining data/genometools-1.6.1+ds/src/extended/io_function_pointers.c
Examining data/genometools-1.6.1+ds/src/extended/inter_feature_visitor.c
Examining data/genometools-1.6.1+ds/src/extended/linearalign.h
Examining data/genometools-1.6.1+ds/src/extended/feature_index_memory_api.h
Examining data/genometools-1.6.1+ds/src/extended/gff3_in_stream.c
Examining data/genometools-1.6.1+ds/src/extended/script_wrapper_stream_api.h
Examining data/genometools-1.6.1+ds/src/extended/gff3_parser.h
Examining data/genometools-1.6.1+ds/src/extended/blast_process_call.h
Examining data/genometools-1.6.1+ds/src/extended/snp_annotator_visitor.c
Examining data/genometools-1.6.1+ds/src/extended/luaserialize.c
Examining data/genometools-1.6.1+ds/src/extended/cds_check_stream.c
Examining data/genometools-1.6.1+ds/src/extended/match_sw.c
Examining data/genometools-1.6.1+ds/src/extended/bitinstream.c
Examining data/genometools-1.6.1+ds/src/extended/ranked_list.c
Examining data/genometools-1.6.1+ds/src/extended/match.c
Examining data/genometools-1.6.1+ds/src/extended/match.h
Examining data/genometools-1.6.1+ds/src/extended/match_blast.h
Examining data/genometools-1.6.1+ds/src/extended/feature_node_api.h
Examining data/genometools-1.6.1+ds/src/extended/linearalign_affinegapcost.c
Examining data/genometools-1.6.1+ds/src/extended/gtf_parser.c
Examining data/genometools-1.6.1+ds/src/extended/rmq.h
Examining data/genometools-1.6.1+ds/src/extended/add_introns_stream.c
Examining data/genometools-1.6.1+ds/src/extended/rdb_api.h
Examining data/genometools-1.6.1+ds/src/extended/huffcode.c
Examining data/genometools-1.6.1+ds/src/extended/feature_type_api.h
Examining data/genometools-1.6.1+ds/src/extended/script_filter_api.h
Examining data/genometools-1.6.1+ds/src/extended/gff3_in_stream_plain.c
Examining data/genometools-1.6.1+ds/src/extended/obo_stanza.h
Examining data/genometools-1.6.1+ds/src/extended/cds_check_visitor.c
Examining data/genometools-1.6.1+ds/src/extended/linspace_management.h
Examining data/genometools-1.6.1+ds/src/extended/bed_in_stream_api.h
Examining data/genometools-1.6.1+ds/src/extended/cstr_iterator.c
Examining data/genometools-1.6.1+ds/src/extended/visitor_stream.h
Examining data/genometools-1.6.1+ds/src/extended/region_mapping.c
Examining data/genometools-1.6.1+ds/src/extended/union_find.h
Examining data/genometools-1.6.1+ds/src/extended/spec_visitor.c
Examining data/genometools-1.6.1+ds/src/extended/region_node_builder.h
Examining data/genometools-1.6.1+ds/src/extended/eof_node_api.h
Examining data/genometools-1.6.1+ds/src/extended/gff3_visitor.c
Examining data/genometools-1.6.1+ds/src/extended/intset_8.h
Examining data/genometools-1.6.1+ds/src/extended/aligned_segments_pile.c
Examining data/genometools-1.6.1+ds/src/extended/intset_combined.c
Examining data/genometools-1.6.1+ds/src/extended/csa_visitor.c
Examining data/genometools-1.6.1+ds/src/extended/anno_db_schema_api.h
Examining data/genometools-1.6.1+ds/src/extended/set_source_visitor.h
Examining data/genometools-1.6.1+ds/src/extended/bed_in_stream.c
Examining data/genometools-1.6.1+ds/src/extended/inter_feature_stream_api.h
Examining data/genometools-1.6.1+ds/src/extended/match_last.h
Examining data/genometools-1.6.1+ds/src/extended/extract_feature_stream.c
Examining data/genometools-1.6.1+ds/src/extended/gtf_in_stream_api.h
Examining data/genometools-1.6.1+ds/src/extended/squarealign.h
Examining data/genometools-1.6.1+ds/src/extended/seqid2file.c
Examining data/genometools-1.6.1+ds/src/extended/transcript_bittabs.h
Examining data/genometools-1.6.1+ds/src/extended/merge_feature_stream_api.h
Examining data/genometools-1.6.1+ds/src/extended/fasta_header_iterator.c
Examining data/genometools-1.6.1+ds/src/extended/extract_feature_visitor.c
Examining data/genometools-1.6.1+ds/src/extended/type_checker_obo.h
Examining data/genometools-1.6.1+ds/src/extended/rdb_visitor_rep.h
Examining data/genometools-1.6.1+ds/src/extended/intset_8.c
Examining data/genometools-1.6.1+ds/src/extended/transcript_counts.h
Examining data/genometools-1.6.1+ds/src/extended/match_open_api.h
Examining data/genometools-1.6.1+ds/src/extended/csa_stream_api.h
Examining data/genometools-1.6.1+ds/src/extended/add_ids_stream.c
Examining data/genometools-1.6.1+ds/src/extended/gtf_out_stream.c
Examining data/genometools-1.6.1+ds/src/extended/popcount_tab.h
Examining data/genometools-1.6.1+ds/src/extended/inter_feature_stream.c
Examining data/genometools-1.6.1+ds/src/extended/region_node.h
Examining data/genometools-1.6.1+ds/src/extended/reconstructalignment.c
Examining data/genometools-1.6.1+ds/src/extended/extract_feature_stream_api.h
Examining data/genometools-1.6.1+ds/src/extended/seqid2seqnum_mapping.h
Examining data/genometools-1.6.1+ds/src/extended/permute_words.h
Examining data/genometools-1.6.1+ds/src/extended/aligned_segments_pile.h
Examining data/genometools-1.6.1+ds/src/extended/intset_16.c
Examining data/genometools-1.6.1+ds/src/extended/region_mapping_api.h
Examining data/genometools-1.6.1+ds/src/extended/gtf_in_stream.h
Examining data/genometools-1.6.1+ds/src/extended/gff3_linesorted_out_stream.c
Examining data/genometools-1.6.1+ds/src/extended/node_visitor_api.h
Examining data/genometools-1.6.1+ds/src/extended/dup_feature_stream.c
Examining data/genometools-1.6.1+ds/src/extended/transcript_bittabs.c
Examining data/genometools-1.6.1+ds/src/extended/match_visitor_rep.h
Examining data/genometools-1.6.1+ds/src/extended/transcript_evaluators.c
Examining data/genometools-1.6.1+ds/src/extended/bitoutstream.c
Examining data/genometools-1.6.1+ds/src/extended/array_out_stream.c
Examining data/genometools-1.6.1+ds/src/extended/feature_out_stream.c
Examining data/genometools-1.6.1+ds/src/extended/scorehandler.c
Examining data/genometools-1.6.1+ds/src/extended/condenseq_rep.h
Examining data/genometools-1.6.1+ds/src/extended/globalchaining_api.h
Examining data/genometools-1.6.1+ds/src/extended/scorehandler.h
Examining data/genometools-1.6.1+ds/src/extended/node_visitor.c
Examining data/genometools-1.6.1+ds/src/extended/linearalign_affinegapcost.h
Examining data/genometools-1.6.1+ds/src/extended/regular_seqid_api.h
Examining data/genometools-1.6.1+ds/src/extended/priority_queue.h
Examining data/genometools-1.6.1+ds/src/extended/gff3_out_stream.c
Examining data/genometools-1.6.1+ds/src/extended/orphanage.c
Examining data/genometools-1.6.1+ds/src/extended/gap_str.c
Examining data/genometools-1.6.1+ds/src/extended/type_checker.c
Examining data/genometools-1.6.1+ds/src/extended/safe_popen.c
Examining data/genometools-1.6.1+ds/src/extended/evaluator.h
Examining data/genometools-1.6.1+ds/src/extended/safe_popen.h
Examining data/genometools-1.6.1+ds/src/extended/sequence_node_out_visitor.c
Examining data/genometools-1.6.1+ds/src/extended/spec_visitor.h
Examining data/genometools-1.6.1+ds/src/extended/diagonalbandalign.c
Examining data/genometools-1.6.1+ds/src/extended/tag_value_map.h
Examining data/genometools-1.6.1+ds/src/extended/anno_db_schema_rep.h
Examining data/genometools-1.6.1+ds/src/extended/node_stream_api.h
Examining data/genometools-1.6.1+ds/src/extended/md5_to_id_visitor.h
Examining data/genometools-1.6.1+ds/src/extended/cds_check_visitor.h
Examining data/genometools-1.6.1+ds/src/annotationsketch/text_width_calculator_cairo.h
Examining data/genometools-1.6.1+ds/src/annotationsketch/element.h
Examining data/genometools-1.6.1+ds/src/annotationsketch/text_width_calculator_rep.h
Examining data/genometools-1.6.1+ds/src/annotationsketch/image_info.h
Examining data/genometools-1.6.1+ds/src/annotationsketch/diagram.h
Examining data/genometools-1.6.1+ds/src/annotationsketch/style.h
Examining data/genometools-1.6.1+ds/src/annotationsketch/canvas.c
Examining data/genometools-1.6.1+ds/src/annotationsketch/text_width_calculator.c
Examining data/genometools-1.6.1+ds/src/annotationsketch/layout.c
Examining data/genometools-1.6.1+ds/src/annotationsketch/color_api.h
Examining data/genometools-1.6.1+ds/src/annotationsketch/feature_index_rep.h
Examining data/genometools-1.6.1+ds/src/annotationsketch/canvas_cairo.c
Examining data/genometools-1.6.1+ds/src/annotationsketch/gt_sketch.c
Examining data/genometools-1.6.1+ds/src/annotationsketch/color.c
Examining data/genometools-1.6.1+ds/src/annotationsketch/canvas_rep.h
Examining data/genometools-1.6.1+ds/src/annotationsketch/style_api.h
Examining data/genometools-1.6.1+ds/src/annotationsketch/diagram_api.h
Examining data/genometools-1.6.1+ds/src/annotationsketch/image_info.c
Examining data/genometools-1.6.1+ds/src/annotationsketch/text_width_calculator.h
Examining data/genometools-1.6.1+ds/src/annotationsketch/rec_map.h
Examining data/genometools-1.6.1+ds/src/annotationsketch/cliptype.h
Examining data/genometools-1.6.1+ds/src/annotationsketch/canvas_api.h
Examining data/genometools-1.6.1+ds/src/annotationsketch/graphics_cairo.h
Examining data/genometools-1.6.1+ds/src/annotationsketch/feature_index_memory.h
Examining data/genometools-1.6.1+ds/src/annotationsketch/line_breaker_bases.c
Examining data/genometools-1.6.1+ds/src/annotationsketch/gt_sketch_page.c
Examining data/genometools-1.6.1+ds/src/annotationsketch/coords.c
Examining data/genometools-1.6.1+ds/src/annotationsketch/canvas_members.h
Examining data/genometools-1.6.1+ds/src/annotationsketch/gt_sketch.h
Examining data/genometools-1.6.1+ds/src/annotationsketch/custom_track_script_wrapper_api.h
Examining data/genometools-1.6.1+ds/src/annotationsketch/block.h
Examining data/genometools-1.6.1+ds/src/annotationsketch/custom_track_example.h
Examining data/genometools-1.6.1+ds/src/annotationsketch/custom_track_example.c
Examining data/genometools-1.6.1+ds/src/annotationsketch/line_breaker.c
Examining data/genometools-1.6.1+ds/src/annotationsketch/line_breaker.h
Examining data/genometools-1.6.1+ds/src/annotationsketch/custom_track_gc_content.h
Examining data/genometools-1.6.1+ds/src/annotationsketch/drawing_range.c
Examining data/genometools-1.6.1+ds/src/annotationsketch/custom_track.c
Examining data/genometools-1.6.1+ds/src/annotationsketch/canvas_cairo_file_api.h
Examining data/genometools-1.6.1+ds/src/annotationsketch/feature_index_api.h
Examining data/genometools-1.6.1+ds/src/annotationsketch/text_width_calculator_cairo_api.h
Examining data/genometools-1.6.1+ds/src/annotationsketch/custom_track_script_wrapper.h
Examining data/genometools-1.6.1+ds/src/annotationsketch/layout_api.h
Examining data/genometools-1.6.1+ds/src/annotationsketch/graphics_cairo.c
Examining data/genometools-1.6.1+ds/src/annotationsketch/custom_track_rep.h
Examining data/genometools-1.6.1+ds/src/annotationsketch/coords.h
Examining data/genometools-1.6.1+ds/src/annotationsketch/line_breaker_rep.h
Examining data/genometools-1.6.1+ds/src/annotationsketch/layout.h
Examining data/genometools-1.6.1+ds/src/annotationsketch/graphics.c
Examining data/genometools-1.6.1+ds/src/annotationsketch/custom_track_api.h
Examining data/genometools-1.6.1+ds/src/annotationsketch/graphics.h
Examining data/genometools-1.6.1+ds/src/annotationsketch/line.c
Examining data/genometools-1.6.1+ds/src/annotationsketch/image_info_api.h
Examining data/genometools-1.6.1+ds/src/annotationsketch/feature_index.h
Examining data/genometools-1.6.1+ds/src/annotationsketch/custom_track_gc_content_api.h
Examining data/genometools-1.6.1+ds/src/annotationsketch/luastyle.c
Examining data/genometools-1.6.1+ds/src/annotationsketch/canvas_cairo_file.c
Examining data/genometools-1.6.1+ds/src/annotationsketch/canvas_cairo_context_api.h
Examining data/genometools-1.6.1+ds/src/annotationsketch/drawing_range.h
Examining data/genometools-1.6.1+ds/src/annotationsketch/rec_map.c
Examining data/genometools-1.6.1+ds/src/annotationsketch/style.c
Examining data/genometools-1.6.1+ds/src/annotationsketch/feature_stream_api.h
Examining data/genometools-1.6.1+ds/src/annotationsketch/canvas_cairo_context.h
Examining data/genometools-1.6.1+ds/src/annotationsketch/graphics_api.h
Examining data/genometools-1.6.1+ds/src/annotationsketch/block_api.h
Examining data/genometools-1.6.1+ds/src/annotationsketch/line_breaker_captions.c
Examining data/genometools-1.6.1+ds/src/annotationsketch/canvas_cairo_file.h
Examining data/genometools-1.6.1+ds/src/annotationsketch/diagram.c
Examining data/genometools-1.6.1+ds/src/annotationsketch/graphics_cairo_api.h
Examining data/genometools-1.6.1+ds/src/annotationsketch/luastyle.h
Examining data/genometools-1.6.1+ds/src/annotationsketch/track.h
Examining data/genometools-1.6.1+ds/src/annotationsketch/gt_sketch_page.h
Examining data/genometools-1.6.1+ds/src/annotationsketch/line_breaker_captions.h
Examining data/genometools-1.6.1+ds/src/annotationsketch/feature_index_memory_api.h
Examining data/genometools-1.6.1+ds/src/annotationsketch/default_formats.h
Examining data/genometools-1.6.1+ds/src/annotationsketch/rec_map_api.h
Examining data/genometools-1.6.1+ds/src/annotationsketch/canvas_cairo_context.c
Examining data/genometools-1.6.1+ds/src/annotationsketch/custom_track_script_wrapper.c
Examining data/genometools-1.6.1+ds/src/annotationsketch/line_breaker_bases.h
Examining data/genometools-1.6.1+ds/src/annotationsketch/canvas.h
Examining data/genometools-1.6.1+ds/src/annotationsketch/custom_track.h
Examining data/genometools-1.6.1+ds/src/annotationsketch/line.h
Examining data/genometools-1.6.1+ds/src/annotationsketch/block.c
Examining data/genometools-1.6.1+ds/src/annotationsketch/track.c
Examining data/genometools-1.6.1+ds/src/annotationsketch/text_width_calculator_api.h
Examining data/genometools-1.6.1+ds/src/annotationsketch/custom_track_gc_content.c
Examining data/genometools-1.6.1+ds/src/annotationsketch/graphics_rep.h
Examining data/genometools-1.6.1+ds/src/annotationsketch/canvas_cairo.h
Examining data/genometools-1.6.1+ds/src/annotationsketch/element.c
Examining data/genometools-1.6.1+ds/src/annotationsketch/text_width_calculator_cairo.c
Examining data/genometools-1.6.1+ds/src/gt.c
Examining data/genometools-1.6.1+ds/src/core/bioseq_col.c
Examining data/genometools-1.6.1+ds/src/core/minmax_api.h
Examining data/genometools-1.6.1+ds/src/core/fasta.h
Examining data/genometools-1.6.1+ds/src/core/bsearch_api.h
Examining data/genometools-1.6.1+ds/src/core/array.c
Examining data/genometools-1.6.1+ds/src/core/cstr_array_api.h
Examining data/genometools-1.6.1+ds/src/core/fa_api.h
Examining data/genometools-1.6.1+ds/src/core/bitpackstringop8.c
Examining data/genometools-1.6.1+ds/src/core/strand.h
Examining data/genometools-1.6.1+ds/src/core/sequence_buffer_plain.c
Examining data/genometools-1.6.1+ds/src/core/splitter_api.h
Examining data/genometools-1.6.1+ds/src/core/output_file_api.h
Examining data/genometools-1.6.1+ds/src/core/encseq_access_type.h
Examining data/genometools-1.6.1+ds/src/core/mail_address.h
Examining data/genometools-1.6.1+ds/src/core/seq_iterator_api.h
Examining data/genometools-1.6.1+ds/src/core/compact_ulong_store.c
Examining data/genometools-1.6.1+ds/src/core/encseq_rep.h
Examining data/genometools-1.6.1+ds/src/core/example_a.h
Examining data/genometools-1.6.1+ds/src/core/seq.c
Examining data/genometools-1.6.1+ds/src/core/sequence_buffer_embl.h
Examining data/genometools-1.6.1+ds/src/core/progressbar.c
Examining data/genometools-1.6.1+ds/src/core/mapspec.h
Examining data/genometools-1.6.1+ds/src/core/ebzlib.h
Examining data/genometools-1.6.1+ds/src/core/fileutils.c
Examining data/genometools-1.6.1+ds/src/core/symbol_api.h
Examining data/genometools-1.6.1+ds/src/core/alphabet.c
Examining data/genometools-1.6.1+ds/src/core/gc_content.h
Examining data/genometools-1.6.1+ds/src/core/fileutils_api.h
Examining data/genometools-1.6.1+ds/src/core/range_api.h
Examining data/genometools-1.6.1+ds/src/core/timer.c
Examining data/genometools-1.6.1+ds/src/core/cstr.h
Examining data/genometools-1.6.1+ds/src/core/byte_select_api.h
Examining data/genometools-1.6.1+ds/src/core/sequence_buffer_gb.c
Examining data/genometools-1.6.1+ds/src/core/disc_distri.c
Examining data/genometools-1.6.1+ds/src/core/eansi.h
Examining data/genometools-1.6.1+ds/src/core/str_array.h
Examining data/genometools-1.6.1+ds/src/core/translator.c
Examining data/genometools-1.6.1+ds/src/core/stack-inlined.h
Examining data/genometools-1.6.1+ds/src/core/logger_api.h
Examining data/genometools-1.6.1+ds/src/core/fasta_reader_seqit.h
Examining data/genometools-1.6.1+ds/src/core/score_function.c
Examining data/genometools-1.6.1+ds/src/core/checkbitpackstring16.c
Examining data/genometools-1.6.1+ds/src/core/fastq.c
Examining data/genometools-1.6.1+ds/src/core/toolbox.h
Examining data/genometools-1.6.1+ds/src/core/assert_api.h
Examining data/genometools-1.6.1+ds/src/core/readmode.c
Examining data/genometools-1.6.1+ds/src/core/class_alloc_lock.c
Examining data/genometools-1.6.1+ds/src/core/ezlib.h
Examining data/genometools-1.6.1+ds/src/core/interval_tree_api.h
Examining data/genometools-1.6.1+ds/src/core/str_cache.c
Examining data/genometools-1.6.1+ds/src/core/md5_fingerprint_api.h
Examining data/genometools-1.6.1+ds/src/core/colorspace.c
Examining data/genometools-1.6.1+ds/src/core/sequence_buffer_fasta.h
Examining data/genometools-1.6.1+ds/src/core/sig.h
Examining data/genometools-1.6.1+ds/src/core/md5_fingerprint.c
Examining data/genometools-1.6.1+ds/src/core/option.h
Examining data/genometools-1.6.1+ds/src/core/mathsupport.c
Examining data/genometools-1.6.1+ds/src/core/gtdatapath.h
Examining data/genometools-1.6.1+ds/src/core/multithread.c
Examining data/genometools-1.6.1+ds/src/core/translator_api.h
Examining data/genometools-1.6.1+ds/src/core/example_a.c
Examining data/genometools-1.6.1+ds/src/core/sequence_buffer_rep.h
Examining data/genometools-1.6.1+ds/src/core/fasta_reader_fsm.h
Examining data/genometools-1.6.1+ds/src/core/disc_distri_api.h
Examining data/genometools-1.6.1+ds/src/core/tool.h
Examining data/genometools-1.6.1+ds/src/core/xbzlib.c
Examining data/genometools-1.6.1+ds/src/core/array3dim.c
Examining data/genometools-1.6.1+ds/src/core/divmodmul_api.h
Examining data/genometools-1.6.1+ds/src/core/sequence_buffer_fastq.h
Examining data/genometools-1.6.1+ds/src/core/str_array.c
Examining data/genometools-1.6.1+ds/src/core/radix_sort.h
Examining data/genometools-1.6.1+ds/src/core/seq_iterator_rep.h
Examining data/genometools-1.6.1+ds/src/core/warning_api.h
Examining data/genometools-1.6.1+ds/src/core/grep_api.h
Examining data/genometools-1.6.1+ds/src/core/endianess.c
Examining data/genometools-1.6.1+ds/src/core/thread_api.h
Examining data/genometools-1.6.1+ds/src/core/bitpackstringop32.c
Examining data/genometools-1.6.1+ds/src/core/io.c
Examining data/genometools-1.6.1+ds/src/core/csvline_reader.c
Examining data/genometools-1.6.1+ds/src/core/tool_api.h
Examining data/genometools-1.6.1+ds/src/core/qsort_r.c
Examining data/genometools-1.6.1+ds/src/core/checkencchar.h
Examining data/genometools-1.6.1+ds/src/core/codon_iterator_encseq.c
Examining data/genometools-1.6.1+ds/src/core/string_distri.h
Examining data/genometools-1.6.1+ds/src/core/complement.h
Examining data/genometools-1.6.1+ds/src/core/dlist_api.h
Examining data/genometools-1.6.1+ds/src/core/interval_tree.h
Examining data/genometools-1.6.1+ds/src/core/alphabet.h
Examining data/genometools-1.6.1+ds/src/core/bitbuffer.c
Examining data/genometools-1.6.1+ds/src/core/ebzlib.c
Examining data/genometools-1.6.1+ds/src/core/intbits.h
Examining data/genometools-1.6.1+ds/src/core/hashtable.h
Examining data/genometools-1.6.1+ds/src/core/seq_iterator_sequence_buffer.c
Examining data/genometools-1.6.1+ds/src/core/encseq.h
Examining data/genometools-1.6.1+ds/src/core/file.c
Examining data/genometools-1.6.1+ds/src/core/array_api.h
Examining data/genometools-1.6.1+ds/src/core/class_alloc_lock.h
Examining data/genometools-1.6.1+ds/src/core/array2dim_sparse.c
Examining data/genometools-1.6.1+ds/src/core/score_matrix.c
Examining data/genometools-1.6.1+ds/src/core/fasta_reader_rep.h
Examining data/genometools-1.6.1+ds/src/core/encseq_metadata.h
Examining data/genometools-1.6.1+ds/src/core/unit_testing.c
Examining data/genometools-1.6.1+ds/src/core/version_api.h
Examining data/genometools-1.6.1+ds/src/core/symbol.c
Examining data/genometools-1.6.1+ds/src/core/orf.c
Examining data/genometools-1.6.1+ds/src/core/init_api.h
Examining data/genometools-1.6.1+ds/src/core/bioseq.c
Examining data/genometools-1.6.1+ds/src/core/quality.c
Examining data/genometools-1.6.1+ds/src/core/array2dim_sparse_api.h
Examining data/genometools-1.6.1+ds/src/core/encseq_metadata.c
Examining data/genometools-1.6.1+ds/src/core/tool_iterator.h
Examining data/genometools-1.6.1+ds/src/core/chardef_api.h
Examining data/genometools-1.6.1+ds/src/core/fasta_reader.c
Examining data/genometools-1.6.1+ds/src/core/spacecalc.h
Examining data/genometools-1.6.1+ds/src/core/queue_api.h
Examining data/genometools-1.6.1+ds/src/core/qsort_r_api.h
Examining data/genometools-1.6.1+ds/src/core/countingsort.c
Examining data/genometools-1.6.1+ds/src/core/checkbitpackstring8.c
Examining data/genometools-1.6.1+ds/src/core/deprecated_api.h
Examining data/genometools-1.6.1+ds/src/core/readmode_api.h
Examining data/genometools-1.6.1+ds/src/core/dynalloc.c
Examining data/genometools-1.6.1+ds/src/core/sequence_buffer_plain.h
Examining data/genometools-1.6.1+ds/src/core/md5_tab.c
Examining data/genometools-1.6.1+ds/src/core/md5_encoder_api.h
Examining data/genometools-1.6.1+ds/src/core/process.h
Examining data/genometools-1.6.1+ds/src/core/phase_api.h
Examining data/genometools-1.6.1+ds/src/core/example.h
Examining data/genometools-1.6.1+ds/src/core/log.c
Examining data/genometools-1.6.1+ds/src/core/checkbitpackstring64.c
Examining data/genometools-1.6.1+ds/src/core/logger.h
Examining data/genometools-1.6.1+ds/src/core/qsort-ulong.c
Examining data/genometools-1.6.1+ds/src/core/ulongbound.h
Examining data/genometools-1.6.1+ds/src/core/cstr_array.c
Examining data/genometools-1.6.1+ds/src/core/bioseq_col.h
Examining data/genometools-1.6.1+ds/src/core/parseutils.h
Examining data/genometools-1.6.1+ds/src/core/tokenizer.h
Examining data/genometools-1.6.1+ds/src/core/bioseq_iterator.c
Examining data/genometools-1.6.1+ds/src/core/bittab_api.h
Examining data/genometools-1.6.1+ds/src/core/trans_table.c
Examining data/genometools-1.6.1+ds/src/core/bittab.h
Examining data/genometools-1.6.1+ds/src/core/xposix_api.h
Examining data/genometools-1.6.1+ds/src/core/str_api.h
Examining data/genometools-1.6.1+ds/src/core/multithread_api.h
Examining data/genometools-1.6.1+ds/src/core/bitpackstringop16.c
Examining data/genometools-1.6.1+ds/src/core/qsort-ulong.h
Examining data/genometools-1.6.1+ds/src/core/str.c
Examining data/genometools-1.6.1+ds/src/core/codetype.h
Examining data/genometools-1.6.1+ds/src/core/spacepeak.h
Examining data/genometools-1.6.1+ds/src/core/unused_api.h
Examining data/genometools-1.6.1+ds/src/core/class_alloc.c
Examining data/genometools-1.6.1+ds/src/core/splitter.c
Examining data/genometools-1.6.1+ds/src/core/fastq.h
Examining data/genometools-1.6.1+ds/src/core/pairbwtidx.h
Examining data/genometools-1.6.1+ds/src/core/versionfunc_api.h
Examining data/genometools-1.6.1+ds/src/core/versionfunc.c
Examining data/genometools-1.6.1+ds/src/core/colorspace.h
Examining data/genometools-1.6.1+ds/src/core/seq_iterator_fastq_api.h
Examining data/genometools-1.6.1+ds/src/core/md5_seqid_api.h
Examining data/genometools-1.6.1+ds/src/core/basename_api.h
Examining data/genometools-1.6.1+ds/src/core/queue.h
Examining data/genometools-1.6.1+ds/src/core/encseq_col.c
Examining data/genometools-1.6.1+ds/src/core/sequence_buffer_embl.c
Examining data/genometools-1.6.1+ds/src/core/toolbox.c
Examining data/genometools-1.6.1+ds/src/core/hashtable-siop.h
Examining data/genometools-1.6.1+ds/src/core/fasta_reader_api.h
Examining data/genometools-1.6.1+ds/src/core/strcmp.c
Examining data/genometools-1.6.1+ds/src/core/parseutils.c
Examining data/genometools-1.6.1+ds/src/core/basename.c
Examining data/genometools-1.6.1+ds/src/core/version.c
Examining data/genometools-1.6.1+ds/src/core/symbol.h
Examining data/genometools-1.6.1+ds/src/core/array2dim_api.h
Examining data/genometools-1.6.1+ds/src/core/timer_api.h
Examining data/genometools-1.6.1+ds/src/core/seq_iterator_sequence_buffer.h
Examining data/genometools-1.6.1+ds/src/core/spacepeak.c
Examining data/genometools-1.6.1+ds/src/core/csvline_reader.h
Examining data/genometools-1.6.1+ds/src/core/bitpackarray.h
Examining data/genometools-1.6.1+ds/src/core/thread.c
Examining data/genometools-1.6.1+ds/src/core/checkbitpackstring.c
