data/hisat2-2.2.1/.gitattributes: ASCII text data/hisat2-2.2.1/.gitignore: ASCII text data/hisat2-2.2.1/AUTHORS: ASCII text data/hisat2-2.2.1/CMakeLists.txt: ASCII text data/hisat2-2.2.1/HISAT2-genotype.png: PNG image data, 2989 x 1609, 8-bit/color RGBA, non-interlaced data/hisat2-2.2.1/LICENSE: ASCII text data/hisat2-2.2.1/MANUAL: ASCII text, with very long lines data/hisat2-2.2.1/MANUAL.markdown: exported SGML document, ASCII text, with very long lines data/hisat2-2.2.1/NEWS: ASCII text data/hisat2-2.2.1/README.md: UTF-8 Unicode text, with very long lines data/hisat2-2.2.1/TUTORIAL: ASCII text data/hisat2-2.2.1/VERSION: ASCII text data/hisat2-2.2.1/_config.yml: ASCII text, with no line terminators data/hisat2-2.2.1/aligner_bt.cpp: C++ source, ASCII text data/hisat2-2.2.1/aligner_bt.h: C++ source, ASCII text data/hisat2-2.2.1/aligner_cache.cpp: C++ source, ASCII text data/hisat2-2.2.1/aligner_cache.h: C++ source, ASCII text data/hisat2-2.2.1/aligner_driver.cpp: C source, ASCII text data/hisat2-2.2.1/aligner_driver.h: C++ source, ASCII text data/hisat2-2.2.1/aligner_metrics.h: C++ source, ASCII text data/hisat2-2.2.1/aligner_report.h: C++ source, ASCII text data/hisat2-2.2.1/aligner_result.cpp: C++ source, ASCII text data/hisat2-2.2.1/aligner_result.h: C++ source, ASCII text data/hisat2-2.2.1/aligner_seed.cpp: C++ source, ASCII text data/hisat2-2.2.1/aligner_seed.h: C source, ASCII text data/hisat2-2.2.1/aligner_seed2.cpp: C++ source, ASCII text data/hisat2-2.2.1/aligner_seed2.h: C source, ASCII text data/hisat2-2.2.1/aligner_seed_policy.cpp: C++ source, ASCII text data/hisat2-2.2.1/aligner_seed_policy.h: C++ source, ASCII text data/hisat2-2.2.1/aligner_sw.cpp: C source, ASCII text data/hisat2-2.2.1/aligner_sw_common.h: C source, ASCII text data/hisat2-2.2.1/aligner_sw_driver.cpp: ASCII text data/hisat2-2.2.1/aligner_sw_driver.h: C++ source, ASCII text data/hisat2-2.2.1/aligner_sw_nuc.h: C++ source, ASCII text data/hisat2-2.2.1/aligner_swsse.cpp: C source, ASCII text data/hisat2-2.2.1/aligner_swsse.h: C source, ASCII text data/hisat2-2.2.1/aligner_swsse_ee_i16.cpp: C source, ASCII text data/hisat2-2.2.1/aligner_swsse_ee_u8.cpp: C source, ASCII text data/hisat2-2.2.1/aligner_swsse_loc_i16.cpp: C source, ASCII text data/hisat2-2.2.1/aligner_swsse_loc_u8.cpp: C source, ASCII text data/hisat2-2.2.1/aln_sink.cpp: C++ source, ASCII text data/hisat2-2.2.1/aln_sink.h: C++ source, ASCII text data/hisat2-2.2.1/alphabet.cpp: C++ source, ASCII text data/hisat2-2.2.1/alphabet.h: C++ source, ASCII text data/hisat2-2.2.1/alt.h: C++ source, ASCII text data/hisat2-2.2.1/assert_helpers.h: C++ source, ASCII text data/hisat2-2.2.1/banded.cpp: C source, ASCII text data/hisat2-2.2.1/banded.h: C++ source, ASCII text data/hisat2-2.2.1/binary_sa_search.h: C source, ASCII text data/hisat2-2.2.1/bit_packed_array.cpp: C source, ASCII text data/hisat2-2.2.1/bit_packed_array.h: C++ source, ASCII text data/hisat2-2.2.1/bitpack.h: C source, ASCII text data/hisat2-2.2.1/blockwise_sa.h: C++ source, ASCII text data/hisat2-2.2.1/bp_aligner.h: C++ source, ASCII text data/hisat2-2.2.1/btypes.h: C source, ASCII text data/hisat2-2.2.1/ccnt_lut.cpp: C source, ASCII text data/hisat2-2.2.1/diff_sample.cpp: C source, ASCII text data/hisat2-2.2.1/diff_sample.h: C++ source, ASCII text data/hisat2-2.2.1/docs/404.html: ASCII text data/hisat2-2.2.1/docs/Gemfile: ASCII text data/hisat2-2.2.1/docs/LICENSE: ASCII text data/hisat2-2.2.1/docs/README.md: exported SGML document, ASCII text data/hisat2-2.2.1/docs/_config.yml: exported SGML document, ASCII text data/hisat2-2.2.1/docs/_data/collaborate.yml: ASCII text data/hisat2-2.2.1/docs/_data/contributor.yml: ASCII text data/hisat2-2.2.1/docs/_data/download-binary.yml: ASCII text data/hisat2-2.2.1/docs/_data/download-index.yml: ASCII text data/hisat2-2.2.1/docs/_includes/article-footer.html: ASCII text data/hisat2-2.2.1/docs/_includes/article-header.html: HTML document, ASCII text data/hisat2-2.2.1/docs/_includes/disqus.html: HTML document, ASCII text data/hisat2-2.2.1/docs/_includes/fb-root.html: HTML