Examining data/genometools-1.6.1+ds/src/core/seq_iterator.c
Examining data/genometools-1.6.1+ds/src/core/option.c
Examining data/genometools-1.6.1+ds/src/core/translator.h
Examining data/genometools-1.6.1+ds/src/core/strand.c
Examining data/genometools-1.6.1+ds/src/core/sequence_buffer_gb.h
Examining data/genometools-1.6.1+ds/src/core/encseq_options.c
Examining data/genometools-1.6.1+ds/src/core/array2dim.c
Examining data/genometools-1.6.1+ds/src/core/endianess_api.h
Examining data/genometools-1.6.1+ds/src/core/bitbuffer.h
Examining data/genometools-1.6.1+ds/src/core/splitter.h
Examining data/genometools-1.6.1+ds/src/core/byte_popcount_api.h
Examining data/genometools-1.6.1+ds/src/core/dyn_bittab.c
Examining data/genometools-1.6.1+ds/src/core/mapspec.c
Examining data/genometools-1.6.1+ds/src/core/fa.c
Examining data/genometools-1.6.1+ds/src/core/strcmp_api.h
Examining data/genometools-1.6.1+ds/src/core/bioseq_api.h
Examining data/genometools-1.6.1+ds/src/core/encseq.c
Examining data/genometools-1.6.1+ds/src/core/grep.h
Examining data/genometools-1.6.1+ds/src/core/xzlib.h
Examining data/genometools-1.6.1+ds/src/core/safecast-gen.h
Examining data/genometools-1.6.1+ds/src/core/checkbitpackstring32.c
Examining data/genometools-1.6.1+ds/src/core/encseq_api.h
Examining data/genometools-1.6.1+ds/src/core/bsearch.h
Examining data/genometools-1.6.1+ds/src/core/combinatorics.c
Examining data/genometools-1.6.1+ds/src/core/sig.c
Examining data/genometools-1.6.1+ds/src/core/strand_api.h
Examining data/genometools-1.6.1+ds/src/core/msort.c
Examining data/genometools-1.6.1+ds/src/core/bool_matrix.c
Examining data/genometools-1.6.1+ds/src/core/grep.c
Examining data/genometools-1.6.1+ds/src/core/dual-pivot-qsort.c
Examining data/genometools-1.6.1+ds/src/core/logger.c
Examining data/genometools-1.6.1+ds/src/core/file_api.h
Examining data/genometools-1.6.1+ds/src/core/mathsupport_api.h
Examining data/genometools-1.6.1+ds/src/core/sequence_buffer.h
Examining data/genometools-1.6.1+ds/src/core/range.c
Examining data/genometools-1.6.1+ds/src/core/cstr_table_api.h
Examining data/genometools-1.6.1+ds/src/core/score_matrix_api.h
Examining data/genometools-1.6.1+ds/src/core/example_b.h
Examining data/genometools-1.6.1+ds/src/core/encseq_ptr.c
Examining data/genometools-1.6.1+ds/src/core/unit_testing_api.h
Examining data/genometools-1.6.1+ds/src/core/seq_info_cache.h
Examining data/genometools-1.6.1+ds/src/core/tooldriver.c
Examining data/genometools-1.6.1+ds/src/core/dual-pivot-qsort.h
Examining data/genometools-1.6.1+ds/src/core/xansi_api.h
Examining data/genometools-1.6.1+ds/src/core/fasta_reader_seqit.c
Examining data/genometools-1.6.1+ds/src/core/safearith_api.h
Examining data/genometools-1.6.1+ds/src/core/string_distri.c
Examining data/genometools-1.6.1+ds/src/core/cstr_table.c
Examining data/genometools-1.6.1+ds/src/core/tokenizer.c
Examining data/genometools-1.6.1+ds/src/core/codon_iterator_api.h
Examining data/genometools-1.6.1+ds/src/core/seq_col.h
Examining data/genometools-1.6.1+ds/src/core/progressbar.h
Examining data/genometools-1.6.1+ds/src/core/compat.c
Examining data/genometools-1.6.1+ds/src/core/log_api.h
Examining data/genometools-1.6.1+ds/src/core/fptr_api.h
Examining data/genometools-1.6.1+ds/src/core/ensure_api.h
Examining data/genometools-1.6.1+ds/src/core/xzlib.c
Examining data/genometools-1.6.1+ds/src/core/yarandom.c
Examining data/genometools-1.6.1+ds/src/core/example.c
Examining data/genometools-1.6.1+ds/src/core/warning.c
Examining data/genometools-1.6.1+ds/src/core/trans_table_api.h
Examining data/genometools-1.6.1+ds/src/core/hashmap_api.h
Examining data/genometools-1.6.1+ds/src/core/bittab.c
Examining data/genometools-1.6.1+ds/src/core/hashtable.c
Examining data/genometools-1.6.1+ds/src/core/md5_encoder.c
Examining data/genometools-1.6.1+ds/src/core/desc_buffer.h
Examining data/genometools-1.6.1+ds/src/core/bsearch.c
Examining data/genometools-1.6.1+ds/src/core/xbsd.h
Examining data/genometools-1.6.1+ds/src/core/dynalloc.h
Examining data/genometools-1.6.1+ds/src/core/log.h
Examining data/genometools-1.6.1+ds/src/core/array.h
Examining data/genometools-1.6.1+ds/src/core/phase.c
Examining data/genometools-1.6.1+ds/src/core/alphabet_api.h
Examining data/genometools-1.6.1+ds/src/core/showtime.h
Examining data/genometools-1.6.1+ds/src/core/byte_select.c
Examining data/genometools-1.6.1+ds/src/core/quality.h
Examining data/genometools-1.6.1+ds/src/core/xposix.c
Examining data/genometools-1.6.1+ds/src/core/io.h
Examining data/genometools-1.6.1+ds/src/core/codon_iterator_encseq_api.h
Examining data/genometools-1.6.1+ds/src/core/compat_api.h
Examining data/genometools-1.6.1+ds/src/core/dyn_bittab.h
Examining data/genometools-1.6.1+ds/src/core/cstr_api.h
Examining data/genometools-1.6.1+ds/src/core/option_api.h
Examining data/genometools-1.6.1+ds/src/core/array3dim_api.h
Examining data/genometools-1.6.1+ds/src/core/countingsort.h
Examining data/genometools-1.6.1+ds/src/core/compact_ulong_store.h
Examining data/genometools-1.6.1+ds/src/core/undef_api.h
Examining data/genometools-1.6.1+ds/src/core/ma.c
Examining data/genometools-1.6.1+ds/src/core/password_entry.h
Examining data/genometools-1.6.1+ds/src/core/seq_col_rep.h
Examining data/genometools-1.6.1+ds/src/core/combinatorics_impl.h
Examining data/genometools-1.6.1+ds/src/core/bitpackstring.h
Examining data/genometools-1.6.1+ds/src/core/encseq_options.h
Examining data/genometools-1.6.1+ds/src/core/arraydef_api.h
Examining data/genometools-1.6.1+ds/src/core/eansi.c
Examining data/genometools-1.6.1+ds/src/core/str_array_api.h
Examining data/genometools-1.6.1+ds/src/core/class_alloc_api.h
Examining data/genometools-1.6.1+ds/src/core/tooldriver_api.h
Examining data/genometools-1.6.1+ds/src/core/codon_iterator_rep.h
Examining data/genometools-1.6.1+ds/src/core/byte_popcount.c
Examining data/genometools-1.6.1+ds/src/core/yarandom_api.h
Examining data/genometools-1.6.1+ds/src/core/disc_distri.h
Examining data/genometools-1.6.1+ds/src/core/msort_api.h
Examining data/genometools-1.6.1+ds/src/core/gtdatapath.c
Examining data/genometools-1.6.1+ds/src/core/parseutils_api.h
Examining data/genometools-1.6.1+ds/src/core/sequence_buffer_fastq.c
Examining data/genometools-1.6.1+ds/src/core/hashmap.c
Examining data/genometools-1.6.1+ds/src/core/fasta_reader_rec.h
Examining data/genometools-1.6.1+ds/src/core/bitpackstringop64.c
Examining data/genometools-1.6.1+ds/src/core/sequence_buffer_fasta.c
Examining data/genometools-1.6.1+ds/src/core/tool.c
Examining data/genometools-1.6.1+ds/src/core/msort.h
Examining data/genometools-1.6.1+ds/src/core/codon_iterator_simple_api.h
Examining data/genometools-1.6.1+ds/src/core/interval_tree.c
Examining data/genometools-1.6.1+ds/src/core/gc_content.c
Examining data/genometools-1.6.1+ds/src/core/bool_matrix_api.h
Examining data/genometools-1.6.1+ds/src/core/cstr.c
Examining data/genometools-1.6.1+ds/src/core/trans_table.h
Examining data/genometools-1.6.1+ds/src/core/xbsd.c
Examining data/genometools-1.6.1+ds/src/core/sequence_buffer_inline.h
Examining data/genometools-1.6.1+ds/src/core/bitpackstringop.c
Examining data/genometools-1.6.1+ds/src/core/cstr_table.h
Examining data/genometools-1.6.1+ds/src/core/dlist.c
Examining data/genometools-1.6.1+ds/src/core/fasta.c
Examining data/genometools-1.6.1+ds/src/core/checkbitpackarray.c
Examining data/genometools-1.6.1+ds/src/core/encseq_access_type.c
Examining data/genometools-1.6.1+ds/src/core/seq_info_cache.c
Examining data/genometools-1.6.1+ds/src/core/fasta_api.h
Examining data/genometools-1.6.1+ds/src/core/xbzlib.h
Examining data/genometools-1.6.1+ds/src/core/complement.c
Examining data/genometools-1.6.1+ds/src/core/readmode.h
Examining data/genometools-1.6.1+ds/src/core/output_file.h
Examining data/genometools-1.6.1+ds/src/core/xansi.c
Examining data/genometools-1.6.1+ds/src/core/desc_buffer.c
Examining data/genometools-1.6.1+ds/src/core/countingsort_api.h
Examining data/genometools-1.6.1+ds/src/core/bioseq_iterator.h
Examining data/genometools-1.6.1+ds/src/core/combinatorics.h
Examining data/genometools-1.6.1+ds/src/core/md5_tab_api.h
Examining data/genometools-1.6.1+ds/src/core/password_entry.c
Examining data/genometools-1.6.1+ds/src/core/radix_sort.c
Examining data/genometools-1.6.1+ds/src/core/seq_col.c
Examining data/genometools-1.6.1+ds/src/core/toolbox_api.h
Examining data/genometools-1.6.1+ds/src/core/seq_api.h
Examining data/genometools-1.6.1+ds/src/core/codon_iterator_simple.c
Examining data/genometools-1.6.1+ds/src/core/ma_api.h
Examining data/genometools-1.6.1+ds/src/core/fasta_separator.h
Examining data/genometools-1.6.1+ds/src/core/seq_iterator_sequence_buffer_api.h
Examining data/genometools-1.6.1+ds/src/core/fasta_reader_rec.c
Examining data/genometools-1.6.1+ds/src/core/error.c
Examining data/genometools-1.6.1+ds/src/core/types_api.h
Examining data/genometools-1.6.1+ds/src/core/bitpackstringsimpleop.h
Examining data/genometools-1.6.1+ds/src/core/encseq_col.h
Examining data/genometools-1.6.1+ds/src/core/queue.c
Examining data/genometools-1.6.1+ds/src/core/init.c
Examining data/genometools-1.6.1+ds/src/core/str_cache_api.h
Examining data/genometools-1.6.1+ds/src/core/codon_iterator.c
Examining data/genometools-1.6.1+ds/src/core/error_api.h
Examining data/genometools-1.6.1+ds/src/core/codon_api.h
Examining data/genometools-1.6.1+ds/src/core/example_b.c
Examining data/genometools-1.6.1+ds/src/core/ezlib.c
Examining data/genometools-1.6.1+ds/src/core/defined-types.h
Examining data/genometools-1.6.1+ds/src/core/hashmap-generic.h
Examining data/genometools-1.6.1+ds/src/core/format64.h
Examining data/genometools-1.6.1+ds/src/core/md5_seqid.c
Examining data/genometools-1.6.1+ds/src/core/dlist.h
Examining data/genometools-1.6.1+ds/src/core/safearith.c
Examining data/genometools-1.6.1+ds/src/core/process.c
Examining data/genometools-1.6.1+ds/src/core/fasta_reader_fsm.c
Examining data/genometools-1.6.1+ds/src/core/showtime.c
Examining data/genometools-1.6.1+ds/src/core/example_rep.h
Examining data/genometools-1.6.1+ds/src/core/tool_iterator.c
Examining data/genometools-1.6.1+ds/src/core/sequence_buffer.c
Examining data/genometools-1.6.1+ds/src/core/orf_api.h
Examining data/genometools-1.6.1+ds/src/core/filelengthvalues.h
Examining data/genometools-1.6.1+ds/src/core/strcmp.h
Examining data/genometools-1.6.1+ds/src/core/checkbitpackstring-int.c
Examining data/genometools-1.6.1+ds/src/core/score_function.h
Examining data/genometools-1.6.1+ds/src/core/output_file.c
Examining data/genometools-1.6.1+ds/src/core/seq_iterator_fastq.c
Examining data/genometools-1.6.1+ds/src/genometools.h
Examining data/genometools-1.6.1+ds/src/interactive.c
Examining data/genometools-1.6.1+ds/src/gtlua/feature_stream_lua.h
Examining data/genometools-1.6.1+ds/src/gtlua/annotationsketch_lua.c
Examining data/genometools-1.6.1+ds/src/gtlua/score_matrix_lua.h
Examining data/genometools-1.6.1+ds/src/gtlua/canvas_lua.h
Examining data/genometools-1.6.1+ds/src/gtlua/translate_lua.c
Examining data/genometools-1.6.1+ds/src/gtlua/genome_visitor_lua.c
Examining data/genometools-1.6.1+ds/src/gtlua/bittab_lua.h
Examining data/genometools-1.6.1+ds/src/gtlua/gt_lua.h
Examining data/genometools-1.6.1+ds/src/gtlua/feature_index_lua.h
Examining data/genometools-1.6.1+ds/src/gtlua/gtcore_lua.c
Examining data/genometools-1.6.1+ds/src/gtlua/genome_node_lua.h
Examining data/genometools-1.6.1+ds/src/gtlua/gt_lua.c
Examining data/genometools-1.6.1+ds/src/gtlua/csa_stream_lua.h
Examining data/genometools-1.6.1+ds/src/gtlua/layout_lua.h
Examining data/genometools-1.6.1+ds/src/gtlua/gtext_lua.h
Examining data/genometools-1.6.1+ds/src/gtlua/image_info_lua.h
Examining data/genometools-1.6.1+ds/src/gtlua/region_mapping_lua.c
Examining data/genometools-1.6.1+ds/src/gtlua/feature_node_iterator_lua.h
Examining data/genometools-1.6.1+ds/src/gtlua/region_mapping_lua.h
Examining data/genometools-1.6.1+ds/src/gtlua/layout_lua.c
Examining data/genometools-1.6.1+ds/src/gtlua/diagram_lua.h
Examining data/genometools-1.6.1+ds/src/gtlua/annotationsketch_lua.h
Examining data/genometools-1.6.1+ds/src/gtlua/genome_stream_lua.h
Examining data/genometools-1.6.1+ds/src/gtlua/genome_node_lua.c
Examining data/genometools-1.6.1+ds/src/gtlua/image_info_lua.c
Examining data/genometools-1.6.1+ds/src/gtlua/gtext_lua.c
Examining data/genometools-1.6.1+ds/src/gtlua/alphabet_lua.h
Examining data/genometools-1.6.1+ds/src/gtlua/score_matrix_lua.c
Examining data/genometools-1.6.1+ds/src/gtlua/canvas_lua.c
Examining data/genometools-1.6.1+ds/src/gtlua/range_lua.h
Examining data/genometools-1.6.1+ds/src/gtlua/gtcore_lua.h
Examining data/genometools-1.6.1+ds/src/gtlua/stream_evaluator_lua.h
Examining data/genometools-1.6.1+ds/src/gtlua/csa_stream_lua.c
Examining data/genometools-1.6.1+ds/src/gtlua/cds_stream_lua.h
Examining data/genometools-1.6.1+ds/src/gtlua/feature_stream_lua.c
Examining data/genometools-1.6.1+ds/src/gtlua/feature_visitor_lua.h
Examining data/genometools-1.6.1+ds/src/gtlua/feature_node_iterator_lua.c
Examining data/genometools-1.6.1+ds/src/gtlua/cds_stream_lua.c
Examining data/genometools-1.6.1+ds/src/gtlua/stream_evaluator_lua.c
Examining data/genometools-1.6.1+ds/src/gtlua/alphabet_lua.c
Examining data/genometools-1.6.1+ds/src/gtlua/feature_visitor_lua.c
Examining data/genometools-1.6.1+ds/src/gtlua/encseq_lua.c
Examining data/genometools-1.6.1+ds/src/gtlua/mathsupport_lua.h
Examining data/genometools-1.6.1+ds/src/gtlua/diagram_lua.c
Examining data/genometools-1.6.1+ds/src/gtlua/range_lua.c
Examining data/genometools-1.6.1+ds/src/gtlua/encseq_lua.h
Examining data/genometools-1.6.1+ds/src/gtlua/feature_index_lua.c
Examining data/genometools-1.6.1+ds/src/gtlua/mathsupport_lua.c
Examining data/genometools-1.6.1+ds/src/gtlua/genome_visitor_lua.h
Examining data/genometools-1.6.1+ds/src/gtlua/translate_lua.h
Examining data/genometools-1.6.1+ds/src/gtlua/bittab_lua.c
Examining data/genometools-1.6.1+ds/src/gtlua/genome_stream_lua.c
Examining data/genometools-1.6.1+ds/testdata/blosum62.c
Examining data/genometools-1.6.1+ds/debian/tests/gff3validator.c

FINAL RESULTS:

data/genometools-1.6.1+ds/src/annotationsketch/canvas.c:115:12:  [4] (format) snprintf:
  If format strings can be influenced by an attacker, they can be exploited,
  and note that sprintf variations do not always \0-terminate (CWE-134). Use
  a constant for the format specification.
    (void) snprintf(txt, buflen, gt_str_get(formatstring), fpos, unitstr);
data/genometools-1.6.1+ds/src/annotationsketch/canvas.c:129:12:  [4] (format) snprintf:
  If format strings can be influenced by an attacker, they can be exploited,
  and note that sprintf variations do not always \0-terminate (CWE-134). Use
  a constant for the format specification.
    (void) snprintf(txt, buflen, gt_str_get(formatstring), fpos, unitstr);
data/genometools-1.6.1+ds/src/annotationsketch/canvas.c:143:12:  [4] (format) snprintf:
  If format strings can be influenced by an attacker, they can be exploited,
  and note that sprintf variations do not always \0-terminate (CWE-134). Use
  a constant for the format specification.
    (void) snprintf(txt, buflen, gt_str_get(formatstring), fpos, unitstr);
data/genometools-1.6.1+ds/src/annotationsketch/canvas_cairo.c:140:9:  [4] (format) snprintf:
  If format strings can be influenced by an attacker, they can be exploited,
  and note that sprintf variations do not always \0-terminate (CWE-134). Use
  a constant for the format specification.
        snprintf(buf, BUFSIZ, msg, exceeded);
data/genometools-1.6.1+ds/src/core/basename.c:40:3:  [4] (buffer) strcpy:
  Does not check for buffer overflows when copying to destination [MS-banned]
  (CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
  easily misused).
  strcpy(sbuf, path);
data/genometools-1.6.1+ds/src/core/bioseq_col.c:141:14:  [4] (buffer) sscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function. If the scanf format is influenceable by an
  attacker, it's exploitable.
      (void) sscanf(desc, fmt, buf);
data/genometools-1.6.1+ds/src/core/csvline_reader.c:279:5:  [4] (format) printf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
    printf("%c/" GT_WU,cc,csvline_reader->dist.charcount[(int) cc]);
data/genometools-1.6.1+ds/src/core/encseq.c:713:5:  [4] (format) printf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
    printf(GT_WU, range->start);
data/genometools-1.6.1+ds/src/core/encseq.c:715:5:  [4] (format) printf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
    printf(GT_WU ", " GT_WU, range->start, range->end);
data/genometools-1.6.1+ds/src/core/encseq.c:1283:7:  [4] (buffer) strcpy:
  Does not check for buffer overflows when copying to destination [MS-banned]
  (CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
  easily misused).
      strcpy(headerptr->firstfilename+offset,
data/genometools-1.6.1+ds/src/core/encseq.c:8009:5:  [4] (buffer) strcpy:
  Does not check for buffer overflows when copying to destination [MS-banned]
  (CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
  easily misused).
    strcpy(indexnamecopy, indexname);
data/genometools-1.6.1+ds/src/core/error.c:54:10:  [4] (format) vsnprintf:
  If format strings can be influenced by an attacker, they can be exploited,
  and note that sprintf variations do not always \0-terminate (CWE-134). Use
  a constant for the format specification.
  (void) vsnprintf(err->error_string, sizeof (err->error_string), format, ap);
data/genometools-1.6.1+ds/src/core/error_api.h:57:39:  [4] (format) printf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
              __attribute__ ((format (printf, 2, 3)));
data/genometools-1.6.1+ds/src/core/fa.c:316:7:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
  if (access(dirname, R_OK | W_OK | X_OK) == 0)
data/genometools-1.6.1+ds/src/core/file_api.h:50:27:  [4] (format) printf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
  __attribute__ ((format (printf, 2, 3)));
data/genometools-1.6.1+ds/src/core/log_api.h:37:27:  [4] (format) printf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
  __attribute__ ((format (printf, 1, 2)));
data/genometools-1.6.1+ds/src/core/logger.c:100:10:  [4] (format) vfprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
  (void) vfprintf(logger->target, format, ap);
data/genometools-1.6.1+ds/src/core/logger.c:111:10:  [4] (format) vfprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
  (void) vfprintf(logger->target, format, ap);
data/genometools-1.6.1+ds/src/core/logger_api.h:45:35:  [4] (format) printf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
          __attribute__ ((format (printf, 2, 3)));
data/genometools-1.6.1+ds/src/core/logger_api.h:48:35:  [4] (format) printf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
          __attribute__ ((format (printf, 2, 3)));
data/genometools-1.6.1+ds/src/core/ma.c:63:7:  [4] (format) fprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
      fprintf(stderr, GT_WU " bytes were allocated altogether\n", current_size);
data/genometools-1.6.1+ds/src/core/ma.c:78:7:  [4] (format) fprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
      fprintf(stderr, GT_WU " bytes were allocated altogether\n", current_size);
data/genometools-1.6.1+ds/src/core/ma.c:93:7:  [4] (format) fprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
      fprintf(stderr, GT_WU " bytes were allocated altogether\n", current_size);
data/genometools-1.6.1+ds/src/core/option.c:2009:12:  [4] (buffer) sscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function.
    (void) sscanf(gt_str_get(memlimit), "%d%s", &readint, buffer);
data/genometools-1.6.1+ds/src/core/timer.c:145:3:  [4] (format) fprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
  fprintf(fp, fmt,
data/genometools-1.6.1+ds/src/core/timer.c:184:10:  [4] (format) snprintf:
  If format strings can be influenced by an attacker, they can be exploited,
  and note that sprintf variations do not always \0-terminate (CWE-134). Use
  a constant for the format specification.
  (void) snprintf(buf, BUFSIZ-1, fmt,
data/genometools-1.6.1+ds/src/core/timer.c:277:10:  [4] (format) vsnprintf:
  If format strings can be influenced by an attacker, they can be exploited,
  and note that sprintf variations do not always \0-terminate (CWE-134). Use
  a constant for the format specification.
  (void) vsnprintf(buf, BUFSIZ, desc, ap);
data/genometools-1.6.1+ds/src/core/warning.c:53:10:  [4] (format) vfprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
  (void) vfprintf(stderr, format, ap);
data/genometools-1.6.1+ds/src/core/warning_api.h:30:27:  [4] (format) printf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
  __attribute__ ((format (printf, 1, 2)));
data/genometools-1.6.1+ds/src/core/xansi.c:194:7:  [4] (format) vfprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
  if (vfprintf(stream, format, ap) < 0) {
data/genometools-1.6.1+ds/src/core/xansi.c:203:15:  [4] (format) vsnprintf:
  If format strings can be influenced by an attacker, they can be exploited,
  and note that sprintf variations do not always \0-terminate (CWE-134). Use
  a constant for the format specification.
  if ((rval = vsnprintf(str, size, format, ap)) < 0) {
data/genometools-1.6.1+ds/src/extended/blast_process_call.c:275:18:  [4] (shell) popen:
  This causes a new program to execute and is difficult to use safely
  (CWE-78). try using a library call that implements the same functionality
  if available.
  installcheck = popen(call->version_call, "r");
data/genometools-1.6.1+ds/src/extended/blast_process_call.c:313:16:  [4] (shell) popen:
  This causes a new program to execute and is difficult to use safely
  (CWE-78). try using a library call that implements the same functionality
  if available.
    blastout = popen(gt_str_get(call->str), "r");
data/genometools-1.6.1+ds/src/extended/match_iterator_blast.c:92:18:  [4] (buffer) fscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function.
    readvalues = fscanf(mib->pvt->matchfilep,
data/genometools-1.6.1+ds/src/extended/match_iterator_blast.c:119:23:  [4] (buffer) sscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function.
    if ((readvalues = sscanf(buffer, "%s %s %f " GT_WD " " GT_WD " " GT_WD " "
data/genometools-1.6.1+ds/src/extended/match_iterator_last.c:249:15:  [4] (buffer) sscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function. If the scanf format is influenceable by an
  attacker, it's exploitable.
    if (11 != sscanf(gt_str_get(mil->pvt->linebuf),
data/genometools-1.6.1+ds/src/extended/match_iterator_last.c:338:11:  [4] (shell) execvp:
  This causes a new program to execute and is difficult to use safely
  (CWE-78). try using a library call that implements the same functionality
  if available.
          execvp(gt_str_get(lastbinary), args);
data/genometools-1.6.1+ds/src/extended/match_iterator_last.c:440:19:  [4] (shell) system:
  This causes a new program to execute and is difficult to use safely
  (CWE-78). try using a library call that implements the same functionality
  if available.
        had_err = system(gt_str_get(cmdline));
data/genometools-1.6.1+ds/src/extended/match_iterator_open.c:80:16:  [4] (buffer) fscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function.
    readnums = fscanf(mpi->pvt->matchfilep, " " GT_WD " %s " GT_WD " %c " GT_WD
data/genometools-1.6.1+ds/src/extended/match_iterator_open.c:110:9:  [4] (buffer) sscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function.
    if (sscanf(buffer, " " GT_WD " %s " GT_WD " %*c " GT_WD " %s " GT_WD
data/genometools-1.6.1+ds/src/extended/md5set.c:53:5:  [4] (format) fprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
    fprintf(stderr, MD5SET_TOO_LARGE, k);
data/genometools-1.6.1+ds/src/extended/rcr.c:2046:9:  [4] (format) fprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
        fprintf(rcr_dec->fp, "\t" GT_WU, readpos + 1);
data/genometools-1.6.1+ds/src/extended/uint64hashtable.c:50:5:  [4] (format) fprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
    fprintf(stderr, GT_UINT64TABLE_TOO_LARGE, (GtUword)k);
data/genometools-1.6.1+ds/src/gtlua/genome_node_lua.c:809:12:  [4] (format) snprintf:
  If format strings can be influenced by an attacker, they can be exploited,
  and note that sprintf variations do not always \0-terminate (CWE-134). Use
  a constant for the format specification.
    (void) snprintf(buf, BUFSIZ, "region: %s "GT_WU"-"GT_WU,
data/genometools-1.6.1+ds/src/gtlua/range_lua.c:132:10:  [4] (format) snprintf:
  If format strings can be influenced by an attacker, they can be exploited,
  and note that sprintf variations do not always \0-terminate (CWE-134). Use
  a constant for the format specification.
  (void) snprintf(buf, BUFSIZ, GT_WU "-" GT_WU, range->start, range->end);
data/genometools-1.6.1+ds/src/ltr/ltr_refseq_match_stream.c:258:12:  [4] (format) snprintf:
  If format strings can be influenced by an attacker, they can be exploited,
  and note that sprintf variations do not always \0-terminate (CWE-134). Use
  a constant for the format specification.
    (void) snprintf(target, BUFSIZ, "%s " GT_WU " " GT_WU,
data/genometools-1.6.1+ds/src/ltr/ltr_refseq_match_stream.c:289:24:  [4] (shell) popen:
  This causes a new program to execute and is difficult to use safely
  (CWE-78). try using a library call that implements the same functionality
  if available.
  makeblastdb_output = popen(makeblastdb_call, "r");
data/genometools-1.6.1+ds/src/ltr/ltrdigest_pdom_visitor.c:903:20:  [4] (shell) execvp:
  This causes a new program to execute and is difficult to use safely
  (CWE-78). try using a library call that implements the same functionality
  if available.
            (void) execvp("hmmscan", lv->args); /* XXX: read path from env */
data/genometools-1.6.1+ds/src/ltr/ltrdigest_pdom_visitor.c:1024:10:  [4] (shell) system:
  This causes a new program to execute and is difficult to use safely
  (CWE-78). try using a library call that implements the same functionality
  if available.
  rval = system("hmmscan -h > /dev/null");
data/genometools-1.6.1+ds/src/ltr/pdom_model_set.c:76:10:  [4] (shell) system:
  This causes a new program to execute and is difficult to use safely
  (CWE-78). try using a library call that implements the same functionality
  if available.
  rval = system("hmmpress -h > /dev/null");
data/genometools-1.6.1+ds/src/ltr/pdom_model_set.c:82:10:  [4] (shell) system:
  This causes a new program to execute and is difficult to use safely
  (CWE-78). try using a library call that implements the same functionality
  if available.
  rval = system("hmmconvert -h > /dev/null");
data/genometools-1.6.1+ds/src/ltr/pdom_model_set.c:162:18:  [4] (shell) popen:
  This causes a new program to execute and is difficult to use safely
  (CWE-78). try using a library call that implements the same functionality
  if available.
        source = popen(cmd, "r");
data/genometools-1.6.1+ds/src/ltr/pdom_model_set.c:193:14:  [4] (shell) system:
  This causes a new program to execute and is difficult to use safely
  (CWE-78). try using a library call that implements the same functionality
  if available.
      rval = system(gt_str_get(cmdline));
data/genometools-1.6.1+ds/src/match/bcktab.c:755:5:  [4] (format) printf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
    printf("leftborder[" FormatGtCodetype "]="GT_WU,idx,
data/genometools-1.6.1+ds/src/match/bcktab.c:759:7:  [4] (format) printf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
      printf(" size " GT_WU,gt_bcktab_get_leftborder(bcktab,idx) -
data/genometools-1.6.1+ds/src/match/chain2dim.c:1792:3:  [4] (format) fprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
  fprintf(outfp,GT_WU " " GT_WU " " GT_WU " " GT_WU " " GT_WD "\n",
data/genometools-1.6.1+ds/src/match/diagband-struct.c:79:3:  [4] (format) fprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
  fprintf(stream,"# number of resets of all used diagonal bands: " GT_WU,
data/genometools-1.6.1+ds/src/match/diagband-struct.c:84:5:  [4] (format) fprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
    fprintf(stream,"; simple resets: " GT_WU,
data/genometools-1.6.1+ds/src/match/diagband-struct.c:89:5:  [4] (format) fprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
    fprintf(stream,"; resets from matches: " GT_WU,
data/genometools-1.6.1+ds/src/match/diagbandseed.c:2348:3:  [4] (format) printf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
  printf("# total number of seeds: " GT_WU,dbs_state->totalseeds);
data/genometools-1.6.1+ds/src/match/diagbandseed.c:2825:3:  [4] (format) fprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
  fprintf(outfp,GT_WU " " GT_WU " " GT_WU " " GT_WU " " GT_WU " " GT_WU "\n",
data/genometools-1.6.1+ds/src/match/eis-blockcomp.c:2003:3:  [4] (buffer) strcpy:
  Does not check for buffer overflows when copying to destination [MS-banned]
  (CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
  easily misused).
  strcpy(buf, bdxHeader);
data/genometools-1.6.1+ds/src/match/esa-scanprj.c:150:13:  [4] (buffer) sscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function. If the scanf format is influenceable by an
  attacker, it's exploitable.
        if (sscanf((const char *) (linebuffer + idx + 1),
data/genometools-1.6.1+ds/src/match/esa-shulen.c:362:9:  [4] (format) printf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
        printf(Formatuint64_t"\t",
data/genometools-1.6.1+ds/src/match/esa-spmsk.c:106:11:  [4] (format) printf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
          printf(GT_WU " " GT_WU " " GT_WU "\n",lpos,
data/genometools-1.6.1+ds/src/match/ft-eoplist.c:103:5:  [4] (format) sprintf:
  Potential format string problem (CWE-134). Make format string constant.
    sprintf(sbuf->space + sbuf->nextfree,GT_WU "%c",
data/genometools-1.6.1+ds/src/match/ft-eoplist.c:666:5:  [4] (format) fprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
    fprintf(fp,GT_WU "%c",co.iteration,
data/genometools-1.6.1+ds/src/match/ft-eoplist.c:1130:5:  [4] (format) fprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
    fprintf(fp, "# polishing(m=" GT_WD ",d=" GT_WD ",p=" GT_WU
data/genometools-1.6.1+ds/src/match/ft-polish.c:137:7:  [4] (format) printf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
      printf(GT_WU ": sum_score=" GT_WD "\n",idx,sum_score);
data/genometools-1.6.1+ds/src/match/giextract.c:126:11:  [4] (buffer) strcpy:
  Does not check for buffer overflows when copying to destination [MS-banned]
  (CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
  easily misused).
          strcpy(storeptr->fastakey,readptr->fastakey);
data/genometools-1.6.1+ds/src/match/giextract.c:197:9:  [4] (buffer) sscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function. If the scanf format is influenceable by an
  attacker, it's exploitable.
    if (sscanf(lineptr+idx, GT_WD " " GT_WD "\n",
data/genometools-1.6.1+ds/src/match/greedyfwdmat.c:172:3:  [4] (format) printf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
  printf("unit " Formatuint64_t, PRINTuint64_tcast(unitnum));
data/genometools-1.6.1+ds/src/match/hlk-version.c:32:9:  [4] (buffer) strcpy:
  Does not check for buffer overflows when copying to destination [MS-banned]
  (CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
  easily misused).
  (void)strcpy(clean_progname, progname);
data/genometools-1.6.1+ds/src/match/merger-trie.c:279:5:  [4] (format) printf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
    printf("%s " Formatuint64_t,MTRIE_ISLEAF(node) ? "leaf" : "branch",
data/genometools-1.6.1+ds/src/match/prsqualint.c:42:11:  [4] (format) fprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
          fprintf(stderr,ERRORMSG,lparam,option,BESTCHARACTER,\
data/genometools-1.6.1+ds/src/match/prsqualint.c:59:3:  [4] (buffer) strcpy:
  Does not check for buffer overflows when copying to destination [MS-banned]
  (CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
  easily misused).
  strcpy(lparamcopy,lparam);
data/genometools-1.6.1+ds/src/match/querymatch-display.c:221:9:  [4] (buffer) sscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function. If the scanf format is influenceable by an
  attacker, it's exploitable.
    if (sscanf(ptr+1,GT_WD,parameter) != 1)
data/genometools-1.6.1+ds/src/match/querymatch-display.c:541:7:  [4] (format) fprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
      fprintf(stream," -minidentity " GT_WU,minidentity);
data/genometools-1.6.1+ds/src/match/querymatch-display.c:545:7:  [4] (format) fprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
      fprintf(stream," -history " GT_WU,historysize);
data/genometools-1.6.1+ds/src/match/querymatch.c:400:7:  [4] (format) fprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
      fprintf(fp,GT_WU,dtrace ? 0 : trace_delta);
data/genometools-1.6.1+ds/src/match/querymatch.c:458:11:  [4] (format) fprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
          fprintf(querymatch->fp,GT_WU "%c",gt_querymatch_dblen(querymatch),
data/genometools-1.6.1+ds/src/match/querymatch.c:481:9:  [4] (format) fprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
        fprintf(querymatch->fp,GT_WU,gt_querymatch_dblen(querymatch));
data/genometools-1.6.1+ds/src/match/querymatch.c:488:9:  [4] (format) fprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
        fprintf(querymatch->fp,GT_WU,querymatch->dbseqnum);
data/genometools-1.6.1+ds/src/match/querymatch.c:501:11:  [4] (format) fprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
          fprintf(querymatch->fp,GT_WU,querymatch->dbstart_relative + one_off);
data/genometools-1.6.1+ds/src/match/querymatch.c:504:11:  [4] (format) fprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
          fprintf(querymatch->fp,GT_WU,querymatch->db_seqlen - 1 -
data/genometools-1.6.1+ds/src/match/querymatch.c:512:11:  [4] (format) fprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
          fprintf(querymatch->fp,GT_WU,
data/genometools-1.6.1+ds/src/match/querymatch.c:518:11:  [4] (format) fprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
          fprintf(querymatch->fp,GT_WU,querymatch->db_seqlen -
data/genometools-1.6.1+ds/src/match/querymatch.c:528:9:  [4] (format) fprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
        fprintf(querymatch->fp,GT_WU,gt_querymatch_querylen(querymatch));
data/genometools-1.6.1+ds/src/match/querymatch.c:535:9:  [4] (format) fprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
        fprintf(querymatch->fp,GT_WU,querymatch->queryseqnum);
data/genometools-1.6.1+ds/src/match/querymatch.c:546:9:  [4] (format) fprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
        fprintf(querymatch->fp,GT_WU,querymatch->querystart_fwdstrand
data/genometools-1.6.1+ds/src/match/querymatch.c:554:11:  [4] (format) fprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
          fprintf(querymatch->fp,GT_WU,
data/genometools-1.6.1+ds/src/match/querymatch.c:558:11:  [4] (format) fprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
          fprintf(querymatch->fp,GT_WU,
data/genometools-1.6.1+ds/src/match/querymatch.c:564:9:  [4] (format) fprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
        fprintf(querymatch->fp,GT_WU,
data/genometools-1.6.1+ds/src/match/querymatch.c:572:9:  [4] (format) fprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
        fprintf(querymatch->fp,GT_WU,querymatch->mismatches);
data/genometools-1.6.1+ds/src/match/querymatch.c:580:9:  [4] (format) fprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
        fprintf(querymatch->fp,GT_WU,gt_querymatch_indels(querymatch));
data/genometools-1.6.1+ds/src/match/querymatch.c:585:11:  [4] (format) fprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
          fprintf(querymatch->fp,GT_WD,querymatch->score);
data/genometools-1.6.1+ds/src/match/querymatch.c:595:11:  [4] (format) fprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
          fprintf(querymatch->fp,GT_WU,querymatch->distance);
data/genometools-1.6.1+ds/src/match/querymatch.c:612:9:  [4] (format) fprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
        fprintf(querymatch->fp,GT_WU,querymatch->seedlen);
data/genometools-1.6.1+ds/src/match/querymatch.c:615:9:  [4] (format) fprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
        fprintf(querymatch->fp,GT_WU,querymatch->db_seedpos_rel + one_off);
data/genometools-1.6.1+ds/src/match/querymatch.c:618:9:  [4] (format) fprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
        fprintf(querymatch->fp,GT_WU,querymatch->query_seedpos_rel + one_off);
data/genometools-1.6.1+ds/src/match/querymatch.c:621:9:  [4] (format) fprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
        fprintf(querymatch->fp,GT_WU,querymatch->db_seqlen);
data/genometools-1.6.1+ds/src/match/querymatch.c:624:9:  [4] (format) fprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
        fprintf(querymatch->fp,GT_WU,querymatch->query_seqlen);
data/genometools-1.6.1+ds/src/match/querymatch.c:979:15:  [4] (buffer) sscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function. If the scanf format is influenceable by an
  attacker, it's exploitable.
        ret = sscanf(ptr,GT_WU,&querymatch->dblen);
data/genometools-1.6.1+ds/src/match/querymatch.c:982:15:  [4] (buffer) sscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function. If the scanf format is influenceable by an
  attacker, it's exploitable.
        ret = sscanf(ptr,GT_WU,&querymatch->dbseqnum);
data/genometools-1.6.1+ds/src/match/querymatch.c:988:15:  [4] (buffer) sscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function. If the scanf format is influenceable by an
  attacker, it's exploitable.
        ret = sscanf(ptr,GT_WU,&querymatch->dbstart_relative);
data/genometools-1.6.1+ds/src/match/querymatch.c:994:15:  [4] (buffer) sscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function. If the scanf format is influenceable by an
  attacker, it's exploitable.
        ret = sscanf(ptr,GT_WU,&querymatch->querylen);
data/genometools-1.6.1+ds/src/match/querymatch.c:997:15:  [4] (buffer) sscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function. If the scanf format is influenceable by an
  attacker, it's exploitable.
        ret = sscanf(ptr,GT_WU,&queryend_relative);
data/genometools-1.6.1+ds/src/match/querymatch.c:1000:15:  [4] (buffer) sscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function. If the scanf format is influenceable by an
  attacker, it's exploitable.
        ret = sscanf(ptr,GT_WU,&querymatch->queryseqnum);
data/genometools-1.6.1+ds/src/match/querymatch.c:1006:15:  [4] (buffer) sscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function. If the scanf format is influenceable by an
  attacker, it's exploitable.
        ret = sscanf(ptr,GT_WU,&querymatch->querystart_fwdstrand);
data/genometools-1.6.1+ds/src/match/querymatch.c:1009:15:  [4] (buffer) sscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function. If the scanf format is influenceable by an
  attacker, it's exploitable.
        ret = sscanf(ptr,GT_WD,&querymatch->score);
data/genometools-1.6.1+ds/src/match/querymatch.c:1012:15:  [4] (buffer) sscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function. If the scanf format is influenceable by an
  attacker, it's exploitable.
        ret = sscanf(ptr,GT_WU,&querymatch->distance);
data/genometools-1.6.1+ds/src/match/querymatch.c:1015:15:  [4] (buffer) sscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function. If the scanf format is influenceable by an
  attacker, it's exploitable.
        ret = sscanf(ptr,GT_WU,&querymatch->seedlen);
data/genometools-1.6.1+ds/src/match/querymatch.c:1018:15:  [4] (buffer) sscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function. If the scanf format is influenceable by an
  attacker, it's exploitable.
        ret = sscanf(ptr,GT_WU,&querymatch->db_seedpos_rel);
data/genometools-1.6.1+ds/src/match/querymatch.c:1021:15:  [4] (buffer) sscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function. If the scanf format is influenceable by an
  attacker, it's exploitable.
        ret = sscanf(ptr,GT_WU,&querymatch->query_seedpos_rel);
data/genometools-1.6.1+ds/src/match/querymatch.c:1024:15:  [4] (buffer) sscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function. If the scanf format is influenceable by an
  attacker, it's exploitable.
        ret = sscanf(ptr,GT_WU,&querymatch->db_seqlen);
data/genometools-1.6.1+ds/src/match/querymatch.c:1027:15:  [4] (buffer) sscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function. If the scanf format is influenceable by an
  attacker, it's exploitable.
        ret = sscanf(ptr,GT_WU,&querymatch->query_seqlen);
data/genometools-1.6.1+ds/src/match/querymatch.c:1036:15:  [4] (buffer) sscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function. If the scanf format is influenceable by an
  attacker, it's exploitable.
        ret = sscanf(ptr,GT_WU,&querymatch->mismatches);
data/genometools-1.6.1+ds/src/match/querymatch.c:1039:15:  [4] (buffer) sscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function. If the scanf format is influenceable by an
  attacker, it's exploitable.
        ret = sscanf(ptr,GT_WU,&dbend_relative);
data/genometools-1.6.1+ds/src/match/rdj-strgraph.c:289:5:  [4] (format) fprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
    fprintf(stderr, \
data/genometools-1.6.1+ds/src/match/rdj-version.c:32:9:  [4] (buffer) strcpy:
  Does not check for buffer overflows when copying to destination [MS-banned]
  (CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
  easily misused).
  (void)strcpy(clean_progname, progname);
data/genometools-1.6.1+ds/src/match/reads2twobit.c:183:9:  [4] (buffer) strcpy:
  Does not check for buffer overflows when copying to destination [MS-banned]
  (CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
  easily misused).
  (void)strcpy(libspec_copy, gt_str_get(libspec));
data/genometools-1.6.1+ds/src/match/reads2twobit.c:212:11:  [4] (buffer) strcpy:
  Does not check for buffer overflows when copying to destination [MS-banned]
  (CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
  easily misused).
    (void)strcpy(insertspec_copy, insertspec);
data/genometools-1.6.1+ds/src/match/seed-extend-iter.c:141:15:  [4] (buffer) sscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function. If the scanf format is influenceable by an
  attacker, it's exploitable.
          if (sscanf(tok,GT_WD,&readgtword) != 1 ||
data/genometools-1.6.1+ds/src/match/seed-extend-iter.c:167:15:  [4] (buffer) sscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function. If the scanf format is influenceable by an
  attacker, it's exploitable.
          if (sscanf(tok,"trace=" GT_WD,&this_trace_delta) == 1 ||
data/genometools-1.6.1+ds/src/match/seed-extend-iter.c:168:15:  [4] (buffer) sscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function. If the scanf format is influenceable by an
  attacker, it's exploitable.
              sscanf(tok,"dtrace=" GT_WD,&this_trace_delta) == 1)
data/genometools-1.6.1+ds/src/match/seed-extend.c:867:15:  [4] (format) snprintf:
  If format strings can be influenced by an attacker, they can be exploited,
  and note that sprintf variations do not always \0-terminate (CWE-134). Use
  a constant for the format specification.
    offset += snprintf(out + offset,maxstrlen - offset,FORMAT,VALUE)
data/genometools-1.6.1+ds/src/match/sfx-suffixgetset.c:263:3:  [4] (format) printf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
  printf(GT_WU","GT_WU"=",sssp->bucketleftidx+subbucketleft-sssp->partoffset,
data/genometools-1.6.1+ds/src/match/sfx-suffixgetset.c:269:5:  [4] (format) printf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
    printf(" "GT_WU, gt_suffixsortspace_getdirect(sssp,idx));
data/genometools-1.6.1+ds/src/match/shu-genomediff.c:344:13:  [4] (format) fprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
            fprintf(stderr, Formatuint64_t"\t",
data/genometools-1.6.1+ds/src/match/tagerator.c:706:11:  [4] (format) printf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
          printf("\t" Formatuint64_t,PRINTuint64_tcast(tagnumber));
data/genometools-1.6.1+ds/src/match/test-maxpairs.c:232:3:  [4] (format) printf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
  printf(GT_WU " " GT_WU " " GT_WU " " GT_WU "\n",
data/genometools-1.6.1+ds/src/match/tyr-mkindex.c:113:5:  [4] (format) fprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
    fprintf(stderr,"numofmers(distribution) = " Formatuint64_t " != "
data/genometools-1.6.1+ds/src/match/tyr-search.c:118:5:  [4] (format) printf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
    printf(Formatuint64_t,PRINTuint64_tcast(unitnum));
data/genometools-1.6.1+ds/src/tools/gt_condenseq_blast.c:246:16:  [4] (shell) popen:
  This causes a new program to execute and is difficult to use safely
  (CWE-78). try using a library call that implements the same functionality
  if available.
  if ((fpipe = popen(call_str, "r")) == NULL) {
data/genometools-1.6.1+ds/src/tools/gt_condenseq_blast.c:418:9:  [4] (buffer) sscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function. If the scanf format is influenceable by an
  attacker, it's exploitable.
    if (sscanf(dbseqid, GT_WU ",", &hit_seq_id) != 1) {
data/genometools-1.6.1+ds/src/tools/gt_condenseq_blast.c:844:13:  [4] (buffer) sscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function. If the scanf format is influenceable by an
  attacker, it's exploitable.
        if (sscanf(gt_match_get_seqid2(match), GT_WU "|" GT_WU "|" GT_WU,
data/genometools-1.6.1+ds/src/tools/gt_condenseq_hmmsearch.c:402:13:  [4] (buffer) sscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function. If the scanf format is influenceable by an
  attacker, it's exploitable.
        if (sscanf(token, GT_WU ",", &uid) != 1) {
data/genometools-1.6.1+ds/src/tools/gt_condenseq_info.c:127:5:  [4] (format) printf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
    printf(GT_WU "\tunique entries\n", num);
data/genometools-1.6.1+ds/src/tools/gt_condenseq_info.c:128:5:  [4] (format) printf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
    printf(GT_WU "\tunique length\n", total);
data/genometools-1.6.1+ds/src/tools/gt_condenseq_info.c:129:5:  [4] (format) printf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
    printf(GT_WU "\taverage unique length\n", total / num);
data/genometools-1.6.1+ds/src/tools/gt_condenseq_info.c:131:7:  [4] (format) printf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
      printf(GT_WU "\trelevant uniques (>= %u)\n",
data/genometools-1.6.1+ds/src/tools/gt_condenseq_info.c:137:5:  [4] (format) printf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
    printf(GT_WU "\tlink entries\n", num);
data/genometools-1.6.1+ds/src/tools/gt_condenseq_info.c:138:5:  [4] (format) printf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
    printf(GT_WU "\tlink length\n", total);
data/genometools-1.6.1+ds/src/tools/gt_condenseq_info.c:139:5:  [4] (format) printf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
    printf(GT_WU "\taverage link length\n", total / num);
data/genometools-1.6.1+ds/src/tools/gt_condenseq_info.c:140:5:  [4] (format) printf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
    printf(GT_WU "\ttotal length\n", gt_condenseq_total_length(ces));
data/genometools-1.6.1+ds/src/tools/gt_condenseq_info.c:146:5:  [4] (format) printf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
    printf(GT_WU "\tbytes total size\n", size);
data/genometools-1.6.1+ds/src/tools/gt_condenseq_info.c:147:5:  [4] (format) printf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
    printf(GT_WU "\tbytes uniques size\n", uniques);
data/genometools-1.6.1+ds/src/tools/gt_condenseq_info.c:148:5:  [4] (format) printf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
    printf(GT_WU "\tbytes links size (without editscripts)\n", links);
data/genometools-1.6.1+ds/src/tools/gt_condenseq_info.c:149:5:  [4] (format) printf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
    printf(GT_WU "\tbytes editscripts size\n", eds);
data/genometools-1.6.1+ds/src/tools/gt_condenseq_info.c:150:5:  [4] (format) printf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
    printf(GT_WU "\tbytes descriptions size\n", descs);
data/genometools-1.6.1+ds/src/tools/gt_condenseq_info.c:151:5:  [4] (format) printf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
    printf(GT_WU "\tbytes ssptab size\n", ssp);
data/genometools-1.6.1+ds/src/tools/gt_condenseq_info.c:176:7:  [4] (format) printf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
      printf(GT_WU "/" GT_WU " compressed size: %.2f\n",
data/genometools-1.6.1+ds/src/tools/gt_linspace_align.c:444:7:  [4] (buffer) sscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function. If the scanf format is influenceable by an
  attacker, it's exploitable.
  if (sscanf(str, GT_WD, value) != 1 || (non_negative && *value < 0))
data/genometools-1.6.1+ds/src/tools/gt_paircmp.c:199:17:  [4] (buffer) sscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function. If the scanf format is influenceable by an
  attacker, it's exploitable.
            if (sscanf(gt_str_array_get(charlistlen,1UL), GT_WD, &readint) != 1
data/genometools-1.6.1+ds/src/tools/gt_paircmp.c:353:7:  [4] (format) printf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
      printf(GT_WU " " GT_WU " " GT_WU " " GT_WU "%% errors\n",
data/genometools-1.6.1+ds/src/tools/gt_repfind.c:169:7:  [4] (format) printf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
      printf(GT_WU " " GT_WU " " GT_WU "\n",seqnum2,seqnum1,matchlen);
data/genometools-1.6.1+ds/src/tools/gt_repfind.c:179:9:  [4] (format) printf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
        printf(GT_WU " " GT_WU " " GT_WU "\n",seqnum1,seqnum2,matchlen);
data/genometools-1.6.1+ds/src/tools/gt_seq.c:280:18:  [4] (buffer) fscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function. If the scanf format is influenceable by an
  attacker, it's exploitable.
          while (fscanf(fpin,GT_WD,&seqnum_input) == 1)
data/genometools-1.6.1+ds/src/tools/gt_speck.c:153:10:  [4] (format) vsnprintf:
  If format strings can be influenced by an attacker, they can be exploited,
  and note that sprintf variations do not always \0-terminate (CWE-134). Use
  a constant for the format specification.