document, ASCII text data/hisat2-2.2.1/docs/_includes/google-analytics.html: HTML document, ASCII text data/hisat2-2.2.1/docs/_includes/icons.html: HTML document, ASCII text data/hisat2-2.2.1/docs/_includes/page-url-resolver.html: ASCII text data/hisat2-2.2.1/docs/_includes/paginator.html: ASCII text data/hisat2-2.2.1/docs/_includes/share-buttons.html: HTML document, UTF-8 Unicode text, with very long lines data/hisat2-2.2.1/docs/_layouts/default.html: HTML document, UTF-8 Unicode text, with very long lines data/hisat2-2.2.1/docs/_layouts/page.html: ASCII text data/hisat2-2.2.1/docs/_layouts/post.html: ASCII text data/hisat2-2.2.1/docs/_pages/about.md: ASCII text, with very long lines data/hisat2-2.2.1/docs/_pages/archives-all.html: ASCII text data/hisat2-2.2.1/docs/_pages/archives.html: HTML document, ASCII text data/hisat2-2.2.1/docs/_pages/contributors/chanheepark.md: ASCII text data/hisat2-2.2.1/docs/_pages/contributors/yunleozhang.md: ASCII text data/hisat2-2.2.1/docs/_pages/download.md: HTML document, UTF-8 Unicode text data/hisat2-2.2.1/docs/_pages/hisat2.md: UTF-8 Unicode text, with very long lines data/hisat2-2.2.1/docs/_pages/howto.md: ASCII text data/hisat2-2.2.1/docs/_pages/links.md: ASCII text data/hisat2-2.2.1/docs/_pages/manual.md: ASCII text, with very long lines data/hisat2-2.2.1/docs/_pages/search.html: HTML document, ASCII text data/hisat2-2.2.1/docs/_pages/tags.html: HTML document, ASCII text data/hisat2-2.2.1/docs/_posts/2000-01-01-kim.md: ASCII text data/hisat2-2.2.1/docs/_posts/2000-01-02-salzberg.md: UTF-8 Unicode text data/hisat2-2.2.1/docs/_posts/2000-01-03-langmead.md: ASCII text data/hisat2-2.2.1/docs/_posts/2019-07-28-park.md: ASCII text data/hisat2-2.2.1/docs/_sass/_aside.scss: ASCII text data/hisat2-2.2.1/docs/_sass/_common.scss: ASCII text data/hisat2-2.2.1/docs/_sass/_content.scss: ASCII text data/hisat2-2.2.1/docs/_sass/_footer.scss: ASCII text data/hisat2-2.2.1/docs/_sass/_header.scss: ASCII text data/hisat2-2.2.1/docs/_sass/base/_layout.scss: ASCII text data/hisat2-2.2.1/docs/_sass/base/_reset.scss: ASCII text data/hisat2-2.2.1/docs/_sass/base/_syntax.scss: ASCII text data/hisat2-2.2.1/docs/_sass/base/_utilities.scss: ASCII text data/hisat2-2.2.1/docs/_sass/base/_variables.scss: ASCII text data/hisat2-2.2.1/docs/assets/css/style.scss: ASCII text data/hisat2-2.2.1/docs/assets/data/HISAT2-first_release-Sept_8_2015.pdf: PDF document, version 1.3 data/hisat2-2.2.1/docs/assets/img/bioinformatics_utsw_logo.png: PNG image data, 544 x 194, 8-bit/color RGBA, non-interlaced data/hisat2-2.2.1/docs/assets/img/ccb_jhu_logo_tmp.png: PNG image data, 222 x 74, 8-bit/color RGB, non-interlaced data/hisat2-2.2.1/docs/assets/img/ogp.png: PNG image data, 512 x 512, 8-bit/color RGBA, non-interlaced data/hisat2-2.2.1/docs/assets/js/header-link.js: ASCII text data/hisat2-2.2.1/docs/assets/js/script.js: ASCII text data/hisat2-2.2.1/docs/assets/js/search.js: UTF-8 Unicode text data/hisat2-2.2.1/docs/assets/lib/garand-sticky/jquery.sticky.js: ASCII text data/hisat2-2.2.1/docs/favicon.ico: MS Windows icon resource - 2 icons, 16x16, 32 bits/pixel, 32x32, 32 bits/pixel data/hisat2-2.2.1/docs/index.html: ASCII text data/hisat2-2.2.1/docs/search.json: ASCII text data/hisat2-2.2.1/docs_jhu/README: ASCII text data/hisat2-2.2.1/docs_jhu/add.css: ASCII text data/hisat2-2.2.1/docs_jhu/faq.shtml: HTML document, ASCII text data/hisat2-2.2.1/docs_jhu/footer.inc.html: HTML document, ASCII text data/hisat2-2.2.1/docs_jhu/index.html: HTML document, ASCII text data/hisat2-2.2.1/docs_jhu/index.shtml: HTML document, UTF-8 Unicode text, with very long lines data/hisat2-2.2.1/docs_jhu/indexes.txt: ASCII text, with very long lines data/hisat2-2.2.1/docs_jhu/manual.inc.html: HTML document, ASCII text, with very long lines data/hisat2-2.2.1/docs_jhu/manual.shtml: HTML document, ASCII text data/hisat2-2.2.1/docs_jhu/sidebar.inc.shtml: HTML document, ASCII text, with very long lines data/hisat2-2.2.1/docs_jhu/strip_markdown.pl: Perl script text executable data/hisat2-2.2.1/docs_jhu/style.css: ASCII text