  (void) vsnprintf(buf, (BUFSIZ * sizeof (char)), format, ap);
data/genometools-1.6.1+ds/src/core/checkbitpackarray.c:44:14:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    numRnd = random() % MAX_RND_NUMS + 1;
data/genometools-1.6.1+ds/src/core/checkbitpackarray.c:45:12:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    bits = random() % (sizeof (randSrc[0]) * CHAR_BIT + 1);
data/genometools-1.6.1+ds/src/core/checkbitpackarray.c:57:33:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
      uint32_t v = randSrc[i] = random();
data/genometools-1.6.1+ds/src/core/checkbitpackarray.c:88:14:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    numRnd = random() % MAX_RND_NUMS + 1;
data/genometools-1.6.1+ds/src/core/checkbitpackarray.c:89:12:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    bits = random() % (sizeof (randSrc[0]) * CHAR_BIT + 1);
data/genometools-1.6.1+ds/src/core/checkbitpackarray.c:110:44:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
      uint64_t v = randSrc[i] = ((uint64_t)random() << 32 | random());
data/genometools-1.6.1+ds/src/core/checkbitpackarray.c:110:61:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
      uint64_t v = randSrc[i] = ((uint64_t)random() << 32 | random());
data/genometools-1.6.1+ds/src/core/checkbitpackstring-int.c:87:26:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
  offset = offsetStart = random()%(sizeof (unsigned) * CHAR_BIT);
data/genometools-1.6.1+ds/src/core/checkbitpackstring-int.c:88:12:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
  numRnd = random() % (MAX_RND_NUMS_unsigned + 1);
data/genometools-1.6.1+ds/src/core/checkbitpackstring-int.c:103:41:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    unsigned v = randSrc[i] = (unsigned)random() << 32 | random();
data/genometools-1.6.1+ds/src/core/checkbitpackstring-int.c:103:58:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    unsigned v = randSrc[i] = (unsigned)random() << 32 | random();
data/genometools-1.6.1+ds/src/core/checkbitpackstring-int.c:105:31:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    unsigned v = randSrc[i] = random();
data/genometools-1.6.1+ds/src/core/checkbitpackstring-int.c:149:52:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    gt_bsClear(bitStoreCopy, offsetStart, numBits, random()&1);
data/genometools-1.6.1+ds/src/core/checkbitpackstring-int.c:220:24:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    unsigned numBits = random()%32 + 1;
data/genometools-1.6.1+ds/src/core/checkbitpackstring-int.c:302:24:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    unsigned numBits = random()%32 + 1;
data/genometools-1.6.1+ds/src/core/checkbitpackstring-int.c:366:38:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
      bitsTotal += (numBitsList[i] = random()%32 + 1);
data/genometools-1.6.1+ds/src/core/checkbitpackstring-int.c:434:38:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
      bitsTotal += (numBitsList[i] = random()%32 + 1);
data/genometools-1.6.1+ds/src/core/checkbitpackstring-int.c:509:26:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
      unsigned numBits = random()%32 + 1;
data/genometools-1.6.1+ds/src/core/checkbitpackstring-int.c:513:11:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
      if (random()&1)
data/genometools-1.6.1+ds/src/core/checkbitpackstring-int.c:515:26:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        numValueCopies = random()%(numRnd + 1);
data/genometools-1.6.1+ds/src/core/checkbitpackstring-int.c:516:21:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        copyStart = random()%(numRnd - numValueCopies + 1);
data/genometools-1.6.1+ds/src/core/checkbitpackstring-int.c:520:21:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        copyStart = random() % numRnd;
data/genometools-1.6.1+ds/src/core/checkbitpackstring-int.c:521:26:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        numValueCopies = random()%(numRnd - copyStart) + 1;
data/genometools-1.6.1+ds/src/core/checkbitpackstring-int.c:527:20:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
      destOffset = random()%(offsetStart + 32
data/genometools-1.6.1+ds/src/core/checkbitpackstring-int.c:558:26:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
      unsigned numBits = random()%32 + 1;
data/genometools-1.6.1+ds/src/core/checkbitpackstring-int.c:559:20:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
      int bitVal = random()&1;
data/genometools-1.6.1+ds/src/core/checkbitpackstring-int.c:564:11:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
      if (random()&1)
data/genometools-1.6.1+ds/src/core/checkbitpackstring-int.c:566:26:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        numResetValues = random()%(numRnd + 1);
data/genometools-1.6.1+ds/src/core/checkbitpackstring-int.c:567:22:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        resetStart = random()%(numRnd - numResetValues + 1);
data/genometools-1.6.1+ds/src/core/checkbitpackstring-int.c:571:22:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        resetStart = random() % numRnd;
data/genometools-1.6.1+ds/src/core/checkbitpackstring-int.c:572:26:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        numResetValues = random()%(numRnd - resetStart) + 1;
data/genometools-1.6.1+ds/src/core/checkbitpackstring-int.c:635:26:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
      unsigned numBits = random()%32 + 1;
data/genometools-1.6.1+ds/src/core/checkbitpackstring-int.c:639:11:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
      if (random()&1)
data/genometools-1.6.1+ds/src/core/checkbitpackstring-int.c:641:26:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        numCountValues = random()%(numRnd + 1);
data/genometools-1.6.1+ds/src/core/checkbitpackstring-int.c:642:22:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        countStart = random()%(numRnd - numCountValues + 1);
data/genometools-1.6.1+ds/src/core/checkbitpackstring-int.c:646:22:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        countStart = random() % numRnd;
data/genometools-1.6.1+ds/src/core/checkbitpackstring-int.c:647:26:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        numCountValues = random()%(numRnd - countStart) + 1;
data/genometools-1.6.1+ds/src/core/checkbitpackstring16.c:87:26:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
  offset = offsetStart = random()%(sizeof (uint16_t) * CHAR_BIT);
data/genometools-1.6.1+ds/src/core/checkbitpackstring16.c:88:12:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
  numRnd = random() % (MAX_RND_NUMS_uint16_t + 1);
data/genometools-1.6.1+ds/src/core/checkbitpackstring16.c:103:41:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    uint16_t v = randSrc[i] = (uint16_t)random() << 32 | random();
data/genometools-1.6.1+ds/src/core/checkbitpackstring16.c:103:58:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    uint16_t v = randSrc[i] = (uint16_t)random() << 32 | random();
data/genometools-1.6.1+ds/src/core/checkbitpackstring16.c:105:31:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    uint16_t v = randSrc[i] = random();
data/genometools-1.6.1+ds/src/core/checkbitpackstring16.c:149:52:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    gt_bsClear(bitStoreCopy, offsetStart, numBits, random()&1);
data/genometools-1.6.1+ds/src/core/checkbitpackstring16.c:220:24:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    unsigned numBits = random()%16 + 1;
data/genometools-1.6.1+ds/src/core/checkbitpackstring16.c:302:24:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    unsigned numBits = random()%16 + 1;
data/genometools-1.6.1+ds/src/core/checkbitpackstring16.c:366:38:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
      bitsTotal += (numBitsList[i] = random()%16 + 1);
data/genometools-1.6.1+ds/src/core/checkbitpackstring16.c:434:38:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
      bitsTotal += (numBitsList[i] = random()%16 + 1);
data/genometools-1.6.1+ds/src/core/checkbitpackstring16.c:509:26:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
      unsigned numBits = random()%16 + 1;
data/genometools-1.6.1+ds/src/core/checkbitpackstring16.c:513:11:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
      if (random()&1)
data/genometools-1.6.1+ds/src/core/checkbitpackstring16.c:515:26:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        numValueCopies = random()%(numRnd + 1);
data/genometools-1.6.1+ds/src/core/checkbitpackstring16.c:516:21:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        copyStart = random()%(numRnd - numValueCopies + 1);
data/genometools-1.6.1+ds/src/core/checkbitpackstring16.c:520:21:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        copyStart = random() % numRnd;
data/genometools-1.6.1+ds/src/core/checkbitpackstring16.c:521:26:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        numValueCopies = random()%(numRnd - copyStart) + 1;
data/genometools-1.6.1+ds/src/core/checkbitpackstring16.c:527:20:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
      destOffset = random()%(offsetStart + 16
data/genometools-1.6.1+ds/src/core/checkbitpackstring16.c:558:26:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
      unsigned numBits = random()%16 + 1;
data/genometools-1.6.1+ds/src/core/checkbitpackstring16.c:559:20:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
      int bitVal = random()&1;
data/genometools-1.6.1+ds/src/core/checkbitpackstring16.c:564:11:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
      if (random()&1)
data/genometools-1.6.1+ds/src/core/checkbitpackstring16.c:566:26:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        numResetValues = random()%(numRnd + 1);
data/genometools-1.6.1+ds/src/core/checkbitpackstring16.c:567:22:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        resetStart = random()%(numRnd - numResetValues + 1);
data/genometools-1.6.1+ds/src/core/checkbitpackstring16.c:571:22:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        resetStart = random() % numRnd;
data/genometools-1.6.1+ds/src/core/checkbitpackstring16.c:572:26:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        numResetValues = random()%(numRnd - resetStart) + 1;
data/genometools-1.6.1+ds/src/core/checkbitpackstring16.c:635:26:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
      unsigned numBits = random()%16 + 1;
data/genometools-1.6.1+ds/src/core/checkbitpackstring16.c:639:11:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
      if (random()&1)
data/genometools-1.6.1+ds/src/core/checkbitpackstring16.c:641:26:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        numCountValues = random()%(numRnd + 1);
data/genometools-1.6.1+ds/src/core/checkbitpackstring16.c:642:22:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        countStart = random()%(numRnd - numCountValues + 1);
data/genometools-1.6.1+ds/src/core/checkbitpackstring16.c:646:22:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        countStart = random() % numRnd;
data/genometools-1.6.1+ds/src/core/checkbitpackstring16.c:647:26:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        numCountValues = random()%(numRnd - countStart) + 1;
data/genometools-1.6.1+ds/src/core/checkbitpackstring32.c:87:26:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
  offset = offsetStart = random()%(sizeof (uint32_t) * CHAR_BIT);
data/genometools-1.6.1+ds/src/core/checkbitpackstring32.c:88:12:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
  numRnd = random() % (MAX_RND_NUMS_uint32_t + 1);
data/genometools-1.6.1+ds/src/core/checkbitpackstring32.c:103:41:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    uint32_t v = randSrc[i] = (uint32_t)random() << 32 | random();
data/genometools-1.6.1+ds/src/core/checkbitpackstring32.c:103:58:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    uint32_t v = randSrc[i] = (uint32_t)random() << 32 | random();
data/genometools-1.6.1+ds/src/core/checkbitpackstring32.c:105:31:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    uint32_t v = randSrc[i] = random();
data/genometools-1.6.1+ds/src/core/checkbitpackstring32.c:149:52:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    gt_bsClear(bitStoreCopy, offsetStart, numBits, random()&1);
data/genometools-1.6.1+ds/src/core/checkbitpackstring32.c:220:24:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    unsigned numBits = random()%32 + 1;
data/genometools-1.6.1+ds/src/core/checkbitpackstring32.c:302:24:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    unsigned numBits = random()%32 + 1;
data/genometools-1.6.1+ds/src/core/checkbitpackstring32.c:366:38:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
      bitsTotal += (numBitsList[i] = random()%32 + 1);
data/genometools-1.6.1+ds/src/core/checkbitpackstring32.c:434:38:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
      bitsTotal += (numBitsList[i] = random()%32 + 1);
data/genometools-1.6.1+ds/src/core/checkbitpackstring32.c:509:26:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
      unsigned numBits = random()%32 + 1;
data/genometools-1.6.1+ds/src/core/checkbitpackstring32.c:513:11:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
      if (random()&1)
data/genometools-1.6.1+ds/src/core/checkbitpackstring32.c:515:26:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        numValueCopies = random()%(numRnd + 1);
data/genometools-1.6.1+ds/src/core/checkbitpackstring32.c:516:21:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        copyStart = random()%(numRnd - numValueCopies + 1);
data/genometools-1.6.1+ds/src/core/checkbitpackstring32.c:520:21:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        copyStart = random() % numRnd;
data/genometools-1.6.1+ds/src/core/checkbitpackstring32.c:521:26:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        numValueCopies = random()%(numRnd - copyStart) + 1;
data/genometools-1.6.1+ds/src/core/checkbitpackstring32.c:527:20:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
      destOffset = random()%(offsetStart + 32
data/genometools-1.6.1+ds/src/core/checkbitpackstring32.c:558:26:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
      unsigned numBits = random()%32 + 1;
data/genometools-1.6.1+ds/src/core/checkbitpackstring32.c:559:20:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
      int bitVal = random()&1;
data/genometools-1.6.1+ds/src/core/checkbitpackstring32.c:564:11:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
      if (random()&1)
data/genometools-1.6.1+ds/src/core/checkbitpackstring32.c:566:26:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        numResetValues = random()%(numRnd + 1);
data/genometools-1.6.1+ds/src/core/checkbitpackstring32.c:567:22:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        resetStart = random()%(numRnd - numResetValues + 1);
data/genometools-1.6.1+ds/src/core/checkbitpackstring32.c:571:22:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        resetStart = random() % numRnd;
data/genometools-1.6.1+ds/src/core/checkbitpackstring32.c:572:26:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        numResetValues = random()%(numRnd - resetStart) + 1;
data/genometools-1.6.1+ds/src/core/checkbitpackstring32.c:635:26:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
      unsigned numBits = random()%32 + 1;
data/genometools-1.6.1+ds/src/core/checkbitpackstring32.c:639:11:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
      if (random()&1)
data/genometools-1.6.1+ds/src/core/checkbitpackstring32.c:641:26:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        numCountValues = random()%(numRnd + 1);
data/genometools-1.6.1+ds/src/core/checkbitpackstring32.c:642:22:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        countStart = random()%(numRnd - numCountValues + 1);
data/genometools-1.6.1+ds/src/core/checkbitpackstring32.c:646:22:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        countStart = random() % numRnd;
data/genometools-1.6.1+ds/src/core/checkbitpackstring32.c:647:26:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        numCountValues = random()%(numRnd - countStart) + 1;
data/genometools-1.6.1+ds/src/core/checkbitpackstring64.c:87:26:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
  offset = offsetStart = random()%(sizeof (uint64_t) * CHAR_BIT);
data/genometools-1.6.1+ds/src/core/checkbitpackstring64.c:88:12:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
  numRnd = random() % (MAX_RND_NUMS_uint64_t + 1);
data/genometools-1.6.1+ds/src/core/checkbitpackstring64.c:103:41:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    uint64_t v = randSrc[i] = (uint64_t)random() << 32 | random();
data/genometools-1.6.1+ds/src/core/checkbitpackstring64.c:103:58:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    uint64_t v = randSrc[i] = (uint64_t)random() << 32 | random();
data/genometools-1.6.1+ds/src/core/checkbitpackstring64.c:105:31:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    uint64_t v = randSrc[i] = random();
data/genometools-1.6.1+ds/src/core/checkbitpackstring64.c:149:52:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    gt_bsClear(bitStoreCopy, offsetStart, numBits, random()&1);
data/genometools-1.6.1+ds/src/core/checkbitpackstring64.c:220:24:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    unsigned numBits = random()%64 + 1;
data/genometools-1.6.1+ds/src/core/checkbitpackstring64.c:302:24:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    unsigned numBits = random()%64 + 1;
data/genometools-1.6.1+ds/src/core/checkbitpackstring64.c:366:38:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
      bitsTotal += (numBitsList[i] = random()%64 + 1);
data/genometools-1.6.1+ds/src/core/checkbitpackstring64.c:434:38:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
      bitsTotal += (numBitsList[i] = random()%64 + 1);
data/genometools-1.6.1+ds/src/core/checkbitpackstring64.c:509:26:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
      unsigned numBits = random()%64 + 1;
data/genometools-1.6.1+ds/src/core/checkbitpackstring64.c:513:11:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
      if (random()&1)
data/genometools-1.6.1+ds/src/core/checkbitpackstring64.c:515:26:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        numValueCopies = random()%(numRnd + 1);
data/genometools-1.6.1+ds/src/core/checkbitpackstring64.c:516:21:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        copyStart = random()%(numRnd - numValueCopies + 1);
data/genometools-1.6.1+ds/src/core/checkbitpackstring64.c:520:21:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        copyStart = random() % numRnd;
data/genometools-1.6.1+ds/src/core/checkbitpackstring64.c:521:26:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        numValueCopies = random()%(numRnd - copyStart) + 1;
data/genometools-1.6.1+ds/src/core/checkbitpackstring64.c:527:20:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
      destOffset = random()%(offsetStart + 64
data/genometools-1.6.1+ds/src/core/checkbitpackstring64.c:558:26:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
      unsigned numBits = random()%64 + 1;
data/genometools-1.6.1+ds/src/core/checkbitpackstring64.c:559:20:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
      int bitVal = random()&1;
data/genometools-1.6.1+ds/src/core/checkbitpackstring64.c:564:11:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
      if (random()&1)
data/genometools-1.6.1+ds/src/core/checkbitpackstring64.c:566:26:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        numResetValues = random()%(numRnd + 1);
data/genometools-1.6.1+ds/src/core/checkbitpackstring64.c:567:22:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        resetStart = random()%(numRnd - numResetValues + 1);
data/genometools-1.6.1+ds/src/core/checkbitpackstring64.c:571:22:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        resetStart = random() % numRnd;
data/genometools-1.6.1+ds/src/core/checkbitpackstring64.c:572:26:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        numResetValues = random()%(numRnd - resetStart) + 1;
data/genometools-1.6.1+ds/src/core/checkbitpackstring64.c:635:26:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
      unsigned numBits = random()%64 + 1;
data/genometools-1.6.1+ds/src/core/checkbitpackstring64.c:639:11:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
      if (random()&1)
data/genometools-1.6.1+ds/src/core/checkbitpackstring64.c:641:26:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        numCountValues = random()%(numRnd + 1);
data/genometools-1.6.1+ds/src/core/checkbitpackstring64.c:642:22:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        countStart = random()%(numRnd - numCountValues + 1);
data/genometools-1.6.1+ds/src/core/checkbitpackstring64.c:646:22:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        countStart = random() % numRnd;
data/genometools-1.6.1+ds/src/core/checkbitpackstring64.c:647:26:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        numCountValues = random()%(numRnd - countStart) + 1;
data/genometools-1.6.1+ds/src/core/checkbitpackstring8.c:87:26:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
  offset = offsetStart = random()%(sizeof (uint8_t) * CHAR_BIT);
data/genometools-1.6.1+ds/src/core/checkbitpackstring8.c:88:12:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
  numRnd = random() % (MAX_RND_NUMS_uint8_t + 1);
data/genometools-1.6.1+ds/src/core/checkbitpackstring8.c:103:39:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    uint8_t v = randSrc[i] = (uint8_t)random() << 32 | random();
data/genometools-1.6.1+ds/src/core/checkbitpackstring8.c:103:56:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    uint8_t v = randSrc[i] = (uint8_t)random() << 32 | random();
data/genometools-1.6.1+ds/src/core/checkbitpackstring8.c:105:30:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    uint8_t v = randSrc[i] = random();
data/genometools-1.6.1+ds/src/core/checkbitpackstring8.c:149:52:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    gt_bsClear(bitStoreCopy, offsetStart, numBits, random()&1);
data/genometools-1.6.1+ds/src/core/checkbitpackstring8.c:220:24:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    unsigned numBits = random()%8 + 1;
data/genometools-1.6.1+ds/src/core/checkbitpackstring8.c:302:24:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    unsigned numBits = random()%8 + 1;
data/genometools-1.6.1+ds/src/core/checkbitpackstring8.c:366:38:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
      bitsTotal += (numBitsList[i] = random()%8 + 1);
data/genometools-1.6.1+ds/src/core/checkbitpackstring8.c:434:38:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
      bitsTotal += (numBitsList[i] = random()%8 + 1);
data/genometools-1.6.1+ds/src/core/checkbitpackstring8.c:509:26:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
      unsigned numBits = random()%8 + 1;
data/genometools-1.6.1+ds/src/core/checkbitpackstring8.c:513:11:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
      if (random()&1)
data/genometools-1.6.1+ds/src/core/checkbitpackstring8.c:515:26:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        numValueCopies = random()%(numRnd + 1);
data/genometools-1.6.1+ds/src/core/checkbitpackstring8.c:516:21:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        copyStart = random()%(numRnd - numValueCopies + 1);
data/genometools-1.6.1+ds/src/core/checkbitpackstring8.c:520:21:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        copyStart = random() % numRnd;
data/genometools-1.6.1+ds/src/core/checkbitpackstring8.c:521:26:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        numValueCopies = random()%(numRnd - copyStart) + 1;
data/genometools-1.6.1+ds/src/core/checkbitpackstring8.c:527:20:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
      destOffset = random()%(offsetStart + 8
data/genometools-1.6.1+ds/src/core/checkbitpackstring8.c:558:26:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
      unsigned numBits = random()%8 + 1;
data/genometools-1.6.1+ds/src/core/checkbitpackstring8.c:559:20:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
      int bitVal = random()&1;
data/genometools-1.6.1+ds/src/core/checkbitpackstring8.c:564:11:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
      if (random()&1)
data/genometools-1.6.1+ds/src/core/checkbitpackstring8.c:566:26:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        numResetValues = random()%(numRnd + 1);
data/genometools-1.6.1+ds/src/core/checkbitpackstring8.c:567:22:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        resetStart = random()%(numRnd - numResetValues + 1);
data/genometools-1.6.1+ds/src/core/checkbitpackstring8.c:571:22:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        resetStart = random() % numRnd;
data/genometools-1.6.1+ds/src/core/checkbitpackstring8.c:572:26:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        numResetValues = random()%(numRnd - resetStart) + 1;
data/genometools-1.6.1+ds/src/core/checkbitpackstring8.c:635:26:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
      unsigned numBits = random()%8 + 1;
data/genometools-1.6.1+ds/src/core/checkbitpackstring8.c:639:11:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
      if (random()&1)
data/genometools-1.6.1+ds/src/core/checkbitpackstring8.c:641:26:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        numCountValues = random()%(numRnd + 1);
data/genometools-1.6.1+ds/src/core/checkbitpackstring8.c:642:22:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        countStart = random()%(numRnd - numCountValues + 1);
data/genometools-1.6.1+ds/src/core/checkbitpackstring8.c:646:22:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        countStart = random() % numRnd;
data/genometools-1.6.1+ds/src/core/checkbitpackstring8.c:647:26:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        numCountValues = random()%(numRnd - countStart) + 1;
data/genometools-1.6.1+ds/src/core/encseq.c:7816:27:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    startpos = (GtUword) (random() % totallength);
data/genometools-1.6.1+ds/src/core/encseq.c:7837:23:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    pos1 = (GtUword) (random() % totallength);
data/genometools-1.6.1+ds/src/core/encseq.c:7838:23:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    pos2 = (GtUword) (random() % totallength);
data/genometools-1.6.1+ds/src/core/fa.c:341:35:  [3] (buffer) getenv:
  Environment variables are untrustable input if they can be set by an
  attacker. They can have any content and length, and the same variable can
  be set more than once (CWE-807, CWE-20). Check environment variables
  carefully before using them.
        tmpdir = gt_fa_try_tmpdir(getenv("TMPDIR"));
data/genometools-1.6.1+ds/src/core/fa.c:343:35:  [3] (buffer) getenv:
  Environment variables are untrustable input if they can be set by an
  attacker. They can have any content and length, and the same variable can
  be set more than once (CWE-807, CWE-20). Check environment variables
  carefully before using them.
        tmpdir = gt_fa_try_tmpdir(getenv("TMP"));
data/genometools-1.6.1+ds/src/core/fileutils.c:185:18:  [3] (buffer) getenv:
  Environment variables are untrustable input if they can be set by an
  attacker. They can have any content and length, and the same variable can
  be set more than once (CWE-807, CWE-20). Check environment variables
  carefully before using them.
  pathvariable = getenv(env);
data/genometools-1.6.1+ds/src/core/fileutils.c:226:23:  [3] (buffer) realpath:
  This function does not protect against buffer overflows, and some
  implementations can overflow internally (CWE-120/CWE-785!). Ensure that the
  destination buffer is at least of size MAXPATHLEN, andto protect against
  implementation problems, the input argument should also be checked to
  ensure it is no larger than MAXPATHLEN.
      char *abspath = realpath(gt_str_get(path), NULL);
data/genometools-1.6.1+ds/src/core/init.c:74:17:  [3] (buffer) getenv:
  Environment variables are untrustable input if they can be set by an
  attacker. They can have any content and length, and the same variable can
  be set more than once (CWE-807, CWE-20). Check environment variables
  carefully before using them.
  env_options = getenv("GT_ENV_OPTIONS");
data/genometools-1.6.1+ds/src/core/init.c:103:17:  [3] (buffer) getenv:
  Environment variables are untrustable input if they can be set by an
  attacker. They can have any content and length, and the same variable can
  be set more than once (CWE-807, CWE-20). Check environment variables
  carefully before using them.
  bookkeeping = getenv("GT_MEM_BOOKKEEPING");
data/genometools-1.6.1+ds/src/core/mathsupport.c:89:17:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
  r = ((double) random() / ((double) GT_RAND_MAX + 1) * (maximal_value + 1));
data/genometools-1.6.1+ds/src/core/mathsupport.c:98:17:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
  r = ((double) random() / GT_RAND_MAX) * maximal_value; /* XXX */
data/genometools-1.6.1+ds/src/core/mathsupport.c:106:16:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
  r = (double) random() / GT_RAND_MAX;
data/genometools-1.6.1+ds/src/core/xbsd.c:26:8:  [3] (buffer) getenv:
  Environment variables are untrustable input if they can be set by an
  attacker. They can have any content and length, and the same variable can
  be set more than once (CWE-807, CWE-20). Check environment variables
  carefully before using them.
  if (!getenv("GT_NO_FLOCK")) {
data/genometools-1.6.1+ds/src/core/yarandom_api.h:17:8:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
#undef random
data/genometools-1.6.1+ds/src/core/yarandom_api.h:19:8:  [3] (random) drand48:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
#undef drand48
data/genometools-1.6.1+ds/src/core/yarandom_api.h:20:8:  [3] (random) srandom:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
#undef srandom
data/genometools-1.6.1+ds/src/core/yarandom_api.h:21:8:  [3] (random) srand:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
#undef srand
data/genometools-1.6.1+ds/src/core/yarandom_api.h:37:9:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
#define random() \
data/genometools-1.6.1+ds/src/core/yarandom_api.h:45:9:  [3] (random) drand48:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
#define drand48       __ERROR_use_frand_not_drand48_in_GenomeTools__
data/genometools-1.6.1+ds/src/core/yarandom_api.h:46:9:  [3] (random) srandom:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
#define srandom       __ERROR_do_not_call_srandom_in_GenomeTools__
data/genometools-1.6.1+ds/src/core/yarandom_api.h:47:9:  [3] (random) srand:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
#define srand         __ERROR_do_not_call_srand_in_GenomeTools__
data/genometools-1.6.1+ds/src/core/yarandom_api.h:55:31:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
  ({ double tmp = ((((double) random()) * ((double) (f))) /             \
data/genometools-1.6.1+ds/src/core/yarandom_api.h:63:30:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
  (_frand_tmp_ = ((((double) random()) * ((double) (f))) /              \
data/genometools-1.6.1+ds/src/extended/blast_process_call.c:57:9:  [3] (buffer) getenv:
  Environment variables are untrustable input if they can be set by an
  attacker. They can have any content and length, and the same variable can
  be set more than once (CWE-807, CWE-20). Check environment variables
  carefully before using them.
  env = getenv("GT_BLAST_PATH");
data/genometools-1.6.1+ds/src/extended/extract_feature_visitor.c:208:21:  [3] (buffer) getenv:
  Environment variables are untrustable input if they can be set by an
  attacker. They can have any content and length, and the same variable can
  be set more than once (CWE-807, CWE-20). Check environment variables
  carefully before using them.
  efv->retain_ids = getenv("GT_RETAINIDS") ? true : false;
data/genometools-1.6.1+ds/src/extended/feature_index.c:376:15:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
  rng.start = random() % (GT_FI_TEST_END - GT_FI_TEST_QUERY_WIDTH);
data/genometools-1.6.1+ds/src/extended/feature_index.c:377:25:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
  rng.end = rng.start + random() % (GT_FI_TEST_QUERY_WIDTH);
data/genometools-1.6.1+ds/src/extended/feature_index.c:473:13:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    start = random() % (GT_FI_TEST_END - GT_FI_TEST_FEATURE_WIDTH);
data/genometools-1.6.1+ds/src/extended/feature_index.c:474:19:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    end = start + random() % (GT_FI_TEST_FEATURE_WIDTH);
data/genometools-1.6.1+ds/src/extended/gff3_visitor.c:532:30:  [3] (buffer) getenv:
  Environment variables are untrustable input if they can be set by an
  attacker. They can have any content and length, and the same variable can
  be set more than once (CWE-807, CWE-20). Check environment variables
  carefully before using them.
  gff3_visitor->retain_ids = getenv("GT_RETAINIDS") ? true : false;
data/genometools-1.6.1+ds/src/extended/match_iterator_last.c:103:9:  [3] (buffer) getenv:
  Environment variables are untrustable input if they can be set by an
  attacker. They can have any content and length, and the same variable can
  be set more than once (CWE-807, CWE-20). Check environment variables
  carefully before using them.
  env = getenv("GT_LAST_PATH");
data/genometools-1.6.1+ds/src/extended/match_iterator_last.c:423:15:  [3] (buffer) getenv:
  Environment variables are untrustable input if they can be set by an
  attacker. They can have any content and length, and the same variable can
  be set more than once (CWE-807, CWE-20). Check environment variables
  carefully before using them.
        env = getenv("GT_LAST_PATH");
data/genometools-1.6.1+ds/src/extended/match_iterator_last.c:488:22:  [3] (buffer) getenv:
  Environment variables are untrustable input if they can be set by an
  attacker. They can have any content and length, and the same variable can
  be set more than once (CWE-807, CWE-20). Check environment variables
  carefully before using them.
  mil->pvt->tmpdir = getenv("TMPDIR");
data/genometools-1.6.1+ds/src/extended/ranked_list.c:282:33:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
      newstr.score = (GtUword) (random() % (2*nof_best));
data/genometools-1.6.1+ds/src/extended/rbtree.c:845:20:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    j = (GtUword) (random () % GT_RBTREE_SIZE);
data/genometools-1.6.1+ds/src/gtr.c:91:18:  [3] (buffer) getenv:
  Environment variables are untrustable input if they can be set by an
  attacker. They can have any content and length, and the same variable can
  be set more than once (CWE-807, CWE-20). Check environment variables
  carefully before using them.
  if ((seedstr = getenv("GT_SEED"))) {
data/genometools-1.6.1+ds/src/ltr/ltr_refseq_match_stream.c:280:9:  [3] (buffer) getenv:
  Environment variables are untrustable input if they can be set by an
  attacker. They can have any content and length, and the same variable can
  be set more than once (CWE-807, CWE-20). Check environment variables
  carefully before using them.
  env = getenv(GT_BLAST_PATH_ENV);
data/genometools-1.6.1+ds/src/ltr/pdom_model_set.c:137:20:  [3] (buffer) getenv:
  Environment variables are untrustable input if they can be set by an
  attacker. They can have any content and length, and the same variable can
  be set more than once (CWE-807, CWE-20). Check environment variables
  carefully before using them.
    if (!(tmpdir = getenv("TMPDIR")))
data/genometools-1.6.1+ds/src/match/eis-bwtseq.c:640:23:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
          subSeqLen = random()%maxSubSeqLen + 1;
data/genometools-1.6.1+ds/src/match/eis-bwtseq.c:641:19:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
          start = random()%(seqLen - subSeqLen + 1);
data/genometools-1.6.1+ds/src/match/eis-encidxseq.c:167:13:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
      if (!(random() % AVG_RANGE_RANK_INTERVAL))
data/genometools-1.6.1+ds/src/match/eis-encidxseq.c:171:33:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        AlphabetRangeID range = random() % numRanges;
data/genometools-1.6.1+ds/src/match/enum-patt.c:104:37:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
                                   (random() %
data/genometools-1.6.1+ds/src/match/enum-patt.c:109:20:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        (GtUword) (random() % (epi->totallength - *patternlen));
data/genometools-1.6.1+ds/src/match/enum-patt.c:126:23:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
      cc = (GtUchar) (random() % epi->alphasize);
data/genometools-1.6.1+ds/src/match/test-maxpairs.c:78:22:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
  start = (GtUword) (random() % totallength);
data/genometools-1.6.1+ds/src/match/test-maxpairs.c:94:36:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        seqspace[idx] = (GtUchar) (random() % numofchars);
data/genometools-1.6.1+ds/src/tools/gt_sortbench.c:646:40:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
          arraykeypair[idx].uint64_a = random() % (arguments->maxvalue+1);
data/genometools-1.6.1+ds/src/tools/gt_sortbench.c:647:40:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
          arraykeypair[idx].uint64_b = random() % (arguments->maxvalue+1);
data/genometools-1.6.1+ds/src/tools/gt_sortbench.c:657:40:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
            GtUword value = (GtUword) (random() % (arguments->maxvalue+1));
data/genometools-1.6.1+ds/src/tools/gt_sortbench.c:671:26:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
            array[idx] = random() % (arguments->maxvalue+1);
data/genometools-1.6.1+ds/src/annotationsketch/canvas_cairo.c:126:7:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
      char buf[BUFSIZ];
data/genometools-1.6.1+ds/src/annotationsketch/canvas_cairo.c:779:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char str[BUFSIZ];
data/genometools-1.6.1+ds/src/annotationsketch/custom_track_example.c:43:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char buffer[BUFSIZ];
data/genometools-1.6.1+ds/src/annotationsketch/custom_track_example.c:62:3:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
  sprintf(buffer, "Style %p", style);
data/genometools-1.6.1+ds/src/annotationsketch/custom_track_example.c:69:3:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
  sprintf(buffer, "Range "GT_WU" - "GT_WU"", viewrange.start, viewrange.end);
data/genometools-1.6.1+ds/src/annotationsketch/custom_track_example.c:76:3:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
  sprintf(buffer, "Start position y=%u", start_ypos);
data/genometools-1.6.1+ds/src/annotationsketch/custom_track_gc_content.c:211:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char buf[BUFSIZ];
data/genometools-1.6.1+ds/src/annotationsketch/graphics_cairo.c:78:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char buf[BUFSIZ];
data/genometools-1.6.1+ds/src/annotationsketch/graphics_cairo.c:795:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char buf[64];
data/genometools-1.6.1+ds/src/annotationsketch/graphics_cairo.c:815:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char buf[64];
data/genometools-1.6.1+ds/src/annotationsketch/gt_sketch.c:453:13:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
            char buf[BUFSIZ];
data/genometools-1.6.1+ds/src/annotationsketch/gt_sketch_page.c:186:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char buffer[BUFSIZ];
data/genometools-1.6.1+ds/src/annotationsketch/text_width_calculator_cairo.c:109:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char buf[BUFSIZ];
data/genometools-1.6.1+ds/src/core/alphabet.c:429:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
  memcpy(alphabet->mapdomain + alphabet->domainsize, characters,
data/genometools-1.6.1+ds/src/core/alphabet.c:478:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
  memcpy(alpha->mapdomain,(GtUchar *) DNAALPHABETDOMAIN,
data/genometools-1.6.1+ds/src/core/alphabet.c:482:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
  memcpy(alpha->characters,"acgt",(size_t) (MAPSIZEDNA-1));
data/genometools-1.6.1+ds/src/core/alphabet.c:545:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
  memcpy(alpha->mapdomain,
data/genometools-1.6.1+ds/src/core/alphabet.c:549:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
  memcpy(alpha->characters,PROTEINUPPERAMINOACIDS,(size_t) (MAPSIZEPROTEIN-1));
data/genometools-1.6.1+ds/src/core/array.c:55:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
  memcpy(a_copy->space, a->space, a->next_free * a->size_of_elem);
data/genometools-1.6.1+ds/src/core/array.c:99:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy((char*) a->space + (i-1) * a->size_of_elem,
data/genometools-1.6.1+ds/src/core/array.c:115:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy((char*) a->space + (i-len) * a->size_of_elem,
data/genometools-1.6.1+ds/src/core/array.c:131:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy(tmp, front, a->size_of_elem);
data/genometools-1.6.1+ds/src/core/array.c:132:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy(front, back, a->size_of_elem);
data/genometools-1.6.1+ds/src/core/array.c:133:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy(back, tmp, a->size_of_elem);
data/genometools-1.6.1+ds/src/core/array.c:160:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
  memcpy((char*) a->space + a->next_free * size_of_elem, elem, size_of_elem);
data/genometools-1.6.1+ds/src/core/array.c:288:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy((char*) dest->space + (i-1+src->next_free) * dest->size_of_elem,
data/genometools-1.6.1+ds/src/core/array.c:293:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
  memcpy((char*) dest->space, (char*) src->space,
data/genometools-1.6.1+ds/src/core/bioseq.c:114:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char buf[BUFSIZ];
data/genometools-1.6.1+ds/src/core/bioseq.c:117:15:  [2] (tmpfile) tmpfile:
  Function tmpfile() has a security flaw on some systems (e.g., older System
  V systems) (CWE-377).
    gt_assert(tmpfile);
data/genometools-1.6.1+ds/src/core/bioseq.c:121:36:  [2] (tmpfile) tmpfile:
  Function tmpfile() has a security flaw on some systems (e.g., older System
  V systems) (CWE-377).
      if (i > 0) fwrite(buf, 1, i, tmpfile);
data/genometools-1.6.1+ds/src/core/bioseq.c:123:19:  [2] (tmpfile) tmpfile:
  Function tmpfile() has a security flaw on some systems (e.g., older System
  V systems) (CWE-377).
    gt_fa_xfclose(tmpfile);
data/genometools-1.6.1+ds/src/core/bioseq_col.c:129:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char buf[BUFSIZ], fmt[32];
data/genometools-1.6.1+ds/src/core/bioseq_col.c:133:10:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
  (void) sprintf(fmt, "%%%ds", BUFSIZ-1);
data/genometools-1.6.1+ds/src/core/bitpackstringop.c:264:7:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
      memcpy(q, p, completeElems);
data/genometools-1.6.1+ds/src/core/bitpackstringop.c:513:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char buf[sizeof (accum) * CHAR_BIT];
data/genometools-1.6.1+ds/src/core/bittab.c:261:25:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  static const unsigned char bits_in_char[256] = { 0, 1, 1, 2, 1, 2, 2, 3, 1, 2,
data/genometools-1.6.1+ds/src/core/byte_popcount_api.h:25:23:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
extern const unsigned char gt_byte_popcount[256];
data/genometools-1.6.1+ds/src/core/byte_select_api.h:26:23:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
extern const unsigned char gt_byte_select[2048];
data/genometools-1.6.1+ds/src/core/compat.c:31:10:  [2] (tmpfile) mkstemp:
  Potential for temporary file vulnerability in some circumstances. Some
  older Unix-like systems create temp files with permission to write by all
  by default, so be sure to set the umask to override this. Also, some older
  Unix systems might fail to use O_EXCL when opening the file, so make sure
  that O_EXCL is used by the library (CWE-377).
  return mkstemp(templ);
data/genometools-1.6.1+ds/src/core/compat.c:42:10:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  return open(templ, O_RDWR, O_EXCL);
data/genometools-1.6.1+ds/src/core/countingsort.c:48:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy((char*) out + elem_size * (c[k] - 1),
data/genometools-1.6.1+ds/src/core/cstr.c:46:9:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
        memcpy(res[respos], cstr + lastpos, (i - lastpos) * sizeof (char));
data/genometools-1.6.1+ds/src/core/cstr.c:63:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
  memcpy(copy, cstr, size);
data/genometools-1.6.1+ds/src/core/cstr.c:72:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
  memcpy(copy, cstr, length);
data/genometools-1.6.1+ds/src/core/desc_buffer.c:137:7:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
      memcpy(db->buf, db->buf + laststartpos, db->length * sizeof (char));
data/genometools-1.6.1+ds/src/core/eansi.c:24:15:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  if ((file = fopen(path, mode)) == NULL) {
data/genometools-1.6.1+ds/src/core/encseq.c:1029:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy(encseq->exceptionheaderptr.classstartpositionsptr,
data/genometools-1.6.1+ds/src/core/encseq.c:1035:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy(encseq->exceptionheaderptr.maxcharsptr, encseq->maxchars,
data/genometools-1.6.1+ds/src/core/encseq.c:1040:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy(encseq->exceptionheaderptr.allcharsptr, encseq->allchars,
data/genometools-1.6.1+ds/src/core/encseq.c:1045:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy(encseq->exceptionheaderptr.subsymbolmapptr, encseq->subsymbolmap,
data/genometools-1.6.1+ds/src/core/encseq.c:1264:7:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
      memcpy(headerptr->alphadef, alphadef, sizeof (*headerptr->alphadef) *
data/genometools-1.6.1+ds/src/core/encseq.c:5466:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char *desc,
data/genometools-1.6.1+ds/src/core/encseq.c:5469:12:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  unsigned char md5_output[16];
data/genometools-1.6.1+ds/src/core/encseq.c:5706:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char md5_blockbuf[64];
data/genometools-1.6.1+ds/src/core/encseq.c:5707:13:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  GT_UNUSED char md5_outbuf[33];
data/genometools-1.6.1+ds/src/core/encseq.c:5708:12:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  unsigned char md5_output[16];
data/genometools-1.6.1+ds/src/core/encseq.c:7031:7:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
      char buf1[GT_INTWORDSIZE+1], buf2[GT_INTWORDSIZE+1];
data/genometools-1.6.1+ds/src/core/encseq.c:7050:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char buf1[GT_INTWORDSIZE+1],
data/genometools-1.6.1+ds/src/core/encseq.c:7195:9:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
        char buffer[GT_INTWORDSIZE+1];
data/genometools-1.6.1+ds/src/core/encseq.c:7266:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char buf1[GT_INTWORDSIZE+1], buf2[GT_INTWORDSIZE+1];
data/genometools-1.6.1+ds/src/core/encseq.c:7538:12:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  unsigned char subsymbolmap[UCHAR_MAX+1],
data/genometools-1.6.1+ds/src/core/encseq.c:7610:7:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
      char buf[BUFSIZ];
data/genometools-1.6.1+ds/src/core/encseq.c:8734:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char buf[BUFSIZ];
data/genometools-1.6.1+ds/src/core/encseq.c:8887:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy(eb->plainseq, theirseq, (size_t) eb->seqlen);
data/genometools-1.6.1+ds/src/core/encseq.c:8954:7:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
      memcpy(eb->plainseq, str, (size_t) strlen * sizeof (GtUchar));
data/genometools-1.6.1+ds/src/core/encseq.c:8976:7:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
      memcpy(eb->plainseq, theirseq, (size_t) eb->seqlen);
data/genometools-1.6.1+ds/src/core/encseq.c:9128:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy(encseq->destab,
data/genometools-1.6.1+ds/src/core/encseq_col.c:246:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char seqid[GT_MD5_SEQID_HASH_LEN + 1];
data/genometools-1.6.1+ds/src/core/encseq_col.c:285:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char seqid[GT_MD5_SEQID_HASH_LEN + 1];
data/genometools-1.6.1+ds/src/core/encseq_metadata.c:59:15:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
              char buffer[GT_WORDSIZE_INBYTES];\
data/genometools-1.6.1+ds/src/core/error.c:25:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char error_string[BUFSIZ],
data/genometools-1.6.1+ds/src/core/fa.c:495:8:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  fd = open(path, mapwritable?O_RDWR:O_RDONLY, 0);
data/genometools-1.6.1+ds/src/core/fa.c:524:8:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  fd = open(path, mapwritable?O_RDWR:O_RDONLY, 0);
data/genometools-1.6.1+ds/src/core/fa.c:592:8:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  fd = open(path,O_RDONLY); /* open file for read, get filedes */
data/genometools-1.6.1+ds/src/core/file.c:244:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char buf[BUFSIZ];
data/genometools-1.6.1+ds/src/core/file.c:268:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char buf[BUFSIZ];
data/genometools-1.6.1+ds/src/core/fileutils.c:37:15:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  if ((file = fopen(path, "r")) == NULL)
data/genometools-1.6.1+ds/src/core/fileutils.c:61:15:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  if ((file = fopen(path, "r")) == NULL)
data/genometools-1.6.1+ds/src/core/fileutils.c:304:9:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  fp1 = fopen(file1, "rb");
data/genometools-1.6.1+ds/src/core/fileutils.c:305:9:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  fp2 = fopen(file2, "rb");
data/genometools-1.6.1+ds/src/core/grep.c:30:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char sbuf[BUFSIZ], *buf;
data/genometools-1.6.1+ds/src/core/hashtable.c:87:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
  memcpy(gt_ht_elem_ptr(ht, dest_idx), src, ht->table_info.elem_size);
data/genometools-1.6.1+ds/src/core/hashtable.c:236:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy(ht, &new_ht, sizeof (*ht));
data/genometools-1.6.1+ds/src/core/intbits.h:207:23:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
static const unsigned char ReversedByte[256] =
data/genometools-1.6.1+ds/src/core/md5_encoder.c:171:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char buff[64];
data/genometools-1.6.1+ds/src/core/md5_encoder.c:173:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy(buff, pt, num);  /* to avoid changing original string */
data/genometools-1.6.1+ds/src/core/md5_fingerprint.c:28:12:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  unsigned char output[16];
data/genometools-1.6.1+ds/src/core/md5_fingerprint.c:29:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char buf[64];
data/genometools-1.6.1+ds/src/core/option.c:678:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char c,
data/genometools-1.6.1+ds/src/core/option.c:2007:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char buffer[2+1];
data/genometools-1.6.1+ds/src/core/password_entry.c:32:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char buf[255];
data/genometools-1.6.1+ds/src/core/progressbar.c:77:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char buf[MAXIMUM_WINDOW_SIZE + 1];
data/genometools-1.6.1+ds/src/core/queue.c:86:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy(q->contents + q->size, q->contents, q->front * sizeof (void*));
data/genometools-1.6.1+ds/src/core/radix_sort.c:136:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy(dest,source,sizeof (*source) * len);
data/genometools-1.6.1+ds/src/core/score_matrix.c:56:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char *tokenstr, amino_acid, parsed_characters[UCHAR_MAX] = { 0 };
data/genometools-1.6.1+ds/src/core/score_matrix.c:191:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char parsed_characters[UCHAR_MAX] = { 0 };
data/genometools-1.6.1+ds/src/core/seq_iterator_fastq.c:55:12:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  unsigned char ungetchar,
data/genometools-1.6.1+ds/src/core/sequence_buffer.c:68:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char firstcontents[BUFSIZ];
data/genometools-1.6.1+ds/src/core/sequence_buffer_embl.c:73:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char linecode[2];
data/genometools-1.6.1+ds/src/core/sequence_buffer_rep.h:63:12:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  unsigned char ungetchar,
data/genometools-1.6.1+ds/src/core/stack-inlined.h:110:13:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
            memcpy((S)->space,&(S)->staticspace[0],sizeoftype*(S)->staticsize);\
data/genometools-1.6.1+ds/src/core/str.c:76:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
  memcpy(dest->cstr + dest->length, src->cstr, src->length);
data/genometools-1.6.1+ds/src/core/str.c:99:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
  memcpy(dest->cstr + dest->length, cstr, length);
data/genometools-1.6.1+ds/src/core/str.c:145:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char buf[BUFSIZ];
data/genometools-1.6.1+ds/src/core/str.c:155:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char buf[BUFSIZ];
data/genometools-1.6.1+ds/src/core/str.c:165:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char buf[BUFSIZ];
data/genometools-1.6.1+ds/src/core/str.c:175:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char buf[BUFSIZ];
data/genometools-1.6.1+ds/src/core/timer.c:179:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char buf[BUFSIZ];
data/genometools-1.6.1+ds/src/core/timer.c:262:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char buf[BUFSIZ];
data/genometools-1.6.1+ds/src/core/xansi.c:84:15:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  if ((file = fopen(path, mode)) == NULL) {
data/genometools-1.6.1+ds/src/core/xposix.c:101:13:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  if ((fd = open(path, flags, mode)) == -1) {
data/genometools-1.6.1+ds/src/examples/gtkviewer.c:163:30:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  gtk_widget_add_accelerator(open, "activate", accel_group,
data/genometools-1.6.1+ds/src/examples/gtkviewer.c:167:51:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  gtk_menu_shell_append(GTK_MENU_SHELL(filemenu), open);
data/genometools-1.6.1+ds/src/extended/aligned_segment.c:205:9:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
  (void)memcpy(as->d, gt_sam_alignment_identifier(sa), sizeof (*as->d) * dlen);
data/genometools-1.6.1+ds/src/extended/aligned_segment.c:219:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
  memcpy(as->s_orig, as->s, (size_t)(as->alen + 1UL));
data/genometools-1.6.1+ds/src/extended/assembly_stats_calculator.c:87:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char         *name[MAX_NOF_NSTATS];
data/genometools-1.6.1+ds/src/extended/blast_process_call.c:286:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char line[BUFSIZ + 1];
data/genometools-1.6.1+ds/src/extended/condenseq.c:180:12:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    (void) memcpy(cur_id_startptr, desc, (size_t) idlen);
data/genometools-1.6.1+ds/src/extended/editscript.c:40:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char bitbuffer[65] = {0};                         \
data/genometools-1.6.1+ds/src/extended/encdesc.c:1139:10:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    fd = open(gt_str_get(filename), O_RDONLY);
data/genometools-1.6.1+ds/src/extended/gff3_escaping.c:136:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char unescaped_testseq[8],
data/genometools-1.6.1+ds/src/extended/gff3_escaping.c:181:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char code[10];
data/genometools-1.6.1+ds/src/extended/gff3_escaping.c:188:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char code[10];
data/genometools-1.6.1+ds/src/extended/gff3_escaping.c:195:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char code[16];
data/genometools-1.6.1+ds/src/extended/gff3_linesorted_out_stream.c:96:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char buf1[BUFSIZ], buf2[BUFSIZ];
data/genometools-1.6.1+ds/src/extended/gff3_output.c:59:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char buf[BUFSIZ];
data/genometools-1.6.1+ds/src/extended/hcr.c:1031:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char qual[BUFSIZ] = {0},
data/genometools-1.6.1+ds/src/extended/match_iterator_blast.c:77:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char query_seq[BUFSIZ], db_seq[BUFSIZ], buffer[BUFSIZ];
data/genometools-1.6.1+ds/src/extended/match_iterator_blast.c:191:30:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
      mpb->pvt->matchfilep = fopen(matchfile, "r");
data/genometools-1.6.1+ds/src/extended/match_iterator_blast.c:251:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char buffer[BUFSIZ];
data/genometools-1.6.1+ds/src/extended/match_iterator_blast.c:325:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char buffer[BUFSIZ];
data/genometools-1.6.1+ds/src/extended/match_iterator_last.c:330:15:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
      fdout = open(gt_str_get(matchfilename), O_WRONLY | O_CREAT, 0600);
data/genometools-1.6.1+ds/src/extended/match_iterator_open.c:68:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char buffer[BUFSIZ], seqid1[BUFSIZ], seqid2[BUFSIZ], matchtype;
data/genometools-1.6.1+ds/src/extended/match_iterator_open.c:163:30:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
      mpo->pvt->matchfilep = fopen(matchfile, "r");
data/genometools-1.6.1+ds/src/extended/orf_finder_visitor.c:80:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char frame_buf[3];
data/genometools-1.6.1+ds/src/extended/orf_finder_visitor.c:81:3:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
  sprintf(frame_buf, "%d", orf_frame);
data/genometools-1.6.1+ds/src/extended/rdb_mysql.c:190:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char buf[BUFSIZ];
data/genometools-1.6.1+ds/src/extended/rmq.c:153:14:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
static const char gt_rmq_LogTable256[256] =
data/genometools-1.6.1+ds/src/extended/snp_annotator_visitor.c:96:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char codon[3],
data/genometools-1.6.1+ds/src/extended/splice_site_info_visitor.c:64:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char site[5];
data/genometools-1.6.1+ds/src/extended/string_matching.c:196:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char s[STRING_MATCHING_MAX_STRING_LENGTH+1],
data/genometools-1.6.1+ds/src/extended/tag_value_map.c:41:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
  memcpy(map, tag, tag_len + 1);
data/genometools-1.6.1+ds/src/extended/tag_value_map.c:42:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
  memcpy(map + tag_len + 1, value, value_len + 1);
data/genometools-1.6.1+ds/src/extended/tag_value_map.c:133:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
  memcpy(*map + map_len, tag, tag_len + 1);
data/genometools-1.6.1+ds/src/extended/tag_value_map.c:134:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
  memcpy(*map + map_len + tag_len + 1, value, value_len + 1);
data/genometools-1.6.1+ds/src/extended/tag_value_map.c:174:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy(old_value, new_value, new_value_len);
data/genometools-1.6.1+ds/src/extended/tag_value_map.c:180:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy(old_value, new_value, new_value_len);
data/genometools-1.6.1+ds/src/extended/tag_value_map.c:189:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy(old_value, new_value, new_value_len);
data/genometools-1.6.1+ds/src/extended/tir_stream.c:798:9:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
        char description_string[BUFSIZ];
data/genometools-1.6.1+ds/src/extended/tir_stream.c:836:7:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
      char buf[BUFSIZ];
data/genometools-1.6.1+ds/src/gtlua/genome_node_lua.c:190:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char strand_char[2];
data/genometools-1.6.1+ds/src/gtlua/genome_node_lua.c:230:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char phasebuf[2];
data/genometools-1.6.1+ds/src/gtlua/genome_node_lua.c:798:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char buf[BUFSIZ];
data/genometools-1.6.1+ds/src/gtlua/range_lua.c:130:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char buf[BUFSIZ];
data/genometools-1.6.1+ds/src/gtr.c:264:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char fulltoolname[BUFSIZ],
data/genometools-1.6.1+ds/src/gtr.c:329:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char fulltoolname[BUFSIZ];
data/genometools-1.6.1+ds/src/interactive.c:112:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char buffer[BUFSIZ];
data/genometools-1.6.1+ds/src/ltr/ltr_classify_stream.c:231:9:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
        char fam[BUFSIZ];
data/genometools-1.6.1+ds/src/ltr/ltr_cluster_prepare_seq_visitor.c:86:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char buffer[BUFSIZ];
data/genometools-1.6.1+ds/src/ltr/ltr_cluster_prepare_seq_visitor.c:110:7:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
      char header[2*BUFSIZ];
data/genometools-1.6.1+ds/src/ltr/ltr_cluster_prepare_seq_visitor.c:138:7:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
      char header[2*BUFSIZ];  /* XXX: use GtStr for safety */
data/genometools-1.6.1+ds/src/ltr/ltr_cluster_stream.c:309:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char buffer[BUFSIZ], *real_feature;
data/genometools-1.6.1+ds/src/ltr/ltr_cluster_stream.c:324:7:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
      char header[2*BUFSIZ];
data/genometools-1.6.1+ds/src/ltr/ltr_cluster_stream.c:367:9:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
        char clid[BUFSIZ];
data/genometools-1.6.1+ds/src/ltr/ltr_cluster_stream.c:401:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char tmp[BUFSIZ];
data/genometools-1.6.1+ds/src/ltr/ltr_refseq_match_stream.c:95:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char header[BUFSIZ];