data/hisat2-2.2.1/dp_framer.cpp: C++ source, ASCII text data/hisat2-2.2.1/dp_framer.h: C++ source, ASCII text data/hisat2-2.2.1/ds.cpp: C++ source, ASCII text data/hisat2-2.2.1/ds.h: C++ source, ASCII text data/hisat2-2.2.1/edit.cpp: C++ source, ASCII text data/hisat2-2.2.1/edit.h: C source, ASCII text data/hisat2-2.2.1/endian_swap.h: C++ source, ASCII text data/hisat2-2.2.1/evaluation/real/calculate_read_cost.py: Python script, ASCII text executable data/hisat2-2.2.1/evaluation/real/init.py: Python script, ASCII text executable data/hisat2-2.2.1/evaluation/simulation/calculate_read_cost.py: Python script, ASCII text executable, with very long lines data/hisat2-2.2.1/evaluation/simulation/init.py: Python script, ASCII text executable data/hisat2-2.2.1/evaluation/tests/CODIS/README: ASCII text data/hisat2-2.2.1/evaluation/tests/HLA_novel/ILMN_StrandSeq_original/README: ASCII text data/hisat2-2.2.1/evaluation/tests/HLA_novel/ILMN_StrandSeq_original/SraRunInfo.txt: ASCII text data/hisat2-2.2.1/evaluation/tests/HLA_novel/README: ASCII text data/hisat2-2.2.1/evaluation/tests/HLA_novel/scripts/run_extract_ILMN_HiSeqX.sh: Bourne-Again shell script, ASCII text executable data/hisat2-2.2.1/evaluation/tests/HLA_novel/hisatgenotype_locus_prev.py: Python script, ASCII text executable data/hisat2-2.2.1/evaluation/tests/genotype_genome/paper_sensitivity/sensitivity.py: Python script, ASCII text executable data/hisat2-2.2.1/evaluation/tests/genotype_genome/hisatgenotype_prev.py: Python script, ASCII text executable data/hisat2-2.2.1/evaluation/tests/one_snp_test/evaluate_one_snp_reads.py: Python script, ASCII text executable data/hisat2-2.2.1/evaluation/tests/one_snp_test/simulate_one_snp_reads.py: Python script, ASCII text executable data/hisat2-2.2.1/evaluation/tests/repeat/commands: ASCII text data/hisat2-2.2.1/evaluation/tests/repeat/generate_repeats.py: Python script, ASCII text executable data/hisat2-2.2.1/evaluation/tests/repeat/test_repeat.py: Python script, ASCII text executable data/hisat2-2.2.1/evaluation/tests/the_small_example/COMMAND: ASCII text data/hisat2-2.2.1/evaluation/tests/the_small_example/small.fa: ASCII text data/hisat2-2.2.1/evaluation/tests/the_small_example/small.snp: ASCII text data/hisat2-2.2.1/evaluation/build_indexes.py: Python script, ASCII text executable data/hisat2-2.2.1/evaluation/generate_reads.py: Python script, ASCII text executable data/hisat2-2.2.1/evaluation/get_data.py: Python script, ASCII text executable data/hisat2-2.2.1/evaluation/get_programs.py: Python script, ASCII text executable data/hisat2-2.2.1/example/index/22_20-21M_snp.1.ht2: data data/hisat2-2.2.1/example/index/22_20-21M_snp.2.ht2: data data/hisat2-2.2.1/example/index/22_20-21M_snp.3.ht2: data data/hisat2-2.2.1/example/index/22_20-21M_snp.4.ht2: data data/hisat2-2.2.1/example/index/22_20-21M_snp.5.ht2: data data/hisat2-2.2.1/example/index/22_20-21M_snp.6.ht2: data data/hisat2-2.2.1/example/index/22_20-21M_snp.7.ht2: data data/hisat2-2.2.1/example/index/22_20-21M_snp.8.ht2: data data/hisat2-2.2.1/example/reads/reads_1.fa: ASCII text data/hisat2-2.2.1/example/reads/reads_2.fa: ASCII text data/hisat2-2.2.1/example/reference/22_20-21M.fa: ASCII text data/hisat2-2.2.1/example/reference/22_20-21M.snp: ASCII text data/hisat2-2.2.1/fast_mutex.h: C++ source, ASCII text, with CRLF line terminators data/hisat2-2.2.1/filebuf.h: C++ source, ASCII text data/hisat2-2.2.1/formats.h: C source, ASCII text data/hisat2-2.2.1/gbwt_graph.h: C++ source, UTF-8 Unicode text data/hisat2-2.2.1/gfm.cpp: C++ source, ASCII text data/hisat2-2.2.1/gfm.h: C++ source, ASCII text data/hisat2-2.2.1/gp.h: C++ source, ASCII text data/hisat2-2.2.1/group_walk.cpp: C source, ASCII text data/hisat2-2.2.1/group_walk.h: C++ source, ASCII text data/hisat2-2.2.1/hgfm.h: C++ source, UTF-8 Unicode text data/hisat2-2.2.1/hi_aligner.h: C++ source, ASCII text data/hisat2-2.2.1/hier_idx_common.h: C source, ASCII text data/hisat2-2.2.1/hisat2.cpp: C++ source, UTF-8 Unicode text data/hisat2-2.2.1/hisat2.sln: UTF-8 Unicode (with BOM) text, with CRLF line terminators