data/genometools-1.6.1+ds/src/ltr/ltr_refseq_match_stream.c:201:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char target[BUFSIZ], *tmp, *tmp2, buf[BUFSIZ];
data/genometools-1.6.1+ds/src/ltr/ltr_refseq_match_stream.c:236:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char params_id[BUFSIZ];
data/genometools-1.6.1+ds/src/ltr/ltr_refseq_match_stream.c:274:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char makeblastdb_call[BUFSIZ],
data/genometools-1.6.1+ds/src/ltr/ltr_refseq_match_stream.c:298:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char buffer[BUFSIZ];
data/genometools-1.6.1+ds/src/ltr/ltrdigest_file_out_stream.c:115:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char tmpstr[BUFSIZ];
data/genometools-1.6.1+ds/src/ltr/ltrdigest_file_out_stream.c:191:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char buf[BUFSIZ];
data/genometools-1.6.1+ds/src/ltr/ltrdigest_file_out_stream.c:255:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char buffer[GT_MAXFILENAMELEN];
data/genometools-1.6.1+ds/src/ltr/ltrdigest_file_out_stream.c:320:7:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
      char buf[BUFSIZ];
data/genometools-1.6.1+ds/src/ltr/ltrdigest_file_out_stream.c:408:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char desc[GT_MAXFASTAHEADER];
data/genometools-1.6.1+ds/src/ltr/ltrdigest_file_out_stream.c:705:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char *buffer,
data/genometools-1.6.1+ds/src/ltr/ltrdigest_file_out_stream.c:819:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char fn[GT_MAXFILENAMELEN];
data/genometools-1.6.1+ds/src/ltr/ltrdigest_pbs_visitor.c:317:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy(trna_from3_full, gt_seq_get_orig(trna_seq),
data/genometools-1.6.1+ds/src/ltr/ltrdigest_pbs_visitor.c:369:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char buffer[BUFSIZ];
data/genometools-1.6.1+ds/src/ltr/ltrdigest_pbs_visitor.c:559:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char *rev_seq,
data/genometools-1.6.1+ds/src/ltr/ltrdigest_pbs_visitor.c:613:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
  memcpy(seq,     fullseq + 20, (size_t) 600);
data/genometools-1.6.1+ds/src/ltr/ltrdigest_pbs_visitor.c:614:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
  memcpy(rev_seq, fullseq + 20, (size_t) 600);
data/genometools-1.6.1+ds/src/ltr/ltrdigest_pbs_visitor.c:637:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
  memcpy(tmp, fullseq + (rng.start * sizeof (char)),
data/genometools-1.6.1+ds/src/ltr/ltrdigest_pbs_visitor.c:656:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
  memcpy(tmp, fullseq + (rng.start * sizeof (char)),
data/genometools-1.6.1+ds/src/ltr/ltrdigest_pdom_visitor.c:344:20:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
      cur_domain = atoi(buf+12);
data/genometools-1.6.1+ds/src/ltr/ltrdigest_pdom_visitor.c:463:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char buf[GT_HMMER_BUF_LEN];
data/genometools-1.6.1+ds/src/ltr/ltrdigest_pdom_visitor.c:474:32:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
    status->frame = (unsigned) atoi(buf+13);
data/genometools-1.6.1+ds/src/ltr/ltrdigest_pdom_visitor.c:585:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char buf[32];
data/genometools-1.6.1+ds/src/ltr/ltrdigest_pdom_visitor.c:908:15:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
              char buf[5];
data/genometools-1.6.1+ds/src/ltr/ltrdigest_pdom_visitor.c:910:22:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
              (void) sprintf(buf, ">"GT_WU"%c\n", i, '+');
data/genometools-1.6.1+ds/src/ltr/ltrdigest_pdom_visitor.c:915:22:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
              (void) sprintf(buf, ">"GT_WU"%c\n", i, '-');
data/genometools-1.6.1+ds/src/ltr/ltrharvest_stream.c:1411:7:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
      char buf[BUFSIZ];
data/genometools-1.6.1+ds/src/ltr/ltrharvest_stream.c:1461:7:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
      char buf[BUFSIZ];
data/genometools-1.6.1+ds/src/ltr/ltrharvest_tabout_visitor.c:87:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char buf[BUFSIZ];
data/genometools-1.6.1+ds/src/ltr/pdom_model_set.c:50:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char filename[BUFSIZ];
data/genometools-1.6.1+ds/src/ltr/pdom_model_set.c:100:7:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
      char line[BUFSIZ];
data/genometools-1.6.1+ds/src/ltr/pdom_model_set.c:104:12:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
      fp = fopen(filename, "r");
data/genometools-1.6.1+ds/src/ltr/pdom_model_set.c:150:12:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    dest = fopen(gt_str_get(pdom_model_set->filename), "w+");
data/genometools-1.6.1+ds/src/ltr/pdom_model_set.c:159:9:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
        char cmd[BUFSIZ];
data/genometools-1.6.1+ds/src/match/eis-blockcomp.c:1342:7:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
      memcpy(retval->cwPart, sBlock->cwData,
data/genometools-1.6.1+ds/src/match/eis-blockcomp.c:1361:9:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
        memcpy(retval->varPart, sBlock->varData,
data/genometools-1.6.1+ds/src/match/eis-blockcomp.c:1508:9:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
        memcpy(rankCounts + rsize, rankCounts, rsize * sizeof (rankCounts[0]));
data/genometools-1.6.1+ds/src/match/eis-blockcomp.c:1600:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
  memcpy(dest, src, sizeof (dest[0]) * alphabetSize);
data/genometools-1.6.1+ds/src/match/eis-bwtseq-context.c:290:7:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
      char buf[1 + 4 + 3 + 3];
data/genometools-1.6.1+ds/src/match/eis-bwtseq-extinfo.c:856:7:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
      memcpy(bwtSeq->rangeSort, defaultRangeSort,
data/genometools-1.6.1+ds/src/match/eis-mrangealphabet.c:134:9:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
        memcpy(newAlpha->mappings, srcAlpha->mappings, UINT8_MAX+1);
data/genometools-1.6.1+ds/src/match/eis-mrangealphabet.c:135:9:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
        memcpy(newAlpha->revMappings, srcAlpha->revMappings, UINT8_MAX+1);
data/genometools-1.6.1+ds/src/match/eis-mrangealphabet.c:136:9:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
        memcpy(newAlpha->baseClass.rangeEndIndices,
data/genometools-1.6.1+ds/src/match/eis-mrangealphabet.c:139:9:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
        memcpy(newAlpha->baseClass.symbolsPerRange,
data/genometools-1.6.1+ds/src/match/eis-seqdatasrc.h:115:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
  memcpy(dest, src, len * xltor.state.elemSize);
data/genometools-1.6.1+ds/src/match/eis-seqranges.c:505:7:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
      memcpy(partialSymSums + i * numSyms, partialSymSums + (i - 1) * numSyms,
data/genometools-1.6.1+ds/src/match/eis-sequencemultiread.c:213:7:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
      memcpy(dest, (char *)readerSet->seqDataBacklog
data/genometools-1.6.1+ds/src/match/ft-front-prune.c:573:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy(fs->space,((GtFtFrontvalue *) fs->space) + trimleft - fs->offset,
data/genometools-1.6.1+ds/src/match/ft-polish.c:78:10:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  static char cs[64+1];
data/genometools-1.6.1+ds/src/match/giextract.c:444:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char key[MAXFIXEDKEYSIZE+1];
data/genometools-1.6.1+ds/src/match/idx-limdfs.c:542:7:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
      memcpy(limdfsresources->copyofcopyofparentstate,
data/genometools-1.6.1+ds/src/match/mssufpat.c:238:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char buffer1[GT_INTWORDSIZE+1], buffer2[GT_INTWORDSIZE+1];
data/genometools-1.6.1+ds/src/match/mssufpat.c:271:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char buffer1[INTWORDSIZE+1], buffer2[INTWORDSIZE+1];
data/genometools-1.6.1+ds/src/match/querymatch-align.c:572:7:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
      memcpy(querymatchoutoptions->vseqbuffer,
data/genometools-1.6.1+ds/src/match/querymatch-display.c:109:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy(copy,str,sizeof *copy * cmplen);
data/genometools-1.6.1+ds/src/match/querymatch-display.c:345:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char copyspace[GT_MAX_DISPLAY_FLAG_LENGTH+1];
data/genometools-1.6.1+ds/src/match/radixsort_str.c:424:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy(bucket.suffixes, rsi->sorted, sizeof (*rsi->sorted) * bucket.width);
data/genometools-1.6.1+ds/src/match/randomcodes-hpcorrect.c:846:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy(sdata->pw_scores_copy, sdata->pw_scores,
data/genometools-1.6.1+ds/src/match/rdj-contigs-graph.c:254:14:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  FILE *fp = fopen(path, "w");
data/genometools-1.6.1+ds/src/match/rdj-contigs-graph.c:268:14:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  FILE *fp = fopen(path, "w");
data/genometools-1.6.1+ds/src/match/rdj-ensure-output.h:34:9:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
        char buffer[MAXOUTSIZE]
data/genometools-1.6.1+ds/src/match/reads2twobit.c:286:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
  memcpy(&(EIDEST), &(EISRC), sizeof (EISRC))
data/genometools-1.6.1+ds/src/match/reads2twobit.c:856:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char line[GT_READS2TWOBIT_READBUFFER_SIZE], *fgetsretval;
data/genometools-1.6.1+ds/src/match/reads2twobit.c:1285:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char line1[GT_READS2TWOBIT_READBUFFER_SIZE],
data/genometools-1.6.1+ds/src/match/reads2twobit.c:1737:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy(outputbuffer + 1, r2t->twobitencoding + firstcodeidx + 1,
data/genometools-1.6.1+ds/src/match/seed-extend-iter.c:118:18:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  defline_infp = fopen(semi->matchfilename, "r");
data/genometools-1.6.1+ds/src/match/seed-extend-iter.c:314:26:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    semi->inputfileptr = fopen(semi->matchfilename, "rb");
data/genometools-1.6.1+ds/src/match/sfx-copysort.c:256:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char buffer[100];
data/genometools-1.6.1+ds/src/match/test-mappedstr.c:137:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char buffer1[64+1], buffer2[64+1];
data/genometools-1.6.1+ds/src/match/twobits2kmers.c:51:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char buffer[2*GT_INTWORDSIZE+1];
data/genometools-1.6.1+ds/src/mgth/mg_combinedscore.c:56:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char contig_triplet[3],              /* Query-Triplet von dem die AS
data/genometools-1.6.1+ds/src/mgth/mg_combinedscore.c:134:18:  [2] (integer) atol:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
    ulhit_from = atol(gt_str_array_get(MATRIXSTRUCT(hit_from), i));
data/genometools-1.6.1+ds/src/mgth/mg_combinedscore.c:135:16:  [2] (integer) atol:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
    ulhit_to = atol(gt_str_array_get(MATRIXSTRUCT(hit_to), i));
data/genometools-1.6.1+ds/src/mgth/mg_outputwriter.c:813:17:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
                atoi(gt_str_array_get(hit_information->hit_from, seq_index));
data/genometools-1.6.1+ds/src/mgth/mg_outputwriter.c:815:17:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
                atoi(gt_str_array_get(hit_information->hit_to, seq_index));
data/genometools-1.6.1+ds/src/mgth/mg_outputwriter.c:1154:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char contig_triplet[3],
data/genometools-1.6.1+ds/src/mgth/mg_xmlparser.c:53:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy(&(mem->memory[mem->size]), ptr, realsize);
data/genometools-1.6.1+ds/src/mgth/mg_xmlparser.c:175:19:  [2] (integer) atol:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
      numb_from = atol(gt_str_array_get(MATRIXSTRUCT(hit_from), hit_counter));
data/genometools-1.6.1+ds/src/mgth/mg_xmlparser.c:176:17:  [2] (integer) atol:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
      numb_to = atol(gt_str_array_get(MATRIXSTRUCT(hit_to), hit_counter));
data/genometools-1.6.1+ds/src/mgth/mg_xmlparser.c:603:26:  [2] (integer) atol:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
        ulong_numb_buf = atol(gt_str_get(PARSESTRUCT(buf_ptr)));
data/genometools-1.6.1+ds/src/mgth/mg_xmlparser.c:613:26:  [2] (integer) atol:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
        ulong_numb_buf = atol(gt_str_get(PARSESTRUCT(buf_ptr)));
data/genometools-1.6.1+ds/src/mgth/mg_xmlparser.c:666:20:  [2] (integer) atol:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
        numb_buf = atol(gt_str_get(PARSESTRUCT(buf_ptr)));
data/genometools-1.6.1+ds/src/mgth/mg_xmlparser.c:682:20:  [2] (integer) atol:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
        numb_buf = atol(gt_str_get(PARSESTRUCT(buf_ptr)));
data/genometools-1.6.1+ds/src/tools/gt_compreads_decompress.c:136:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char qual[BUFSIZ] = {0},
data/genometools-1.6.1+ds/src/tools/gt_condenseq_blast.c:252:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char line[BUFSIZ + 1];
data/genometools-1.6.1+ds/src/tools/gt_convertseq.c:163:9:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
        memcpy(newseq, sequence, (size_t) len*sizeof (GtUchar));
data/genometools-1.6.1+ds/src/tools/gt_encseq_bitextract.c:95:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char buffer[BUFSIZ];
data/genometools-1.6.1+ds/src/tools/gt_encseq_decode.c:224:7:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
      char buf[BUFSIZ];
data/genometools-1.6.1+ds/src/tools/gt_encseq_sample.c:202:9:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
        char buf[BUFSIZ];
data/genometools-1.6.1+ds/src/tools/gt_seqorder.c:216:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char buf[BUFSIZ];
data/genometools-1.6.1+ds/src/tools/gt_skproto.c:106:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
  memcpy(gt_str_get(line), buffer, (size_t) (bufpos + 1));
data/genometools-1.6.1+ds/src/tools/gt_sortbench.c:659:13:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
            memcpy(flba + idx * flba_unitsize,flba_buffer,flba_unitsize);
data/genometools-1.6.1+ds/src/tools/gt_speck.c:151:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char buf[BUFSIZ];
data/genometools-1.6.1+ds/src/tools/gt_splitfasta.c:152:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char buf[BUFSIZ];
data/genometools-1.6.1+ds/src/annotationsketch/canvas_cairo.c:136:9:  [1] (buffer) strncpy:
  Easily used incorrectly; doesn't always \0-terminate or check for invalid
  pointers [MS-banned] (CWE-120).
        strncpy(buf, msg, BUFSIZ);
data/genometools-1.6.1+ds/src/core/alphabet.c:424:23:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  num_of_characters = strlen(characters);
data/genometools-1.6.1+ds/src/core/alphabet.c:474:43:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  alpha->mappedwildcards = (unsigned int) strlen(DNAWILDCARDS);
data/genometools-1.6.1+ds/src/core/alphabet.c:475:38:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  alpha->domainsize = (unsigned int) strlen(DNAALPHABETDOMAIN);
data/genometools-1.6.1+ds/src/core/alphabet.c:541:38:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  alpha->domainsize = (unsigned int) strlen(PROTEINALPHABETDOMAIN);
data/genometools-1.6.1+ds/src/core/alphabet.c:542:43:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  alpha->mappedwildcards = (unsigned int) strlen(PROTEINWILDCARDS);
data/genometools-1.6.1+ds/src/core/array.c:402:34:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
                                 strlen(char_array_test)) == 0);
data/genometools-1.6.1+ds/src/core/basename.c:32:15:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    pathlen = strlen(path);
data/genometools-1.6.1+ds/src/core/basename.c:37:5:  [1] (buffer) strcpy:
  Does not check for buffer overflows when copying to destination [MS-banned]
  (CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
  easily misused). Risk is low because the source is a constant character.
    strcpy(sbuf, ".");
data/genometools-1.6.1+ds/src/core/bioseq.c:337:5:  [1] (buffer) strncpy:
  Easily used incorrectly; doesn't always \0-terminate or check for invalid
  pointers [MS-banned] (CWE-120).
    strncpy(mydesc, desc, desclen);
data/genometools-1.6.1+ds/src/core/codon_iterator_encseq.c:148:31:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  for (j = 0; !had_err && j < strlen(testseq); j++) {
data/genometools-1.6.1+ds/src/core/codon_iterator_encseq.c:149:33:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    for (k = j; !had_err && k < strlen(testseq); k++) {
data/genometools-1.6.1+ds/src/core/codon_iterator_encseq.c:152:55:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
                                                      strlen(testseq) - k,
data/genometools-1.6.1+ds/src/core/codon_iterator_encseq.c:189:43:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  gt_encseq_builder_add_cstr(eb, testseq, strlen(testseq), "foo");
data/genometools-1.6.1+ds/src/core/compat.c:35:34:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  errno_t err = _mktemp_s(templ, strlen(templ) + 1);
data/genometools-1.6.1+ds/src/core/cstr.c:35:19:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  for (i = 0; i < strlen(cstr); i++) {
data/genometools-1.6.1+ds/src/core/cstr.c:41:19:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  for (i = 0; i < strlen(cstr)+1; i++) {
data/genometools-1.6.1+ds/src/core/cstr.c:61:10:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  size = strlen(cstr) + 1;
data/genometools-1.6.1+ds/src/core/cstr.c:104:10:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  return strlen(cstr);
data/genometools-1.6.1+ds/src/core/cstr.c:111:21:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  for (tmp = cstr + strlen(cstr) - 1; tmp >= cstr && *tmp == remove; --tmp);
data/genometools-1.6.1+ds/src/core/cstr_array.c:44:11:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  f_len = strlen(p) + strlen(cstr_array[0]) + 2; /* blank + '\0' */
data/genometools-1.6.1+ds/src/core/cstr_array.c:44:23:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  f_len = strlen(p) + strlen(cstr_array[0]) + 2; /* blank + '\0' */
data/genometools-1.6.1+ds/src/core/csvline_reader.c:102:14:  [1] (buffer) fgetc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    int cc = fgetc(inputfp);
data/genometools-1.6.1+ds/src/core/desc_buffer.c:201:19:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  for (i = 0; i < strlen(strs[0]); i++) {
data/genometools-1.6.1+ds/src/core/desc_buffer.c:213:21:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    for (i = 0; i < strlen(strs[j]); i++) {
data/genometools-1.6.1+ds/src/core/desc_buffer.c:229:21:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    for (i = 0; i < strlen(strs[j]); i++) {
data/genometools-1.6.1+ds/src/core/encseq.c:4897:5:  [1] (buffer) strncpy:
  Easily used incorrectly; doesn't always \0-terminate or check for invalid
  pointers [MS-banned] (CWE-120).
    strncpy(copydestab + offset, desptr, (size_t) desclen);
data/genometools-1.6.1+ds/src/core/encseq.c:5321:5:  [1] (buffer) strncpy:
  Easily used incorrectly; doesn't always \0-terminate or check for invalid
  pointers [MS-banned] (CWE-120).
    strncpy(*allchars + offset,
data/genometools-1.6.1+ds/src/core/encseq.c:5341:3:  [1] (buffer) strncpy:
  Easily used incorrectly; doesn't always \0-terminate or check for invalid
  pointers [MS-banned] (CWE-120).
  strncpy(*allchars + offset,
data/genometools-1.6.1+ds/src/core/encseq.c:8005:28:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    size_t indexname_len = strlen(indexname);
data/genometools-1.6.1+ds/src/core/encseq.c:8440:14:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  if (sat && strlen(sat) > 0
data/genometools-1.6.1+ds/src/core/encseq.c:8879:41:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
                                GtUword strlen, const char *desc)
data/genometools-1.6.1+ds/src/core/encseq.c:8902:32:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
                               strlen * sizeof (GtUchar));
data/genometools-1.6.1+ds/src/core/encseq.c:8904:18:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    eb->seqlen = strlen;
data/genometools-1.6.1+ds/src/core/encseq.c:8920:16:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  for (i=0;i < strlen; i++) {
data/genometools-1.6.1+ds/src/core/encseq.c:8925:42:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  if (eb->minseqlen == GT_UNDEF_UWORD || strlen < eb->minseqlen)
data/genometools-1.6.1+ds/src/core/encseq.c:8926:21:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    eb->minseqlen = strlen;
data/genometools-1.6.1+ds/src/core/encseq.c:8927:42:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  if (eb->maxseqlen == GT_UNDEF_UWORD || strlen > eb->maxseqlen)
data/genometools-1.6.1+ds/src/core/encseq.c:8928:21:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    eb->maxseqlen = strlen;
data/genometools-1.6.1+ds/src/core/encseq.c:8941:59:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
                                                  GtUword strlen,
data/genometools-1.6.1+ds/src/core/encseq.c:8952:41:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
      eb->plainseq = gt_malloc((size_t) strlen * sizeof (GtUchar));
data/genometools-1.6.1+ds/src/core/encseq.c:8953:33:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
      eb->allocated = (size_t) (strlen * sizeof (GtUchar));
data/genometools-1.6.1+ds/src/core/encseq.c:8954:42:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
      memcpy(eb->plainseq, str, (size_t) strlen * sizeof (GtUchar));
data/genometools-1.6.1+ds/src/core/encseq.c:8957:18:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    eb->seqlen = strlen;
data/genometools-1.6.1+ds/src/core/encseq.c:8991:34:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
                                 strlen * sizeof (GtUchar));
data/genometools-1.6.1+ds/src/core/encseq.c:8993:20:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
      eb->seqlen = strlen;
data/genometools-1.6.1+ds/src/core/encseq.c:9009:18:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    for (i=0;i < strlen; i++) {
data/genometools-1.6.1+ds/src/core/encseq.c:9015:42:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  if (eb->minseqlen == GT_UNDEF_UWORD || strlen < eb->minseqlen)
data/genometools-1.6.1+ds/src/core/encseq.c:9016:21:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    eb->minseqlen = strlen;
data/genometools-1.6.1+ds/src/core/encseq.c:9017:42:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  if (eb->maxseqlen == GT_UNDEF_UWORD || strlen > eb->maxseqlen)
data/genometools-1.6.1+ds/src/core/encseq.c:9018:21:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    eb->maxseqlen = strlen;
data/genometools-1.6.1+ds/src/core/encseq.c:9023:44:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
                                   GtUword strlen,
data/genometools-1.6.1+ds/src/core/encseq.c:9026:52:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  gt_assert(memchr(str,(int) GT_SEPARATOR,(size_t) strlen) == NULL);
data/genometools-1.6.1+ds/src/core/encseq.c:9027:50:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  gt_encseq_builder_add_encoded_generic(eb, str, strlen, desc, false);
data/genometools-1.6.1+ds/src/core/encseq.c:9032:48:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
                                       GtUword strlen,
data/genometools-1.6.1+ds/src/core/encseq.c:9035:52:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  gt_assert(memchr(str,(int) GT_SEPARATOR,(size_t) strlen) == NULL);
data/genometools-1.6.1+ds/src/core/encseq.c:9036:50:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  gt_encseq_builder_add_encoded_generic(eb, str, strlen, desc, true);
data/genometools-1.6.1+ds/src/core/encseq.c:9041:53:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
                                            GtUword strlen)
data/genometools-1.6.1+ds/src/core/encseq.c:9045:23:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  for (idx = 0; idx < strlen; idx++)
data/genometools-1.6.1+ds/src/core/encseq_api.h:507:54:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
                                             GtUword strlen,
data/genometools-1.6.1+ds/src/core/encseq_api.h:525:56:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
                                               GtUword strlen,
data/genometools-1.6.1+ds/src/core/encseq_api.h:536:60:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
                                                   GtUword strlen,
data/genometools-1.6.1+ds/src/core/encseq_api.h:544:66:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
                                                         GtUword strlen);
data/genometools-1.6.1+ds/src/core/encseq_col.c:261:7:  [1] (buffer) strncpy:
  Easily used incorrectly; doesn't always \0-terminate or check for invalid
  pointers [MS-banned] (CWE-120).
      strncpy(seqid, cstrseqid + GT_MD5_SEQID_PREFIX_LEN,
data/genometools-1.6.1+ds/src/core/encseq_col.c:300:7:  [1] (buffer) strncpy:
  Easily used incorrectly; doesn't always \0-terminate or check for invalid
  pointers [MS-banned] (CWE-120).
      strncpy(seqid, cstrseqid + GT_MD5_SEQID_PREFIX_LEN,
data/genometools-1.6.1+ds/src/core/fa.c:612:9:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    if (read(fd,ptr,*len) == -1)
data/genometools-1.6.1+ds/src/core/fasta.c:66:46:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  GtUword description_length = description ? strlen(description) : 0;
data/genometools-1.6.1+ds/src/core/fasta.c:78:46:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  GtUword description_length = description ? strlen(description) : 0;
data/genometools-1.6.1+ds/src/core/fasta.c:112:28:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  suffix_length = suffix ? strlen(suffix) : 0;
data/genometools-1.6.1+ds/src/core/fasta.c:152:28:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  suffix_length = suffix ? strlen(suffix) : 0;
data/genometools-1.6.1+ds/src/core/fasta_reader_seqit.c:62:40:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
      had_err = proc_description(desc, strlen(desc), data, err);
data/genometools-1.6.1+ds/src/core/file.c:47:17:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  path_length = strlen(path);
data/genometools-1.6.1+ds/src/core/file.c:78:17:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  path_length = strlen(path);
data/genometools-1.6.1+ds/src/core/fileutils.c:59:16:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  size_t len = strlen(path);
data/genometools-1.6.1+ds/src/core/fileutils.c:141:22:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  for (i = (GtWord) (strlen(file) - 1); i >= 0; i--) {
data/genometools-1.6.1+ds/src/core/fileutils.c:213:33:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
                      (GtUword) strlen(pathvariable), GT_PATH_VAR_SEPARATOR);
data/genometools-1.6.1+ds/src/core/fileutils.c:308:11:  [1] (buffer) fgetc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    cc1 = fgetc(fp1);
data/genometools-1.6.1+ds/src/core/fileutils.c:309:11:  [1] (buffer) fgetc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    cc2 = fgetc(fp2);
data/genometools-1.6.1+ds/src/core/grep.c:100:43:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  return gt_grep_nt(match, pattern, line, strlen(line), err);
data/genometools-1.6.1+ds/src/core/gtdatapath.c:57:53:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
      gt_str_set_length(path, gt_str_length(path) - strlen(GTDATADIR));
data/genometools-1.6.1+ds/src/core/init.c:79:44:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  gt_splitter_split(splitter, env_options, strlen(env_options), ' ');
data/genometools-1.6.1+ds/src/core/option.c:126:27:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  gt_assert(option_str && strlen(option_str));
data/genometools-1.6.1+ds/src/core/option.c:217:13:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
            strlen(one_liner) && isupper((int) one_liner[0]));
data/genometools-1.6.1+ds/src/core/option.c:218:23:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  gt_assert(one_liner[strlen(one_liner)-1] == '.');
data/genometools-1.6.1+ds/src/core/option.c:406:42:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
        if (!option->default_value.s || !strlen(option->default_value.s))
data/genometools-1.6.1+ds/src/core/option.c:459:42:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
        if (!option->default_value.s || !strlen(option->default_value.s))
data/genometools-1.6.1+ds/src/core/option.c:483:19:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  for (i = 0; i < strlen(hdr); i++)
data/genometools-1.6.1+ds/src/core/option.c:490:19:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  for (i = 0; i < strlen(toolname); i++) {
data/genometools-1.6.1+ds/src/core/option.c:543:13:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  gt_assert(strlen(toolname) > 0);
data/genometools-1.6.1+ds/src/core/option.c:554:19:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  for (i = 0; i < strlen(toolname) + 3; i++)
data/genometools-1.6.1+ds/src/core/option.c:597:42:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
        if (!option->default_value.s || !strlen(option->default_value.s))
data/genometools-1.6.1+ds/src/core/option.c:611:42:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
        if (!option->default_value.s || !strlen(option->default_value.s))
data/genometools-1.6.1+ds/src/core/option.c:654:42:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
        if (!option->default_value.s || !strlen(option->default_value.s))
data/genometools-1.6.1+ds/src/core/option.c:713:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    while (read(out_pipe[0], &c, sizeof (char)) > 0)
data/genometools-1.6.1+ds/src/core/option.c:1012:53:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    if (!(argv[argnum] && argv[argnum][0] == '-' && strlen(argv[argnum]) > 1) ||
data/genometools-1.6.1+ds/src/core/output_file.c:60:16:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
               strlen(gt_file_mode_suffix(file_mode)),
data/genometools-1.6.1+ds/src/core/parseutils.c:247:7:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  if (strlen(score) == 1 && score[0] == '.')
data/genometools-1.6.1+ds/src/core/parseutils.c:267:7:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  if (strlen(strand) != 1) {
data/genometools-1.6.1+ds/src/core/parseutils.c:290:7:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  if (strlen(phase) != 1) {
data/genometools-1.6.1+ds/src/core/parseutils.c:328:13:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  desclen = strlen(desc);
data/genometools-1.6.1+ds/src/core/password_entry.c:48:12:  [1] (buffer) scanf:
  It's unclear if the %s limit in the format string is small enough
  (CWE-120). Check that the limit is sufficiently small, or use a different
  input function.
  retval = scanf("%254s", buf);
data/genometools-1.6.1+ds/src/core/progressbar.c:91:27:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    (void) snprintf(buf + strlen(buf), window_size - strlen(buf),
data/genometools-1.6.1+ds/src/core/progressbar.c:91:54:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    (void) snprintf(buf + strlen(buf), window_size - strlen(buf),
data/genometools-1.6.1+ds/src/core/progressbar.c:118:29:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
      (void) snprintf(buf + strlen(buf), window_size - strlen(buf),
data/genometools-1.6.1+ds/src/core/progressbar.c:118:56:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
      (void) snprintf(buf + strlen(buf), window_size - strlen(buf),
data/genometools-1.6.1+ds/src/core/progressbar.c:123:29:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
      (void) snprintf(buf + strlen(buf), window_size - strlen(buf),
data/genometools-1.6.1+ds/src/core/progressbar.c:123:56:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
      (void) snprintf(buf + strlen(buf), window_size - strlen(buf),
data/genometools-1.6.1+ds/src/core/progressbar.c:129:27:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    (void) snprintf(buf + strlen(buf), window_size - strlen(buf),
data/genometools-1.6.1+ds/src/core/progressbar.c:129:54:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    (void) snprintf(buf + strlen(buf), window_size - strlen(buf),
data/genometools-1.6.1+ds/src/core/progressbar.c:154:31:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
        (void) snprintf(buf + strlen(buf), window_size - strlen(buf),
data/genometools-1.6.1+ds/src/core/progressbar.c:154:58:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
        (void) snprintf(buf + strlen(buf), window_size - strlen(buf),
data/genometools-1.6.1+ds/src/core/progressbar.c:159:31:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
        (void) snprintf(buf + strlen(buf), window_size - strlen(buf),
data/genometools-1.6.1+ds/src/core/progressbar.c:159:58:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
        (void) snprintf(buf + strlen(buf), window_size - strlen(buf),
data/genometools-1.6.1+ds/src/core/progressbar.c:165:29:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
      (void) snprintf(buf + strlen(buf), window_size - strlen(buf),
data/genometools-1.6.1+ds/src/core/progressbar.c:165:56:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
      (void) snprintf(buf + strlen(buf), window_size - strlen(buf),
data/genometools-1.6.1+ds/src/core/progressbar.c:171:25:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  (void) snprintf(buf + strlen(buf), window_size - strlen(buf), "%*s",
data/genometools-1.6.1+ds/src/core/progressbar.c:171:52:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  (void) snprintf(buf + strlen(buf), window_size - strlen(buf), "%*s",
data/genometools-1.6.1+ds/src/core/progressbar.c:172:39:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
                  window_size - (int) strlen(buf), "");
data/genometools-1.6.1+ds/src/core/progressbar.c:173:33:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  gt_xwrite(STDOUT_FILENO, buf, strlen(buf));
data/genometools-1.6.1+ds/src/core/sequence_buffer_embl.c:365:45:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  return !strncmp(txt, EMBL_ID_LINE_STRING, strlen(EMBL_ID_LINE_STRING));
data/genometools-1.6.1+ds/src/core/sequence_buffer_fastq.c:161:15:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    desclen = strlen(desc)+1;
data/genometools-1.6.1+ds/src/core/sequence_buffer_fastq.c:168:23:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
      for (i = 0; i < strlen(desc); i++) {
data/genometools-1.6.1+ds/src/core/splitter.c:134:7:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  STR[strlen(STR)] = DELIM
data/genometools-1.6.1+ds/src/core/splitter.c:155:34:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  gt_splitter_split(s, string_1, strlen(string_1), delimiter1);
data/genometools-1.6.1+ds/src/core/splitter.c:166:44:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  gt_splitter_split_non_empty(s, string_1, strlen(string_1), delimiter1);
data/genometools-1.6.1+ds/src/core/splitter.c:177:34:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  gt_splitter_split(s, string_2, strlen(string_2), delimiter2);
data/genometools-1.6.1+ds/src/core/splitter.c:188:44:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  gt_splitter_split_non_empty(s, string_2, strlen(string_2), delimiter2);
data/genometools-1.6.1+ds/src/core/splitter.c:199:34:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  gt_splitter_split(s, string_3, strlen(string_3), delimiter2);
data/genometools-1.6.1+ds/src/core/splitter.c:206:44:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  gt_splitter_split_non_empty(s, string_3, strlen(string_3), delimiter2);
data/genometools-1.6.1+ds/src/core/splitter.c:212:34:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  gt_splitter_split(s, string_4, strlen(string_4), delimiter1);
data/genometools-1.6.1+ds/src/core/splitter.c:221:44:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  gt_splitter_split_non_empty(s, string_4, strlen(string_4), delimiter1);
data/genometools-1.6.1+ds/src/core/splitter.c:229:34:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  gt_splitter_split(s, string_5, strlen(string_5), delimiter1);
data/genometools-1.6.1+ds/src/core/splitter.c:238:44:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  gt_splitter_split_non_empty(s, string_5, strlen(string_5), delimiter1);
data/genometools-1.6.1+ds/src/core/splitter.c:246:34:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  gt_splitter_split(s, string_6, strlen(string_6), delimiter3);
data/genometools-1.6.1+ds/src/core/splitter.c:251:44:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  gt_splitter_split_non_empty(s, string_6, strlen(string_6), delimiter3);
data/genometools-1.6.1+ds/src/core/str.c:62:15:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    cstrlen = strlen(cstr);
data/genometools-1.6.1+ds/src/core/str.c:85:13:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  cstrlen = strlen(cstr);
data/genometools-1.6.1+ds/src/core/str.c:435:13:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  gt_ensure(strlen(gt_str_get(s)) == 0);
data/genometools-1.6.1+ds/src/core/str.c:441:13:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  gt_ensure(strlen(gt_str_get(s)) == 0);
data/genometools-1.6.1+ds/src/core/translator.c:140:22:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    if ((len = (int) strlen(gt_str_array_get(codons, i))) != GT_CODON_LENGTH) {
data/genometools-1.6.1+ds/src/core/translator.c:231:52:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  ci = gt_codon_iterator_simple_new(seq, (GtUword) strlen(seq), test_err);
data/genometools-1.6.1+ds/src/core/translator.c:294:47:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
                                    (GtUword) strlen(invalidseq),
data/genometools-1.6.1+ds/src/core/translator.c:306:47:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
                                    (GtUword) strlen(invalidseq2),
data/genometools-1.6.1+ds/src/core/translator.c:322:47:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
                                    (GtUword) strlen(no_startcodon),
data/genometools-1.6.1+ds/src/core/xansi.c:52:13:  [1] (buffer) fgetc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  if ((cc = fgetc(stream)) == EOF) {
data/genometools-1.6.1+ds/src/core/xbzlib.c:58:13:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  int len = strlen(str);
data/genometools-1.6.1+ds/src/extended/aligned_segment.c:203:10:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  dlen = strlen(gt_sam_alignment_identifier(sa)) + 1UL;
data/genometools-1.6.1+ds/src/extended/alignment.c:844:44:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
                                 (GtUword) strlen(u),
data/genometools-1.6.1+ds/src/extended/alignment.c:846:44:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
                                 (GtUword) strlen(v));
data/genometools-1.6.1+ds/src/extended/condenseq.c:605:9:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    if (strlen(basename) > (size_t) 1 &&
data/genometools-1.6.1+ds/src/extended/editscript.c:333:39:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
                             GtUword *mismatch,
data/genometools-1.6.1+ds/src/extended/editscript.c:375:15:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            (*mismatch)++;
data/genometools-1.6.1+ds/src/extended/editscript.c:1198:20:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
    GtUword match, mismatch, del, ins;
data/genometools-1.6.1+ds/src/extended/editscript.c:1199:42:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
    gt_editscript_get_stats(es, &match, &mismatch, &ins, &del);
data/genometools-1.6.1+ds/src/extended/editscript.h:62:48:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
                                      GtUword *mismatch,
data/genometools-1.6.1+ds/src/extended/encdesc.c:218:9:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  len = strlen(info->descbuffer);
data/genometools-1.6.1+ds/src/extended/encdesc.c:363:28:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    desclength = (GtUword) strlen(descbuffer);
data/genometools-1.6.1+ds/src/extended/encdesc.c:399:28:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    desclength = (GtUword) strlen(longest_desc);
data/genometools-1.6.1+ds/src/extended/encdesc.c:471:30:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
      desclength = (GtUword) strlen(descbuffer);
data/genometools-1.6.1+ds/src/extended/feature_node.c:671:13:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  gt_assert(strlen(attr_name)); /* attribute name cannot be empty */
data/genometools-1.6.1+ds/src/extended/feature_node.c:672:13:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  gt_assert(strlen(attr_value)); /* attribute value cannot be empty */
data/genometools-1.6.1+ds/src/extended/feature_node.c:688:13:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  gt_assert(strlen(attr_name)); /* attribute name cannot be empty */
data/genometools-1.6.1+ds/src/extended/feature_node.c:689:13:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  gt_assert(strlen(attr_value)); /* attribute value cannot be empty */
data/genometools-1.6.1+ds/src/extended/feature_node.c:704:13:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  gt_assert(strlen(attr_name)); /* attribute name cannot be empty */
data/genometools-1.6.1+ds/src/extended/gap_str.c:48:38:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  gt_splitter_split(splitter, mystr, strlen(mystr), ' ');
data/genometools-1.6.1+ds/src/extended/gap_str.c:54:14:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    toklen = strlen(token);
data/genometools-1.6.1+ds/src/extended/gff3_escaping.c:146:52:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    gt_gff3_escape(escaped_seq, unescaped_testseq, strlen(unescaped_testseq));
data/genometools-1.6.1+ds/src/extended/gff3_linesorted_out_stream.c:77:10:  [1] (buffer) strncpy:
  Easily used incorrectly; doesn't always \0-terminate or check for invalid
  pointers [MS-banned] (CWE-120).
  (void) strncpy(buf1, *s1, idlength1);
data/genometools-1.6.1+ds/src/extended/gff3_linesorted_out_stream.c:78:10:  [1] (buffer) strncpy:
  Easily used incorrectly; doesn't always \0-terminate or check for invalid
  pointers [MS-banned] (CWE-120).
  (void) strncpy(buf2, *s2, idlength2);
data/genometools-1.6.1+ds/src/extended/gff3_linesorted_out_stream.c:179:9:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    if (strlen(lsos->outstrings[i]) > 0) {
data/genometools-1.6.1+ds/src/extended/gff3_parser.c:287:47:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  gt_splitter_split(splitter, escaped_target, strlen(escaped_target), ' ');
data/genometools-1.6.1+ds/src/extended/gff3_parser.c:299:32:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
                               strlen(gt_splitter_get_token(splitter, 0)), err);
data/genometools-1.6.1+ds/src/extended/gff3_parser.c:372:40:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  gt_splitter_split(splitter, targets, strlen(targets), ',');
data/genometools-1.6.1+ds/src/extended/gff3_parser.c:828:51:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  gt_splitter_split(parent_splitter, parent_attr, strlen(parent_attr), ',');
data/genometools-1.6.1+ds/src/extended/gff3_parser.c:1207:53:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  gt_splitter_split(attribute_splitter, attributes, strlen(attributes), ';');
data/genometools-1.6.1+ds/src/extended/gff3_parser.c:1229:46:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
      gt_splitter_split(tmp_splitter, token, strlen(token), '=');
data/genometools-1.6.1+ds/src/extended/gff3_parser.c:1259:22:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    if (!had_err && !strlen(attr_tag)) {
data/genometools-1.6.1+ds/src/extended/gff3_parser.c:1271:22:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    if (!had_err && !strlen(attr_value)) {
data/genometools-1.6.1+ds/src/extended/gff3_parser.c:1481:9:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  len = strlen(seqid);
data/genometools-1.6.1+ds/src/extended/gff3_parser.c:1666:44:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  if (strncmp(line, GT_GFF_VERSION_PREFIX, strlen(GT_GFF_VERSION_PREFIX))) {
data/genometools-1.6.1+ds/src/extended/gff3_parser.c:1667:46:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    if (strncmp(line, GT_GVF_VERSION_PREFIX, strlen(GT_GVF_VERSION_PREFIX))) {
data/genometools-1.6.1+ds/src/extended/gff3_parser.c:1783:50:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    gt_splitter_split(splitter, parent_attr_dup, strlen(parent_attr_dup), ',');
data/genometools-1.6.1+ds/src/extended/gff3_parser.c:1809:49:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  return (strncmp(line, GT_GVF_REFERENCE_FASTA, strlen(GT_GVF_REFERENCE_FASTA))
data/genometools-1.6.1+ds/src/extended/gff3_parser.c:1810:51:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
            && strncmp(line, GT_GVF_FEATURE_GFF3, strlen(GT_GVF_FEATURE_GFF3))
data/genometools-1.6.1+ds/src/extended/gff3_parser.c:1811:51:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
            && strncmp(line, GT_GVF_FILE_VERSION, strlen(GT_GVF_FILE_VERSION))
data/genometools-1.6.1+ds/src/extended/gff3_parser.c:1812:48:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
            && strncmp(line, GT_GVF_FILE_DATE, strlen(GT_GVF_FILE_DATE))
data/genometools-1.6.1+ds/src/extended/gff3_parser.c:1813:52:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
            && strncmp(line, GT_GVF_INDIVIDUAL_ID, strlen(GT_GVF_INDIVIDUAL_ID))
data/genometools-1.6.1+ds/src/extended/gff3_parser.c:1814:49:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
            && strncmp(line, GT_GVF_POPULATION, strlen(GT_GVF_POPULATION))
data/genometools-1.6.1+ds/src/extended/gff3_parser.c:1815:42:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
            && strncmp(line, GT_GVF_SEX, strlen(GT_GVF_SEX))
data/genometools-1.6.1+ds/src/extended/gff3_parser.c:1817:24:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
                       strlen(GT_GVF_TECHNOLOGY_PLATFORM))
data/genometools-1.6.1+ds/src/extended/gff3_parser.c:1819:24:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
                       strlen(GT_GVF_TECHNOLOGY_PLATFORM_CLASS))
data/genometools-1.6.1+ds/src/extended/gff3_parser.c:1821:24:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
                       strlen(GT_GVF_TECHNOLOGY_PLATFORM_NAME))
data/genometools-1.6.1+ds/src/extended/gff3_parser.c:1823:24:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
                       strlen(GT_GVF_TECHNOLOGY_PLATFORM_VERSION))
data/genometools-1.6.1+ds/src/extended/gff3_parser.c:1825:24:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
                       strlen(GT_GVF_TECHNOLOGY_PLATFORM_MACHINE_ID))
data/genometools-1.6.1+ds/src/extended/gff3_parser.c:1827:24:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
                       strlen(GT_GVF_TECHNOLOGY_PLATFORM_READ_LENGTH))
data/genometools-1.6.1+ds/src/extended/gff3_parser.c:1829:24:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
                       strlen(GT_GVF_TECHNOLOGY_PLATFORM_READ_TYPE))
data/genometools-1.6.1+ds/src/extended/gff3_parser.c:1831:24:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
                       strlen(GT_GVF_TECHNOLOGY_PLATFORM_READ_PAIR_SPAN))
data/genometools-1.6.1+ds/src/extended/gff3_parser.c:1833:24:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
                       strlen(GT_GVF_TECHNOLOGY_PLATFORM_AVERAGE_COVERAGE))
data/genometools-1.6.1+ds/src/extended/gff3_parser.c:1835:24:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
                       strlen(GT_GVF_SEQUENCING_SCOPE))
data/genometools-1.6.1+ds/src/extended/gff3_parser.c:1837:24:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
                       strlen(GT_GVF_CAPTURE_METHOD))
data/genometools-1.6.1+ds/src/extended/gff3_parser.c:1839:24:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
                       strlen(GT_GVF_CAPTURE_REGIONS))
data/genometools-1.6.1+ds/src/extended/gff3_parser.c:1841:24:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
                       strlen(GT_GVF_SEQUENCE_ALIGNMENT))
data/genometools-1.6.1+ds/src/extended/gff3_parser.c:1843:24:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
                       strlen(GT_GVF_VARIANT_CALLING))
data/genometools-1.6.1+ds/src/extended/gff3_parser.c:1845:24:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
                       strlen(GT_GVF_SAMPLE_DESCRIPTION))
data/genometools-1.6.1+ds/src/extended/gff3_parser.c:1847:24:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
                       strlen(GT_GVF_GENOMIC_SOURCE))
data/genometools-1.6.1+ds/src/extended/gff3_parser.c:1849:24:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
                       strlen(GT_GVF_MULTI_INDIVIDUAL))
data/genometools-1.6.1+ds/src/extended/gff3_parser.c:1850:50:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
            && strncmp(line, GT_GVF_DATA_SOURCE, strlen(GT_GVF_DATA_SOURCE))
data/genometools-1.6.1+ds/src/extended/gff3_parser.c:1851:51:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
            && strncmp(line, GT_GVF_SCORE_METHOD, strlen(GT_GVF_SCORE_METHOD))
data/genometools-1.6.1+ds/src/extended/gff3_parser.c:1852:52:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
            && strncmp(line, GT_GVF_SOURCE_METHOD, strlen(GT_GVF_SOURCE_METHOD))
data/genometools-1.6.1+ds/src/extended/gff3_parser.c:1854:24:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
                       strlen(GT_GVF_ATTRIBUTE_METHOD))
data/genometools-1.6.1+ds/src/extended/gff3_parser.c:1856:24:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
                       strlen(GT_GVF_PHENOTYPE_DESCRIPTION))
data/genometools-1.6.1+ds/src/extended/gff3_parser.c:1858:24:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
                       strlen(GT_GVF_PHASED_GENOTYPES)));
data/genometools-1.6.1+ds/src/extended/gff3_parser.c:1863:41:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  return (strncmp(line, GT_GFF_SPECIES, strlen(GT_GFF_SPECIES))
data/genometools-1.6.1+ds/src/extended/gff3_parser.c:1865:24:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
                       strlen(GT_GFF_FEATURE_ONTOLOGY))
data/genometools-1.6.1+ds/src/extended/gff3_parser.c:1867:24:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
                       strlen(GT_GFF_ATTRIBUTE_ONTOLOGY))
data/genometools-1.6.1+ds/src/extended/gff3_parser.c:1869:24:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
                       strlen(GT_GFF_SOURCE_ONTOLOGY))
data/genometools-1.6.1+ds/src/extended/gff3_parser.c:1871:24:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
                       strlen(GT_GFF_GENOME_BUILD)));
data/genometools-1.6.1+ds/src/extended/gff3_parser.c:1901:21:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
                    strlen(GT_GFF_SEQUENCE_REGION)) == 0)) {
data/genometools-1.6.1+ds/src/extended/gff3_parser.c:1903:22:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    tmpline = line + strlen(GT_GFF_SEQUENCE_REGION);
data/genometools-1.6.1+ds/src/extended/gff3_parser.c:2006:20:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
                   strlen(GT_GFF_TERMINATOR)) == 0) { /* terminator */
data/genometools-1.6.1+ds/src/extended/gff3_parser.c:2007:23:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    if (line_length > strlen(GT_GFF_TERMINATOR)) {
data/genometools-1.6.1+ds/src/extended/gff3_parser.c:2023:20:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
                   strlen(GT_GFF_VERSION_PREFIX)) == 0) {
data/genometools-1.6.1+ds/src/extended/gff3_parser.c:2039:20:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
                   strlen(GT_GVF_VERSION_PREFIX)) == 0) {
data/genometools-1.6.1+ds/src/extended/gff3_visitor.c:405:17:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
                strlen(GT_GFF_VERSION_DIRECTIVE)) == 0
data/genometools-1.6.1+ds/src/extended/gff3_visitor.c:407:22:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
                     strlen(GT_GVF_VERSION_DIRECTIVE)) == 0) {
data/genometools-1.6.1+ds/src/extended/gtdatahelp.c:46:37:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  gt_splitter_split(splitter, prog, strlen(prog), ' ');
data/genometools-1.6.1+ds/src/extended/gtf_parser.c:250:54:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
                              (const char*) key)) && strlen(tname) > 0) {
data/genometools-1.6.1+ds/src/extended/gtf_parser.c:342:54:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
                              (const char*) key)) && strlen(gname) > 0) {
data/genometools-1.6.1+ds/src/extended/gtf_parser.c:551:57:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
      gt_splitter_split(attribute_splitter, attributes, strlen(attributes),
data/genometools-1.6.1+ds/src/extended/gtf_parser.c:574:23:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
          if (attrval[strlen(attrval)-1] == '"')
data/genometools-1.6.1+ds/src/extended/gtf_parser.c:575:21:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
            attrval[strlen(attrval)-1] = '\0';
data/genometools-1.6.1+ds/src/extended/gtf_parser.c:576:32:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
          gt_assert(attrkey && strlen(attrkey) > 0);
data/genometools-1.6.1+ds/src/extended/gtf_parser.c:577:32:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
          gt_assert(attrval && strlen(attrval) > 0);
data/genometools-1.6.1+ds/src/extended/gtf_parser.c:584:47:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
        if (strncmp(token, GENE_ID_ATTRIBUTE, strlen(GENE_ID_ATTRIBUTE)) == 0) {
data/genometools-1.6.1+ds/src/extended/gtf_parser.c:585:15:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
          if (strlen(token) + 2 < strlen(GENE_ID_ATTRIBUTE)) {
data/genometools-1.6.1+ds/src/extended/gtf_parser.c:585:35:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
          if (strlen(token) + 2 < strlen(GENE_ID_ATTRIBUTE)) {
data/genometools-1.6.1+ds/src/extended/gtf_parser.c:592:29:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
          gene_id = token + strlen(GENE_ID_ATTRIBUTE) + 1;
data/genometools-1.6.1+ds/src/extended/gtf_parser.c:595:23:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
          if (gene_id[strlen(gene_id)-1] == '"')
data/genometools-1.6.1+ds/src/extended/gtf_parser.c:596:21:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
            gene_id[strlen(gene_id)-1] = '\0';
data/genometools-1.6.1+ds/src/extended/gtf_parser.c:599:26:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
                         strlen(TRANSCRIPT_ID_ATTRIBUTE)) == 0) {
data/genometools-1.6.1+ds/src/extended/gtf_parser.c:600:15:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
          if (strlen(token) + 2 < strlen(TRANSCRIPT_ID_ATTRIBUTE)) {
data/genometools-1.6.1+ds/src/extended/gtf_parser.c:600:35:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
          if (strlen(token) + 2 < strlen(TRANSCRIPT_ID_ATTRIBUTE)) {
data/genometools-1.6.1+ds/src/extended/gtf_parser.c:607:35:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
          transcript_id = token + strlen(TRANSCRIPT_ID_ATTRIBUTE) + 1;
data/genometools-1.6.1+ds/src/extended/gtf_parser.c:610:29:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
          if (transcript_id[strlen(transcript_id)-1] == '"')
data/genometools-1.6.1+ds/src/extended/gtf_parser.c:611:27:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
            transcript_id[strlen(transcript_id)-1] = '\0';
data/genometools-1.6.1+ds/src/extended/gtf_parser.c:614:26:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
                         strlen(GENE_NAME_ATTRIBUTE)) == 0) {
data/genometools-1.6.1+ds/src/extended/gtf_parser.c:615:15:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
          if (strlen(token) + 2 < strlen(GENE_NAME_ATTRIBUTE)) {
data/genometools-1.6.1+ds/src/extended/gtf_parser.c:615:35:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
          if (strlen(token) + 2 < strlen(GENE_NAME_ATTRIBUTE)) {
data/genometools-1.6.1+ds/src/extended/gtf_parser.c:622:31:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
          gene_name = token + strlen(GENE_NAME_ATTRIBUTE) + 1;
data/genometools-1.6.1+ds/src/extended/gtf_parser.c:626:25:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
          if (gene_name[strlen(gene_name)-1] == '"')
data/genometools-1.6.1+ds/src/extended/gtf_parser.c:627:23:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
            gene_name[strlen(gene_name)-1] = '\0';
data/genometools-1.6.1+ds/src/extended/gtf_parser.c:630:26:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
                         strlen(TRANSCRIPT_NAME_ATTRIBUTE)) == 0) {
data/genometools-1.6.1+ds/src/extended/gtf_parser.c:631:15:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
          if (strlen(token) + 2 < strlen(TRANSCRIPT_NAME_ATTRIBUTE)) {
data/genometools-1.6.1+ds/src/extended/gtf_parser.c:631:35:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
          if (strlen(token) + 2 < strlen(TRANSCRIPT_NAME_ATTRIBUTE)) {
data/genometools-1.6.1+ds/src/extended/gtf_parser.c:638:37:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
          transcript_name = token + strlen(TRANSCRIPT_NAME_ATTRIBUTE) + 1;
data/genometools-1.6.1+ds/src/extended/gtf_parser.c:642:31:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
          if (transcript_name[strlen(transcript_name)-1] == '"')
data/genometools-1.6.1+ds/src/extended/gtf_parser.c:643:29:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
            transcript_name[strlen(transcript_name)-1] = '\0';
data/genometools-1.6.1+ds/src/extended/gtf_parser.c:682:30:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
      if (transcript_name && strlen(transcript_name) > 0
data/genometools-1.6.1+ds/src/extended/gtf_parser.c:689:24:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
      if (gene_name && strlen(gene_name) > 0
data/genometools-1.6.1+ds/src/extended/hcr.c:189:20:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  GT_UNUSED size_t read,
data/genometools-1.6.1+ds/src/extended/hcr.c:585:20:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  GT_UNUSED size_t read,
data/genometools-1.6.1+ds/src/extended/hcr.c:762:20:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  GT_UNUSED size_t read;
data/genometools-1.6.1+ds/src/extended/hcr.c:1062:38:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
      for (i = 0, cur_width = 0; i < strlen(seq); i++, cur_width++) {
data/genometools-1.6.1+ds/src/extended/hcr.c:1072:38:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
      for (i = 0, cur_width = 0; i < strlen(qual); i++, cur_width++) {
data/genometools-1.6.1+ds/src/extended/hmm.c:635:42:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  encoded_seq = gt_malloc(sizeof (int) * strlen(coin_tosses[size-1]));
data/genometools-1.6.1+ds/src/extended/hmm.c:638:11:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    len = strlen(coin_tosses[i]);
data/genometools-1.6.1+ds/src/extended/hmm.c:668:42:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  encoded_seq = gt_malloc(sizeof (int) * strlen(dice_rolls[size-1]));
data/genometools-1.6.1+ds/src/extended/hmm.c:671:11:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    len = strlen(dice_rolls[i]);
data/genometools-1.6.1+ds/src/extended/hpol_processor.c:112:19:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  slen = (GtUword)strlen(gt_aligned_segment_seq(as));
data/genometools-1.6.1+ds/src/extended/hpol_processor.c:113:30:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  gt_assert(slen == (GtUword)strlen(gt_aligned_segment_qual(as)));
data/genometools-1.6.1+ds/src/extended/hpol_processor.c:125:24:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    gt_assert((GtUword)strlen(gt_aligned_segment_qual(as)) == slen);
data/genometools-1.6.1+ds/src/extended/hpol_processor.c:252:19:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  rlen = (GtUword)strlen(r);
data/genometools-1.6.1+ds/src/extended/hpol_processor.c:916:30:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    for (i = 0; i < (GtUword)strlen(d); i++)
data/genometools-1.6.1+ds/src/extended/match_iterator_blast.c:84:13:  [1] (buffer) fgetc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        if (fgetc(mib->pvt->matchfilep) == '#') {
data/genometools-1.6.1+ds/src/extended/match_iterator_last.c:188:7:  [1] (buffer) strncpy:
  Easily used incorrectly; doesn't always \0-terminate or check for invalid
  pointers [MS-banned] (CWE-120).