data/hisat2-2.2.1/hisat2.xcodeproj/project.pbxproj: ASCII text data/hisat2-2.2.1/hisat2_build.cpp: C source, ASCII text data/hisat2-2.2.1/hisat2_build_main.cpp: C++ source, ASCII text data/hisat2-2.2.1/hisat2_inspect.cpp: C++ source, ASCII text data/hisat2-2.2.1/hisat2_main.cpp: C++ source, ASCII text data/hisat2-2.2.1/hisat2_read_statistics.py: Python script, ASCII text executable data/hisat2-2.2.1/hisat2_repeat.cpp: C source, ASCII text data/hisat2-2.2.1/hisat2_repeat_main.cpp: C++ source, ASCII text data/hisat2-2.2.1/hisat2lib/ht2.h: C source, ASCII text data/hisat2-2.2.1/hisat2lib/ht2_alignment.cpp: ASCII text data/hisat2-2.2.1/hisat2lib/ht2_handle.h: C source, ASCII text data/hisat2-2.2.1/hisat2lib/ht2_index.cpp: C source, ASCII text data/hisat2-2.2.1/hisat2lib/ht2_init.cpp: C++ source, ASCII text data/hisat2-2.2.1/hisat2lib/ht2_repeat.cpp: C source, ASCII text data/hisat2-2.2.1/hisat2lib/java_jni/HT2Module.java: Java source, ASCII text data/hisat2-2.2.1/hisat2lib/java_jni/HT2ModuleExample.java: C source, ASCII text data/hisat2-2.2.1/hisat2lib/java_jni/Makefile: makefile script, ASCII text data/hisat2-2.2.1/hisat2lib/java_jni/ht2module.c: C source, ASCII text data/hisat2-2.2.1/hisat2lib/pymodule/Makefile: makefile script, ASCII text data/hisat2-2.2.1/hisat2lib/pymodule/ht2module.c: C source, ASCII text data/hisat2-2.2.1/hisat2lib/pymodule/ht2example.py: Python script, ASCII text executable data/hisat2-2.2.1/hisat2lib/pymodule/setup.py: Python script, ASCII text executable data/hisat2-2.2.1/hisat_bp.cpp: C++ source, ASCII text data/hisat2-2.2.1/ival_list.cpp: C++ source, ASCII text data/hisat2-2.2.1/ival_list.h: C++ source, ASCII text data/hisat2-2.2.1/li_hla/Makefile: makefile script, ASCII text data/hisat2-2.2.1/li_hla/alignments.hpp: C++ source, ASCII text data/hisat2-2.2.1/li_hla/defs.h: C source, ASCII text data/hisat2-2.2.1/li_hla/main.cpp: C source, ASCII text data/hisat2-2.2.1/limit.cpp: C source, ASCII text data/hisat2-2.2.1/limit.h: C source, ASCII text data/hisat2-2.2.1/ls.cpp: C++ source, ASCII text data/hisat2-2.2.1/ls.h: C++ source, ASCII text data/hisat2-2.2.1/mask.cpp: C source, ASCII text data/hisat2-2.2.1/mask.h: C source, ASCII text data/hisat2-2.2.1/mem_ids.h: ASCII text data/hisat2-2.2.1/mm.h: C source, ASCII text data/hisat2-2.2.1/msvcc/CodeStubs.vcxproj.filters: XML 1.0 document, UTF-8 Unicode (with BOM) text, with CRLF line terminators data/hisat2-2.2.1/msvcc/CoreDefs.props: XML 1.0 document, UTF-8 Unicode (with BOM) text, with CRLF line terminators data/hisat2-2.2.1/msvcc/SetVersion.vbs: ASCII text, with CRLF line terminators data/hisat2-2.2.1/msvcc/SysDefs.props: XML 1.0 document, UTF-8 Unicode (with BOM) text, with CRLF line terminators data/hisat2-2.2.1/msvcc/codeStubs.vcxproj: XML 1.0 document, UTF-8 Unicode (with BOM) text, with CRLF line terminators data/hisat2-2.2.1/msvcc/codeStubs/getopt.c: C source, ASCII text data/hisat2-2.2.1/msvcc/codeStubs/getopt.h: C source, ASCII text data/hisat2-2.2.1/msvcc/codeStubs/getopt1.c: C source, ASCII text data/hisat2-2.2.1/msvcc/codeStubs/sys/time.cpp: C source, ASCII text, with CRLF, LF line terminators data/hisat2-2.2.1/msvcc/codeStubs/sys/time.h: C source, ASCII text, with CRLF line terminators data/hisat2-2.2.1/msvcc/codeStubs/unistd.h: empty data/hisat2-2.2.1/msvcc/hisat2-align-l.vcxproj: XML 1.0 document, UTF-8 Unicode (with BOM) text, with CRLF line terminators data/hisat2-2.2.1/msvcc/hisat2-align-l.vcxproj.filters: XML 1.0 document, UTF-8 Unicode (with BOM) text, with CRLF line terminators data/hisat2-2.2.1/msvcc/hisat2-align-s.vcxproj: XML 1.0 document, UTF-8 Unicode (with BOM) text, with CRLF line terminators data/hisat2-2.2.1/msvcc/hisat2-align-s.vcxproj.filters: XML 1.0 document, UTF-8 Unicode (with BOM) text, with CRLF line terminators data/hisat2-2.2.1/msvcc/hisat2-build-l.vcxproj: XML 1.0 document, UTF-8 Unicode (with BOM) text, with CRLF line terminators data/hisat2-2.2.1/msvcc/hisat2-build-l.vcxproj.filters: XML 1.0 document, UTF-8 Unicode (with BOM) text, with CRLF line terminators data/hisat2-2.2.1/msvcc/hisat2-build-s.vcxproj: XML 1.0 document, UTF-8 Unicode (with BOM) text, with CRLF line terminators data/hisat2-2.2.1/msvcc/hisat2-build-s.vcxproj.filters: XML 1.0 document, UTF-8 Unicode (with BOM) text, with CRLF line terminators data/hisat2-2.2.1/msvcc/hisat2-inspect-l.vcxproj: XML 1.0 document, UTF-8 Unicode (with BOM) text, with CRLF line terminators data/hisat2-2.2.1/msvcc/hisat2-inspect-l.vcxproj.filters: XML 1.0 document, UTF-8 Unicode (with BOM) text, with CRLF line terminators data/hisat2-2.2.1/msvcc/hisat2-inspect-s.vcxproj: XML 1.0 document, UTF-8 Unicode (with BOM) text, with CRLF line terminators data/hisat2-2.2.1/msvcc/hisat2-inspect-s.vcxproj.filters: XML 1.0 document, UTF-8 Unicode (with BOM) text, with CRLF line terminators data/hisat2-2.2.1/msvcc/search.vcxproj: XML 1.0 document, UTF-8 Unicode (with BOM) text, with CRLF line terminators data/hisat2-2.2.1/msvcc/search.vcxproj.filters: XML 1.0 document, UTF-8 Unicode (with BOM) text, with CRLF line terminators data/hisat2-2.2.1/msvcc/search64.vcxproj: XML 1.0 document, UTF-8 Unicode (with BOM) text, with CRLF line terminators data/hisat2-2.2.1/msvcc/search64.vcxproj.filters: XML 1.0 document, UTF-8 Unicode (with BOM) text, with CRLF line terminators data/hisat2-2.2.1/msvcc/shared.vcxproj: XML 1.0 document, UTF-8 Unicode (with BOM) text, with CRLF line terminators data/hisat2-2.2.1/msvcc/shared.vcxproj.filters: XML 1.0 document, UTF-8 Unicode (with BOM) text, with CRLF line terminators data/hisat2-2.2.1/msvcc/shared64.vcxproj: XML 1.0 document, UTF-8 Unicode (with BOM) text, with CRLF line terminators data/hisat2-2.2.1/msvcc/shared64.vcxproj.filters: XML 1.0 document, UTF-8 Unicode (with BOM) text, with CRLF line terminators data/hisat2-2.2.1/multikey_qsort.cpp: C source, ASCII text data/hisat2-2.2.1/multikey_qsort.h: C++ source, ASCII text data/hisat2-2.2.1/opts.h: C source, ASCII text data/hisat2-2.2.1/outq.cpp: C++ source, ASCII text data/hisat2-2.2.1/outq.h: C++ source, ASCII text data/hisat2-2.2.1/pat.cpp: C++ source, ASCII text data/hisat2-2.2.1/pat.h: C++ source, ASCII text data/hisat2-2.2.1/pe.cpp: C++ source, ASCII text data/hisat2-2.2.1/pe.h: C++ source, ASCII text data/hisat2-2.2.1/presets.cpp: C++ source, ASCII text data/hisat2-2.2.1/presets.h: C++ source, ASCII text data/hisat2-2.2.1/qual.cpp: ASCII text data/hisat2-2.2.1/qual.h: C++ source, ASCII text data/hisat2-2.2.1/radix_sort.h: C++ source, ASCII text data/hisat2-2.2.1/random_source.cpp: C++ source, ASCII text data/hisat2-2.2.1/random_source.h: C++ source, ASCII text data/hisat2-2.2.1/random_util.cpp: C source, ASCII text data/hisat2-2.2.1/random_util.h: C++ source, ASCII text data/hisat2-2.2.1/read.h: C source, ASCII text data/hisat2-2.2.1/read_qseq.cpp: C source, ASCII text data/hisat2-2.2.1/ref_coord.cpp: C++ source, ASCII text data/hisat2-2.2.1/ref_coord.h: C++ source, ASCII text data/hisat2-2.2.1/ref_read.cpp: C source, ASCII text data/hisat2-2.2.1/ref_read.h: C++ source, ASCII text data/hisat2-2.2.1/reference.cpp: C++ source, ASCII text data/hisat2-2.2.1/reference.h: C++ source, ASCII text data/hisat2-2.2.1/repeat.h: C++ source, ASCII text data/hisat2-2.2.1/repeat_builder.cpp: C++ source, ASCII text data/hisat2-2.2.1/repeat_builder.h: C++ source, ASCII text data/hisat2-2.2.1/repeat_kmer.h: C++ source, ASCII text data/hisat2-2.2.1/rfm.h: C++ source, UTF-8 Unicode text data/hisat2-2.2.1/sam.h: C++ source, UTF-8 Unicode text data/hisat2-2.2.1/scoring.cpp: C++ source, ASCII text data/hisat2-2.2.1/scoring.h: C++ source, ASCII text data/hisat2-2.2.1/scripts/convert_quals.pl: Perl script text executable data/hisat2-2.2.1/scripts/gen_2b_occ_lookup.pl: Perl script text executable data/hisat2-2.2.1/scripts/gen_occ_lookup.pl: Perl script text executable data/hisat2-2.2.1/scripts/gen_solqual_lookup.pl: Perl script text executable data/hisat2-2.2.1/scripts/infer_fraglen.pl: Perl script text executable data/hisat2-2.2.1/scripts/make_a_thaliana_tair.sh: POSIX shell script, ASCII text executable data/hisat2-2.2.1/scripts/make_b_taurus_UMD3.sh: POSIX shell script, ASCII text