      strncpy(desccpy, desc, desclen);
data/genometools-1.6.1+ds/src/extended/match_iterator_last.c:320:34:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
      gt_assert(matchfilehash && strlen(matchfilehash) > 0);
data/genometools-1.6.1+ds/src/extended/match_iterator_open.c:74:11:  [1] (buffer) fgetc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      if (fgetc(mpi->pvt->matchfilep) == '#') {
data/genometools-1.6.1+ds/src/extended/mutate.c:36:29:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  mutated_description_len = strlen(description) + strlen(MUTATED_DESC_PRIMER)
data/genometools-1.6.1+ds/src/extended/mutate.c:36:51:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  mutated_description_len = strlen(description) + strlen(MUTATED_DESC_PRIMER)
data/genometools-1.6.1+ds/src/extended/mutate.c:116:37:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  seq = gt_seq_new_own(mutated_seq, strlen(mutated_seq), alphabet);
data/genometools-1.6.1+ds/src/extended/rcr.c:1413:20:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  GT_UNUSED size_t read,
data/genometools-1.6.1+ds/src/extended/rcr.c:1580:22:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  while (!had_err && read < length) {
data/genometools-1.6.1+ds/src/extended/rdb_mysql.c:127:48:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  if ((retval = mysql_stmt_prepare(tmp, query, strlen(query)))) {
data/genometools-1.6.1+ds/src/extended/rdb_mysql.c:346:19:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  str = gt_calloc(strlen(val)+1, sizeof (char));
data/genometools-1.6.1+ds/src/extended/rdb_mysql.c:347:3:  [1] (buffer) strncpy:
  Easily used incorrectly; doesn't always \0-terminate or check for invalid
  pointers [MS-banned] (CWE-120).
  strncpy(str, val, strlen(val));
data/genometools-1.6.1+ds/src/extended/rdb_mysql.c:347:21:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  strncpy(str, val, strlen(val));
data/genometools-1.6.1+ds/src/extended/rdb_mysql.c:351:13:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  *length = strlen(str);
data/genometools-1.6.1+ds/src/extended/rdb_mysql.c:357:41:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  stm->params[param_no].buffer_length = strlen(str);
data/genometools-1.6.1+ds/src/extended/rdb_sqlite.c:203:58:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  rval = sqlite3_bind_text(sts->stmt, param_no + 1, val, strlen(val),
data/genometools-1.6.1+ds/src/extended/region_mapping.c:230:5:  [1] (buffer) strncpy:
  Easily used incorrectly; doesn't always \0-terminate or check for invalid
  pointers [MS-banned] (CWE-120).
    strncpy(*seq, rm->rawseq + start - 1, (end - start + 1) * sizeof (char));
data/genometools-1.6.1+ds/src/extended/region_mapping.c:323:7:  [1] (buffer) strncpy:
  Easily used incorrectly; doesn't always \0-terminate or check for invalid
  pointers [MS-banned] (CWE-120).
      strncpy(*seq, rm->rawseq + start - 1, (end - start + 1) * sizeof (char));
data/genometools-1.6.1+ds/src/extended/sam_query_name_iterator.c:41:10:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  while (read > 0 && gt_sam_alignment_is_unmapped(sqi->alignment)) {
data/genometools-1.6.1+ds/src/extended/sam_query_name_iterator.c:44:7:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  if (read > 0) {
data/genometools-1.6.1+ds/src/extended/sam_query_name_iterator.c:46:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    return read;
data/genometools-1.6.1+ds/src/extended/samfile_iterator.c:104:7:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  int read;
data/genometools-1.6.1+ds/src/extended/samfile_iterator.c:109:7:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  if (read > 0) {
data/genometools-1.6.1+ds/src/extended/samfile_iterator.c:115:10:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  return read;
data/genometools-1.6.1+ds/src/extended/seqid2seqnum_mapping.c:142:5:  [1] (buffer) strncpy:
  Easily used incorrectly; doesn't always \0-terminate or check for invalid
  pointers [MS-banned] (CWE-120).
    strncpy(dup, desc, j);
data/genometools-1.6.1+ds/src/extended/snp_annotator_visitor.c:104:15:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    mrnalen = strlen(mrnaseq);
data/genometools-1.6.1+ds/src/extended/snp_annotator_visitor.c:216:28:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
              mrnasnppos = strlen(mRNA) - mrnasnppos - 1;
data/genometools-1.6.1+ds/src/extended/snp_annotator_visitor.c:217:36:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
            gt_assert(mrnasnppos < strlen(mRNA));
data/genometools-1.6.1+ds/src/extended/snp_annotator_visitor.c:313:16:  [1] (buffer) strncpy:
  Easily used incorrectly; doesn't always \0-terminate or check for invalid
  pointers [MS-banned] (CWE-120).
        (void) strncpy(mrna_charseq, gt_str_get(mrnaseq),
data/genometools-1.6.1+ds/src/extended/snp_annotator_visitor.c:346:12:  [1] (buffer) strncpy:
  Easily used incorrectly; doesn't always \0-terminate or check for invalid
  pointers [MS-banned] (CWE-120).
    (void) strncpy(mrna_charseq, gt_str_get(mrnaseq), gt_str_length(mrnaseq));
data/genometools-1.6.1+ds/src/extended/splice_site_info_visitor.c:162:23:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  gt_assert(string && strlen(string) == 4);
data/genometools-1.6.1+ds/src/extended/splice_site_info_visitor.c:174:23:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  gt_assert(string && strlen(string) == 2);
data/genometools-1.6.1+ds/src/extended/stream_evaluator.c:590:8:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
  bool equal;
data/genometools-1.6.1+ds/src/extended/stream_evaluator.c:621:10:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
  return equal;
data/genometools-1.6.1+ds/src/extended/stream_evaluator.c:652:8:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
  bool equal;
data/genometools-1.6.1+ds/src/extended/stream_evaluator.c:686:7:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
  if (equal && gt_array_size(mRNAs_1) == gt_array_size(mRNAs_2)) {
data/genometools-1.6.1+ds/src/extended/stream_evaluator.c:691:17:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
      gt_assert(equal);
data/genometools-1.6.1+ds/src/extended/stream_evaluator.c:695:12:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
      if (!equal)
data/genometools-1.6.1+ds/src/extended/stream_evaluator.c:706:10:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
  return equal;
data/genometools-1.6.1+ds/src/extended/string_matching.c:213:40:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  gt_string_matching_brute_force(text, strlen(text), "", 0, store_match,
data/genometools-1.6.1+ds/src/extended/string_matching.c:215:32:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  gt_string_matching_bmh(text, strlen(text), "", 0, store_match, bmh_matches);
data/genometools-1.6.1+ds/src/extended/string_matching.c:216:32:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  gt_string_matching_kmp(text, strlen(text), "", 0, store_match, kmp_matches);
data/genometools-1.6.1+ds/src/extended/string_matching.c:217:38:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  gt_string_matching_shift_and(text, strlen(text), "", 0, store_match,
data/genometools-1.6.1+ds/src/extended/tag_value_map.c:37:13:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  tag_len = strlen(tag);
data/genometools-1.6.1+ds/src/extended/tag_value_map.c:38:15:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  value_len = strlen(value);
data/genometools-1.6.1+ds/src/extended/tag_value_map.c:124:13:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  tag_len = strlen(tag);
data/genometools-1.6.1+ds/src/extended/tag_value_map.c:125:15:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  value_len = strlen(value);
data/genometools-1.6.1+ds/src/extended/tag_value_map.c:143:13:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  tag_len = strlen(tag);
data/genometools-1.6.1+ds/src/extended/tag_value_map.c:149:15:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  value_len = strlen(value);
data/genometools-1.6.1+ds/src/extended/tag_value_map.c:163:13:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  gt_assert(strlen(tag));
data/genometools-1.6.1+ds/src/extended/tag_value_map.c:164:19:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  new_value_len = strlen(new_value);
data/genometools-1.6.1+ds/src/extended/tag_value_map.c:171:19:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  old_value_len = strlen(old_value);
data/genometools-1.6.1+ds/src/extended/tag_value_map.c:196:27:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  gt_assert(map && tag && strlen(tag));
data/genometools-1.6.1+ds/src/extended/tag_value_map.c:351:45:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    gt_ensure(!(old_map_len - new_map_len - strlen("tag 1") - 1
data/genometools-1.6.1+ds/src/extended/tag_value_map.c:352:24:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
                     - strlen("value XXX") -1));
data/genometools-1.6.1+ds/src/extended/tag_value_map.c:369:45:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    gt_ensure(!(old_map_len - new_map_len - strlen("tag 2") - 1
data/genometools-1.6.1+ds/src/extended/tag_value_map.c:370:24:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
                     - strlen("value YYY") -1));
data/genometools-1.6.1+ds/src/extended/tag_value_map.c:387:45:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    gt_ensure(!(old_map_len - new_map_len - strlen("tag 3") - 1
data/genometools-1.6.1+ds/src/extended/tag_value_map.c:388:24:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
                     - strlen("value ZZZ") -1));
data/genometools-1.6.1+ds/src/extended/tir_stream.c:805:15:  [1] (buffer) strncpy:
  Easily used incorrectly; doesn't always \0-terminate or check for invalid
  pointers [MS-banned] (CWE-120).
       (void) strncpy(description_string, description,
data/genometools-1.6.1+ds/src/extended/type_graph.c:105:34:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
      if (!strncmp(rel, PART_OF, strlen(PART_OF))) {
data/genometools-1.6.1+ds/src/extended/type_graph.c:106:37:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
        const char *part_of = rel + strlen(PART_OF) + 1;
data/genometools-1.6.1+ds/src/extended/type_graph.c:112:36:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
      if (!strncmp(rel, MEMBER_OF, strlen(MEMBER_OF))) {
data/genometools-1.6.1+ds/src/extended/type_graph.c:113:39:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
        const char *member_of = rel + strlen(MEMBER_OF) + 1;
data/genometools-1.6.1+ds/src/extended/type_graph.c:119:43:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
      if (!strncmp(rel, INTEGRAL_PART_OF, strlen(INTEGRAL_PART_OF))) {
data/genometools-1.6.1+ds/src/extended/type_graph.c:120:46:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
        const char *integral_part_of = rel + strlen(INTEGRAL_PART_OF) + 1;
data/genometools-1.6.1+ds/src/extended/uniq_stream.c:60:12:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
    return equal;
data/genometools-1.6.1+ds/src/extended/xrf_abbr_parse_tree.c:119:11:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
      if (strlen(value) >= 10) {
data/genometools-1.6.1+ds/src/extended/xrf_checker.c:55:45:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  gt_splitter_split(xrc->splitter, myvalue, strlen(myvalue), ',');
data/genometools-1.6.1+ds/src/gtlua/alphabet_lua.c:69:20:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  luaL_argcheck(L, strlen(characters), 2,
data/genometools-1.6.1+ds/src/gtlua/alphabet_lua.c:81:20:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  luaL_argcheck(L, strlen(wildcard) == 1, 2,
data/genometools-1.6.1+ds/src/gtlua/encseq_lua.c:790:45:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  gt_encseq_builder_add_cstr(*builder, str, strlen(str), desc);
data/genometools-1.6.1+ds/src/gtlua/genome_node_lua.c:326:20:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  luaL_argcheck(L, strlen(str) == 1 && strchr(GT_STRAND_CHARS, str[0]),
data/genometools-1.6.1+ds/src/gtlua/genome_node_lua.c:354:20:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  luaL_argcheck(L, strlen(p) == 1 && strchr(GT_PHASE_CHARS, p[0]),
data/genometools-1.6.1+ds/src/gtlua/genome_node_lua.c:433:20:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  luaL_argcheck(L, strlen(key) > 0, 2,
data/genometools-1.6.1+ds/src/gtlua/genome_node_lua.c:436:20:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  luaL_argcheck(L, strlen(key) > 0, 3,
data/genometools-1.6.1+ds/src/gtlua/genome_node_lua.c:557:20:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  luaL_argcheck(L, strlen(type) > 0, 2, "must not be empty");
data/genometools-1.6.1+ds/src/gtlua/translate_lua.c:36:20:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  luaL_argcheck(L, strlen(dna) >= 3, 1,
data/genometools-1.6.1+ds/src/gtlua/translate_lua.c:42:54:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
                                                     strlen(dna),
data/genometools-1.6.1+ds/src/interactive.c:120:7:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  l = strlen(b);
data/genometools-1.6.1+ds/src/ltr/ltr_cluster_stream.c:373:16:  [1] (buffer) strncpy:
  Easily used incorrectly; doesn't always \0-terminate or check for invalid
  pointers [MS-banned] (CWE-120).
        (void) strncpy(encseqid, encseqdesc, (size_t) desclen);
data/genometools-1.6.1+ds/src/ltr/ltr_cluster_stream.c:448:7:  [1] (buffer) strncpy:
  Easily used incorrectly; doesn't always \0-terminate or check for invalid
  pointers [MS-banned] (CWE-120).
      strncpy(output, description, (size_t) desclen);
data/genometools-1.6.1+ds/src/ltr/ltr_refseq_match_stream.c:293:12:  [1] (buffer) fgetc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    while (fgetc(makeblastdb_output) != EOF);
data/genometools-1.6.1+ds/src/ltr/ltrdigest_file_out_stream.c:326:45:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
      gt_file_xwrite(alifile, buf, (size_t) strlen(buf) * sizeof (char));
data/genometools-1.6.1+ds/src/ltr/ltrdigest_file_out_stream.c:720:23:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  gt_assert(buffer && strlen(buffer) > 0);
data/genometools-1.6.1+ds/src/ltr/ltrdigest_pbs_visitor.c:185:50:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
                                             int mismatch, int insertion,
data/genometools-1.6.1+ds/src/ltr/ltrdigest_pbs_visitor.c:196:59:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
      gt_score_matrix_set_score(sm, m, n, (n==m ? match : mismatch));
data/genometools-1.6.1+ds/src/ltr/ltrdigest_pbs_visitor.c:202:29:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
                            mismatch);
data/genometools-1.6.1+ds/src/ltr/ltrdigest_pbs_visitor.c:473:7:  [1] (buffer) strncpy:
  Easily used incorrectly; doesn't always \0-terminate or check for invalid
  pointers [MS-banned] (CWE-120).
      strncpy(rev_seq, gt_str_get(seq), (size_t) seqlen * sizeof (char));
data/genometools-1.6.1+ds/src/ltr/ltrdigest_pdom_visitor.c:377:25:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
              gt_assert(strlen(b) > 0);
data/genometools-1.6.1+ds/src/ltr/ltrdigest_pdom_visitor.c:861:9:  [1] (buffer) strncpy:
  Easily used incorrectly; doesn't always \0-terminate or check for invalid
  pointers [MS-banned] (CWE-120).
        strncpy(rev_seq, gt_str_get(seq), (size_t) seqlen * sizeof (char));
data/genometools-1.6.1+ds/src/ltr/ltrdigest_ppt_visitor.c:575:7:  [1] (buffer) strncpy:
  Easily used incorrectly; doesn't always \0-terminate or check for invalid
  pointers [MS-banned] (CWE-120).
      strncpy(rev_seq, gt_str_get(seq), (size_t) seqlen * sizeof (char));
data/genometools-1.6.1+ds/src/ltr/ltrharvest_stream.c:1436:16:  [1] (buffer) strncpy:
  Easily used incorrectly; doesn't always \0-terminate or check for invalid
  pointers [MS-banned] (CWE-120).
        (void) strncpy(buf, desc, (size_t) (desclen * sizeof (char)));
data/genometools-1.6.1+ds/src/ltr/pdom_model_set.c:113:15:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
        len = strlen(line);
data/genometools-1.6.1+ds/src/ltr/pdom_model_set.c:171:24:  [1] (buffer) fgetc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
          while ((ch = fgetc(source)) != EOF) {
data/genometools-1.6.1+ds/src/match/chainofin.c:44:16:  [1] (buffer) getc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  while ((cc = getc(fp)) != EOF)
data/genometools-1.6.1+ds/src/match/diagbandseed.c:5058:18:  [1] (buffer) fgetc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    while ((cc = fgetc(stream_tab[tidx])) != EOF) {
data/genometools-1.6.1+ds/src/match/eis-encidxseq.c:139:26:  [1] (buffer) getc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
           && (symRead = getc(bwtFP)) != EOF)
data/genometools-1.6.1+ds/src/match/eis-mrangealphabet.c:284:17:  [1] (buffer) getc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        int c = getc(fp);
data/genometools-1.6.1+ds/src/match/esa-map.c:63:22:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  size_t dbfilelen = strlen(DBFILEKEY);
data/genometools-1.6.1+ds/src/match/fmi-sufbwtstream.c:69:20:  [1] (buffer) fgetc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      while ((cc = fgetc(fpsource)) != EOF)
data/genometools-1.6.1+ds/src/match/fmi-sufbwtstream.c:79:19:  [1] (buffer) fgetc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        if ((cc = fgetc(fpsource)) == EOF)
data/genometools-1.6.1+ds/src/match/gfa_writer.c:84:16:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
      (GtUword)strlen(sequence), sequence);
data/genometools-1.6.1+ds/src/match/giextract.c:123:17:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
          len = strlen(readptr->fastakey);
data/genometools-1.6.1+ds/src/match/giextract.c:193:5:  [1] (buffer) strncpy:
  Easily used incorrectly; doesn't always \0-terminate or check for invalid
  pointers [MS-banned] (CWE-120).
    strncpy(fastakeyptr->fastakey,lineptr,idx);
data/genometools-1.6.1+ds/src/match/giextract.c:584:7:  [1] (buffer) strncpy:
  Easily used incorrectly; doesn't always \0-terminate or check for invalid
  pointers [MS-banned] (CWE-120).
      strncpy(keytabptr->key,keyptr,(size_t) constantkeylen);
data/genometools-1.6.1+ds/src/match/giextract.c:589:5:  [1] (buffer) strncpy:
  Easily used incorrectly; doesn't always \0-terminate or check for invalid
  pointers [MS-banned] (CWE-120).
    strncpy(previouskey,keyptr,(size_t) constantkeylen);
data/genometools-1.6.1+ds/src/match/giextract.c:895:7:  [1] (buffer) strncpy:
  Easily used incorrectly; doesn't always \0-terminate or check for invalid
  pointers [MS-banned] (CWE-120).
      strncpy(keyspace,keyptr,(size_t) keylen);
data/genometools-1.6.1+ds/src/match/giextract.c:912:26:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
          headerlength = strlen(desc);
data/genometools-1.6.1+ds/src/match/hlk-version.c:26:19:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  size_t pnsize = strlen(progname), hlksize = strlen(" "GT_HARLEKIN_CMD);
data/genometools-1.6.1+ds/src/match/hlk-version.c:26:47:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  size_t pnsize = strlen(progname), hlksize = strlen(" "GT_HARLEKIN_CMD);
data/genometools-1.6.1+ds/src/match/optionargmode.c:83:11:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    len = strlen(modedesc[modecount].name);
data/genometools-1.6.1+ds/src/match/optionargmode.c:93:14:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  spacelen = strlen(space);
data/genometools-1.6.1+ds/src/match/optionargmode.c:98:11:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    len = strlen(modedesc[modecount].name);
data/genometools-1.6.1+ds/src/match/prsqualint.c:57:43:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  lparamcopy = gt_malloc(sizeof (char) * (strlen(lparam)+1));
data/genometools-1.6.1+ds/src/match/querymatch-display.c:608:29:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  const size_t header_len = strlen(header);
data/genometools-1.6.1+ds/src/match/rdj-ensure-output.h:44:59:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
        outsize = (size_t)gt_file_xread((GTFILE), buffer, strlen(EXPOUT)); \
data/genometools-1.6.1+ds/src/match/rdj-ensure-output.h:45:30:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
        gt_ensure(outsize == strlen(EXPOUT));                     \
data/genometools-1.6.1+ds/src/match/rdj-ensure-output.h:53:26:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
               (GtUword) strlen(EXPOUT), buffer);                    \
data/genometools-1.6.1+ds/src/match/rdj-spmlist.c:138:7:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  if (strlen(source) != (size_t)1)
data/genometools-1.6.1+ds/src/match/rdj-version.c:26:19:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  size_t pnsize = strlen(progname), rdjsize = strlen(" "GT_READJOINER_CMD);
data/genometools-1.6.1+ds/src/match/rdj-version.c:26:47:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  size_t pnsize = strlen(progname), rdjsize = strlen(" "GT_READJOINER_CMD);
data/genometools-1.6.1+ds/src/match/reads2twobit.c:211:10:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
        (strlen(insertspec) + 1UL));
data/genometools-1.6.1+ds/src/match/reads2twobit.c:213:53:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    gt_splitter_split(s2, insertspec_copy, (GtUword)strlen(insertspec),
data/genometools-1.6.1+ds/src/match/reads2twobit.c:524:10:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  while (strlen(LINE) == GT_READS2TWOBIT_READBUFFER_SIZE - (size_t) 1 \
data/genometools-1.6.1+ds/src/match/reads2twobit.c:2027:22:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
      len = (GtUword)strlen(desc);
data/genometools-1.6.1+ds/src/match/sfx-bentsedg.c:674:35:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
  for (equalpart = 0; equalpart < equal; equalpart++)
data/genometools-1.6.1+ds/src/match/sfx-bentsedg.c:699:19:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
                  equal,smaller,larger);
data/genometools-1.6.1+ds/src/match/test-pairwise.c:71:19:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  len = (GtUword) strlen(text);
data/genometools-1.6.1+ds/src/match/test-pairwise.c:108:35:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
                asize = (GtUword) strlen(alpha);
data/genometools-1.6.1+ds/src/match/tyr-mkindex.c:549:7:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  if (strlen(storeindex) == 0)
data/genometools-1.6.1+ds/src/match/tyr-mkindex.c:577:9:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    if (strlen(storeindex) == 0)
data/genometools-1.6.1+ds/src/match/tyr-mkindex.c:617:11:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
      if (strlen(storeindex) == 0)
data/genometools-1.6.1+ds/src/mgth/mg_combinedscore.c:132:15:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    hit_len = strlen(gt_str_array_get(MATRIXSTRUCT(hit_dna), i));
data/genometools-1.6.1+ds/src/mgth/mg_outputwriter.c:1168:16:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  contig_len = strlen(contig_seq);
data/genometools-1.6.1+ds/src/tools/gt_encseq_decode.c:234:21:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
          desclen = strlen(buf);
data/genometools-1.6.1+ds/src/tools/gt_encseq_decode.c:251:21:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
          desclen = strlen(buf);
data/genometools-1.6.1+ds/src/tools/gt_encseq_sample.c:204:19:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
        desclen = strlen(buf);
data/genometools-1.6.1+ds/src/tools/gt_extracttarget.c:111:47:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  gt_splitter_split(splitter, escaped_target, strlen(escaped_target), ',');
data/genometools-1.6.1+ds/src/tools/gt_extracttarget.c:116:46:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    gt_splitter_split(blank_splitter, token, strlen(token), ' ');
data/genometools-1.6.1+ds/src/tools/gt_extracttarget.c:119:32:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
                               strlen(gt_splitter_get_token(blank_splitter, 0)),
data/genometools-1.6.1+ds/src/tools/gt_extracttarget.c:135:40:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
          gt_string_matching_bmh(desc, strlen(desc),
data/genometools-1.6.1+ds/src/tools/gt_paircmp.c:258:31:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
                    (GtUword) strlen(gt_str_array_get(opt->strings,0)),
data/genometools-1.6.1+ds/src/tools/gt_paircmp.c:260:31:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
                    (GtUword) strlen(gt_str_array_get(opt->strings,1UL)));
data/genometools-1.6.1+ds/src/tools/gt_paircmp.c:280:31:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
                    (GtUword) strlen(gt_str_array_get(opt->fastasequences0,i)),
data/genometools-1.6.1+ds/src/tools/gt_paircmp.c:282:31:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
                    (GtUword) strlen(gt_str_array_get(opt->fastasequences1,j)));
data/genometools-1.6.1+ds/src/tools/gt_seqorder.c:219:10:  [1] (buffer) strncpy:
  Easily used incorrectly; doesn't always \0-terminate or check for invalid
  pointers [MS-banned] (CWE-120).
  (void) strncpy(buf, desc1, GT_MIN(BUFSIZ, desclen1) * sizeof (char));
data/genometools-1.6.1+ds/src/tools/gt_seqorder.c:222:10:  [1] (buffer) strncpy:
  Easily used incorrectly; doesn't always \0-terminate or check for invalid
  pointers [MS-banned] (CWE-120).
  (void) strncpy(buf, desc2, GT_MIN(BUFSIZ, desclen2) * sizeof (char));
data/genometools-1.6.1+ds/src/tools/gt_simreads.c:387:18:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    gt_str_reset(read);
data/genometools-1.6.1+ds/src/tools/gt_simreads.c:421:28:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        gt_str_append_char(read, gt_alphabet_decode(
data/genometools-1.6.1+ds/src/tools/gt_simreads.c:436:38:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                          gt_str_get(read),
data/genometools-1.6.1+ds/src/tools/gt_simreads.c:437:41:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                          gt_str_length(read),
data/genometools-1.6.1+ds/src/tools/gt_simreads.c:440:37:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      output_bases += gt_str_length(read);
data/genometools-1.6.1+ds/src/tools/gt_simreads.c:497:17:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  gt_str_delete(read);
data/genometools-1.6.1+ds/src/tools/gt_skproto.c:54:12:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    slen = strlen(forbid[i]);

ANALYSIS SUMMARY:

Hits = 1054
Lines analyzed = 347773 in approximately 8.28 seconds (41997 lines/second)
Physical Source Lines of Code (SLOC) = 271277
Hits@level = [0] 1427 [1] 428 [2] 259 [3] 208 [4] 159 [5]   0
Hits@level+ = [0+] 2481 [1+] 1054 [2+] 626 [3+] 367 [4+] 159 [5+]   0
Hits/KSLOC@level+ = [0+] 9.14563 [1+] 3.88533 [2+] 2.3076 [3+] 1.35286 [4+] 0.586117 [5+]   0
Dot directories skipped = 2 (--followdotdir overrides)
Minimum risk level = 1
Not every hit is necessarily a security vulnerability.
There may be other security vulnerabilities; review your code!
See 'Secure Programming HOWTO'
(https://dwheeler.com/secure-programs) for more information.