executable data/hisat2-2.2.1/scripts/make_bdgp6.sh: POSIX shell script, ASCII text executable data/hisat2-2.2.1/scripts/make_bdgp6_tran.sh: POSIX shell script, ASCII text executable data/hisat2-2.2.1/scripts/make_canFam2.sh: POSIX shell script, ASCII text executable data/hisat2-2.2.1/scripts/make_ce10.sh: POSIX shell script, ASCII text executable data/hisat2-2.2.1/scripts/make_dm6.sh: POSIX shell script, ASCII text executable data/hisat2-2.2.1/scripts/make_e_coli.sh: POSIX shell script, ASCII text executable data/hisat2-2.2.1/scripts/make_grch37.sh: POSIX shell script, ASCII text executable data/hisat2-2.2.1/scripts/make_grch37_snp.sh: POSIX shell script, ASCII text executable data/hisat2-2.2.1/scripts/make_grch37_snp_tran.sh: POSIX shell script, ASCII text executable data/hisat2-2.2.1/scripts/make_grch37_snp_tran_ercc.sh: POSIX shell script, ASCII text executable data/hisat2-2.2.1/scripts/make_grch37_tran.sh: POSIX shell script, ASCII text executable data/hisat2-2.2.1/scripts/make_grch38.sh: POSIX shell script, ASCII text executable data/hisat2-2.2.1/scripts/make_grch38_rep.sh: POSIX shell script, ASCII text executable data/hisat2-2.2.1/scripts/make_grch38_snp.sh: POSIX shell script, ASCII text executable data/hisat2-2.2.1/scripts/make_grch38_snp_rep.sh: POSIX shell script, ASCII text executable data/hisat2-2.2.1/scripts/make_grch38_snp_tran.sh: POSIX shell script, ASCII text executable data/hisat2-2.2.1/scripts/make_grch38_snp_tran_ercc.sh: POSIX shell script, ASCII text executable data/hisat2-2.2.1/scripts/make_grch38_tran.sh: POSIX shell script, ASCII text executable data/hisat2-2.2.1/scripts/make_grcm38.sh: POSIX shell script, ASCII text executable data/hisat2-2.2.1/scripts/make_grcm38_snp.sh: POSIX shell script, ASCII text executable data/hisat2-2.2.1/scripts/make_grcm38_snp_tran.sh: POSIX shell script, ASCII text executable data/hisat2-2.2.1/scripts/make_grcm38_tran.sh: POSIX shell script, ASCII text executable data/hisat2-2.2.1/scripts/make_hg19.sh: POSIX shell script, ASCII text executable data/hisat2-2.2.1/scripts/make_hg38.sh: POSIX shell script, ASCII text executable data/hisat2-2.2.1/scripts/make_hg38_allsnp.sh: POSIX shell script, ASCII text executable data/hisat2-2.2.1/scripts/make_hg38_snp.sh: POSIX shell script, ASCII text executable data/hisat2-2.2.1/scripts/make_hg38_snp_tran.sh: POSIX shell script, ASCII text executable data/hisat2-2.2.1/scripts/make_mm10.sh: POSIX shell script, ASCII text executable data/hisat2-2.2.1/scripts/make_mm9.sh: POSIX shell script, ASCII text executable data/hisat2-2.2.1/scripts/make_r64.sh: POSIX shell script, ASCII text executable data/hisat2-2.2.1/scripts/make_r64_tran.sh: POSIX shell script, ASCII text executable data/hisat2-2.2.1/scripts/make_rn4.sh: POSIX shell script, ASCII text executable data/hisat2-2.2.1/scripts/make_rn6.sh: POSIX shell script, ASCII text executable data/hisat2-2.2.1/scripts/make_rnor6.sh: POSIX shell script, ASCII text executable data/hisat2-2.2.1/scripts/make_rnor6_tran.sh: POSIX shell script, ASCII text executable data/hisat2-2.2.1/scripts/make_sc3.sh: POSIX shell script, ASCII text executable data/hisat2-2.2.1/scripts/make_wbcel235.sh: POSIX shell script, ASCII text executable data/hisat2-2.2.1/scripts/make_wbcel235_tran.sh: POSIX shell script, ASCII text executable data/hisat2-2.2.1/scripts/make_zm3_snp_tran_ercc.sh: POSIX shell script, ASCII text executable data/hisat2-2.2.1/scripts/sim/AlignmentCheck.pm: Perl script text executable data/hisat2-2.2.1/scripts/sim/DNA.pm: Perl script text executable data/hisat2-2.2.1/scripts/sim/Mutate.pm: Perl script text executable data/hisat2-2.2.1/scripts/sim/RandDNA.pm: Perl script text executable data/hisat2-2.2.1/scripts/sim/SampleRead.pm: Perl script text executable data/hisat2-2.2.1/scripts/sim/Sim.pm: Perl script text executable data/hisat2-2.2.1/scripts/sim/Test.pm: Perl script text executable data/hisat2-2.2.1/scripts/sim/contrib/ForkManager.pm: Perl5 module source, ISO-8859 text data/hisat2-2.2.1/scripts/sim/run.pl: Perl script text executable data/hisat2-2.2.1/scripts/sim/run.sh: POSIX shell script, ASCII text executable data/hisat2-2.2.1/scripts/sim/unit.sh: POSIX shell script, ASCII text executable data/hisat2-2.2.1/scripts/test/DNA.pm: Perl script text executable data/hisat2-2.2.1/scripts/test/Read.pm: Perl script text executable data/hisat2-2.2.1/scripts/test/args.pl: Perl script text executable data/hisat2-2.2.1/scripts/test/simple_tests.pl: Perl script text executable data/hisat2-2.2.1/scripts/test/simple_tests.sh: POSIX shell script, ASCII text executable data/hisat2-2.2.1/scripts/sa.py: Python script, ASCII text executable data/hisat2-2.2.1/scripts/validate_repeat.py: Python script, ASCII text executable data/hisat2-2.2.1/search_globals.h: C source, ASCII text data/hisat2-2.2.1/sequence_io.h: C++ source, ASCII text data/hisat2-2.2.1/shmem.cpp: C++ source, ASCII text data/hisat2-2.2.1/shmem.h: C++ source, ASCII text data/hisat2-2.2.1/simple_func.cpp: C source, ASCII text data/hisat2-2.2.1/simple_func.h: C++ source, ASCII text data/hisat2-2.2.1/splice_site.cpp: C source, ASCII text data/hisat2-2.2.1/splice_site.h: C++ source, ASCII text data/hisat2-2.2.1/splice_site_mem.h: C source, ASCII text data/hisat2-2.2.1/splice_site_new.cpp: C source, ASCII text data/hisat2-2.2.1/spliced_aligner.h: C++ source, ASCII text data/hisat2-2.2.1/sse_util.cpp: C source, ASCII text data/hisat2-2.2.1/sstring.cpp: C++ source, ASCII text data/hisat2-2.2.1/sstring.h: C++ source, ASCII text, with very long lines data/hisat2-2.2.1/str_util.h: C source, ASCII text data/hisat2-2.2.1/third_party/cpuid.h: C source, ASCII text data/hisat2-2.2.1/threading.h: C++ source, ASCII text data/hisat2-2.2.1/timer.h: C++ source, ASCII text data/hisat2-2.2.1/tinythread.cpp: C++ source, ASCII text data/hisat2-2.2.1/tinythread.h: C++ source, ASCII text data/hisat2-2.2.1/tokenize.h: C++ source, ASCII text data/hisat2-2.2.1/tp.h: C++ source, ASCII text data/hisat2-2.2.1/unique.cpp: C++ source, ASCII text data/hisat2-2.2.1/unique.h: C++ source, ASCII text data/hisat2-2.2.1/util.h: C++ source, ASCII text data/hisat2-2.2.1/word_io.h: C++ source, ASCII text data/hisat2-2.2.1/zbox.h: C++ source, ASCII text data/hisat2-2.2.1/debian/changelog: ASCII text data/hisat2-2.2.1/debian/clean: ASCII text data/hisat2-2.2.1/debian/control: ASCII text data/hisat2-2.2.1/debian/copyright: UTF-8 Unicode text data/hisat2-2.2.1/debian/docs: ASCII text data/hisat2-2.2.1/debian/examples: ASCII text data/hisat2-2.2.1/debian/hisat2.install: ASCII text data/hisat2-2.2.1/debian/manpages: ASCII text data/hisat2-2.2.1/debian/patches/compilerflags: unified diff output, ASCII text data/hisat2-2.2.1/debian/patches/fix-freebsd: unified diff output, ASCII text data/hisat2-2.2.1/debian/patches/fix-manual: unified diff output, ASCII text data/hisat2-2.2.1/debian/patches/hardening: unified diff output, ASCII text data/hisat2-2.2.1/debian/patches/python3: unified diff output, ASCII text data/hisat2-2.2.1/debian/patches/reproducibile: unified diff output, ASCII text data/hisat2-2.2.1/debian/patches/series: ASCII text data/hisat2-2.2.1/debian/patches/simde: unified diff output, ASCII text data/hisat2-2.2.1/debian/python3-hisat2.install: ASCII text data/hisat2-2.2.1/debian/python3-hisat2.lintian-overrides: ASCII text data/hisat2-2.2.1/debian/rules: a /usr/bin/make -f script, ASCII text executable data/hisat2-2.2.1/debian/salsa-ci.yml: ASCII text data/hisat2-2.2.1/debian/source/format: ASCII text data/hisat2-2.2.1/debian/source/lintian-overrides: ASCII text data/hisat2-2.2.1/debian/tests/control: ASCII text data/hisat2-2.2.1/debian/tests/run-unit-tests: Bourne-Again shell script, ASCII text executable data/hisat2-2.2.1/debian/upstream/metadata: ASCII text data/hisat2-2.2.1/debian/watch: ASCII text data/hisat2-2.2.1/.pc/.version: ASCII text data/hisat2-2.2.1/.pc/.quilt_patches: ASCII text data/hisat2-2.2.1/.pc/.quilt_series: ASCII text data/hisat2-2.2.1/.pc/applied-patches: ASCII text data/hisat2-2.2.1/.pc/hardening/Makefile: ASCII text data/hisat2-2.2.1/.pc/reproducibile/Makefile: ASCII text data/hisat2-2.2.1/.pc/fix-freebsd/hisat2: Perl script text executable data/hisat2-2.2.1/.pc/compilerflags/Makefile: ASCII text data/hisat2-2.2.1/.pc/simde/aligner_sw.h: C++ source, ASCII text data/hisat2-2.2.1/.pc/simde/sse_util.h: C++ source, ASCII text data/hisat2-2.2.1/.pc/simde/Makefile: ASCII text data/hisat2-2.2.1/.pc/simde/processor_support.h: C++ source, UTF-8 Unicode text data/hisat2-2.2.1/.pc/python3/evaluation/build_indexes.py: Python script, ASCII text executable data/hisat2-2.2.1/.pc/python3/evaluation/generate_reads.py: Python script, ASCII text executable data/hisat2-2.2.1/.pc/python3/evaluation/get_data.py: Python script, ASCII text executable data/hisat2-2.2.1/.pc/python3/evaluation/get_programs.py: Python script, ASCII text executable data/hisat2-2.2.1/.pc/python3/evaluation/real/calculate_read_cost.py: Python script, ASCII text executable data/hisat2-2.2.1/.pc/python3/evaluation/real/init.py: Python script, ASCII text executable data/hisat2-2.2.1/.pc/python3/evaluation/simulation/calculate_read_cost.py: Python script, ASCII text executable, with very long lines data/hisat2-2.2.1/.pc/python3/evaluation/simulation/init.py: Python script, ASCII text executable data/hisat2-2.2.1/.pc/python3/evaluation/tests/HLA_novel/hisatgenotype_locus_prev.py: Python script, ASCII text executable data/hisat2-2.2.1/.pc/python3/evaluation/tests/genotype_genome/hisatgenotype_prev.py: Python script, ASCII text executable data/hisat2-2.2.1/.pc/python3/evaluation/tests/genotype_genome/paper_sensitivity/sensitivity.py: Python script, ASCII text executable data/hisat2-2.2.1/.pc/python3/evaluation/tests/one_snp_test/evaluate_one_snp_reads.py: Python script, ASCII text executable data/hisat2-2.2.1/.pc/python3/evaluation/tests/one_snp_test/simulate_one_snp_reads.py: Python script, ASCII text executable data/hisat2-2.2.1/.pc/python3/evaluation/tests/repeat/generate_repeats.py: Python script, ASCII text executable data/hisat2-2.2.1/.pc/python3/evaluation/tests/repeat/test_repeat.py: Python script, ASCII text executable data/hisat2-2.2.1/.pc/python3/hisat2-build: Python script, ASCII text executable data/hisat2-2.2.1/.pc/python3/hisat2-build-new: Python script, ASCII text executable data/hisat2-2.2.1/.pc/python3/hisat2-inspect: Python script, ASCII text executable data/hisat2-2.2.1/.pc/python3/hisat2_extract_exons.py: Python script, ASCII text executable data/hisat2-2.2.1/.pc/python3/hisat2_extract_snps_haplotypes_UCSC.py: Python script, ASCII text executable data/hisat2-2.2.1/.pc/python3/hisat2_extract_snps_haplotypes_VCF.py: Python script, ASCII text executable data/hisat2-2.2.1/.pc/python3/hisat2_extract_splice_sites.py: Python script, ASCII text executable data/hisat2-2.2.1/.pc/python3/hisat2_simulate_reads.py: Python script, ASCII text executable data/hisat2-2.2.1/.pc/python3/hisat2lib/pymodule/ht2example.py: Python script, ASCII text executable data/hisat2-2.2.1/.pc/python3/hisat2lib/pymodule/setup.py: Python script, ASCII text executable data/hisat2-2.2.1/.pc/python3/scripts/sa.py: Python script, ASCII text executable data/hisat2-2.2.1/.pc/python3/scripts/validate_repeat.py: Python script, ASCII text executable data/hisat2-2.2.1/.pc/fix-manual/Makefile: ASCII text data/hisat2-2.2.1/hisat2: Perl script text executable data/hisat2-2.2.1/aligner_sw.h: C++ source, ASCII text data/hisat2-2.2.1/sse_util.h: C++ source, ASCII text data/hisat2-2.2.1/processor_support.h: C++ source, UTF-8 Unicode text data/hisat2-2.2.1/hisat2-build: Python script, ASCII text executable data/hisat2-2.2.1/hisat2-build-new: Python script, ASCII text executable data/hisat2-2.2.1/hisat2-inspect: Python script, ASCII text executable data/hisat2-2.2.1/hisat2_extract_exons.py: Python script, ASCII text executable data/hisat2-2.2.1/hisat2_extract_snps_haplotypes_UCSC.py: Python script, ASCII text executable data/hisat2-2.2.1/hisat2_extract_snps_haplotypes_VCF.py: Python script, ASCII text executable data/hisat2-2.2.1/hisat2_extract_splice_sites.py: Python script, ASCII text executable data/hisat2-2.2.1/hisat2_simulate_reads.py: Python script, ASCII text executable data/hisat2-2.2.1/Makefile: ASCII text