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/ /_/ > | \// __ \| | / /_/ | | || |
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grep rough audit - static analysis tool
v2.8 written by @Wireghoul
=================================[justanotherhacker.com]===
bio-rainbow-2.0.4+dfsg/main.c-48- "Input File Format: <seqid:int>\\t<cluster_id:int>\\t<read1:string>\\t<read2:string>[\\t<pre_cluster_id:int>]\n"
bio-rainbow-2.0.4+dfsg/main.c:49: " -i <string> Input rbasm output file [stdin]\n"
bio-rainbow-2.0.4+dfsg/main.c-50- " -a output assembly\n"
##############################################
bio-rainbow-2.0.4+dfsg/main.c-194- uint32_t max_cluster = 300;
bio-rainbow-2.0.4+dfsg/main.c:195: uint32_t need_asm = 0;
bio-rainbow-2.0.4+dfsg/main.c-196- float min_sm = 0.90;
##############################################
bio-rainbow-2.0.4+dfsg/main.c-211- case 'N': max_cluster = atoi(optarg); break;
bio-rainbow-2.0.4+dfsg/main.c:212: case 'a': need_asm = 1; break;
bio-rainbow-2.0.4+dfsg/main.c-213- case 'r': min_read = atoi(optarg); break;
##############################################
bio-rainbow-2.0.4+dfsg/mergectg.c-473- merger->max_read = max_read;
bio-rainbow-2.0.4+dfsg/mergectg.c:474: merger->need_asm = need_asm;
bio-rainbow-2.0.4+dfsg/mergectg.c-475- merger->max_cluster = max_cluster;
##############################################
bio-rainbow-2.0.4+dfsg/tags-186-begin_iter_bitvec bitvec.h /^static inline void begin_iter_bitvec(BitVec *bitv){ bitv->iter_idx = 0; }$/;" f
bio-rainbow-2.0.4+dfsg/tags:187:begin_iter_simpasm simp_asm.h /^static inline void begin_iter_simpasm(SimpAssembler *sa){ sa->iter_idx = 0; }$/;" f
bio-rainbow-2.0.4+dfsg/tags-188-bit2bits dna.h 144;" d
##############################################
bio-rainbow-2.0.4+dfsg/tags-373-free_sequence file_reader.h 59;" d
bio-rainbow-2.0.4+dfsg/tags:374:free_simpasm simp_asm.h /^static inline void free_simpasm(SimpAssembler *sa){$/;" f
bio-rainbow-2.0.4+dfsg/tags-375-free_string string.h /^static inline void free_string(String *str){ free(str->string); free(str); }$/;" f
##############################################
bio-rainbow-2.0.4+dfsg/tags-454-init_merger mergectg.c /^merge_t* init_merger(uint32_t min_kmer, uint32_t min_overlap, float het, uint32_t kmersize, uint32_t max_cluster, uint32_t need_asm) {$/;" f
bio-rainbow-2.0.4+dfsg/tags:455:init_simpasm simp_asm.h /^static inline SimpAssembler* init_simpasm(uint32_t n_cpu, uint32_t kmer_size, uint32_t rd_len, uint32_t strand, uint32_t min_ol, float min_sm, uint32_t max_mm, int allow_gap){$/;" f
bio-rainbow-2.0.4+dfsg/tags-456-init_string string.h /^static inline String* init_string(int cap){$/;" f
##############################################
bio-rainbow-2.0.4+dfsg/tags-465-iter_idx simp_asm.h /^ uint32_t iter_idx;$/;" m struct:__anon51
bio-rainbow-2.0.4+dfsg/tags:466:iter_simpasm simp_asm.h /^static inline SimpContigInfo* iter_simpasm(SimpAssembler *sa){$/;" f
bio-rainbow-2.0.4+dfsg/tags-467-j stdaln.h /^ int i, j;$/;" m struct:__anon15
##############################################
bio-rainbow-2.0.4+dfsg/tags-569-native_number_cmp list.h 216;" d
bio-rainbow-2.0.4+dfsg/tags:570:need_asm mergectg.h /^ uint32_t need_asm; \/\/ parameter$/;" m struct:__anon8
bio-rainbow-2.0.4+dfsg/tags-571-nst_nt4_table ezmsim.c /^uint8_t nst_nt4_table[256] = {$/;" v
##############################################
bio-rainbow-2.0.4+dfsg/tags-620-print_alignments asm_R2.c /^void print_alignments(EF *ef){$/;" f
bio-rainbow-2.0.4+dfsg/tags:621:print_asm mergectg.c /^void print_asm(merge_t *merger, FILE *out) {$/;" f
bio-rainbow-2.0.4+dfsg/tags-622-print_asm2 mergectg.c /^void print_asm2(merge_t *merger, FILE *out) {$/;" f
##############################################
bio-rainbow-2.0.4+dfsg/tags-630-push_heap heap.h /^static inline void push_heap(Heap *heap, void *p){$/;" f
bio-rainbow-2.0.4+dfsg/tags:631:push_simpasm simp_asm.h /^static inline void push_simpasm(SimpAssembler *sa, uint32_t seqid, char *seq, uint32_t seqlen, uint8_t rank){$/;" f
bio-rainbow-2.0.4+dfsg/tags-632-push_vec vector.h /^static inline void push_vec(Vector *vec, void *e){$/;" f
##############################################
bio-rainbow-2.0.4+dfsg/tags-677-reset_merger mergectg.c /^void reset_merger(merge_t *merger) {$/;" f
bio-rainbow-2.0.4+dfsg/tags:678:reset_simpasm simp_asm.h /^static inline void reset_simpasm(SimpAssembler *sa){$/;" f
bio-rainbow-2.0.4+dfsg/tags-679-reset_vec vector.h /^static inline void reset_vec(Vector *vec){$/;" f
##############################################
bio-rainbow-2.0.4+dfsg/debian/bio-rainbow.install-1-select* usr/bin/
bio-rainbow-2.0.4+dfsg/debian/bio-rainbow.install:2:rbasm usr/bin/
bio-rainbow-2.0.4+dfsg/debian/bio-rainbow.install-3-bio-rainbow usr/bin/
##############################################
bio-rainbow-2.0.4+dfsg/debian/createmanpages-4-
bio-rainbow-2.0.4+dfsg/debian/createmanpages:5:VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*://' -e 's/-.*//' -e 's/[+~]dfsg$//'`
bio-rainbow-2.0.4+dfsg/debian/createmanpages-6-NAME=`grep "^Description:" debian/control | sed 's/^Description: *//'`
##############################################
bio-rainbow-2.0.4+dfsg/debian/mans/bio-rainbow.1-53-.HP
bio-rainbow-2.0.4+dfsg/debian/mans/bio-rainbow.1:54:\fB\-i\fR <string> Input rbasm output file [stdin]
bio-rainbow-2.0.4+dfsg/debian/mans/bio-rainbow.1-55-.TP
##############################################
bio-rainbow-2.0.4+dfsg/debian/mans/rbasm.1-1-.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.6.
bio-rainbow-2.0.4+dfsg/debian/mans/rbasm.1:2:.TH RBASM "1" "July 2018" "rbasm 2.0.4" "User Commands"
bio-rainbow-2.0.4+dfsg/debian/mans/rbasm.1-3-.SH NAME
bio-rainbow-2.0.4+dfsg/debian/mans/rbasm.1:4:rbasm \- local assemble fragments around restriction sites
bio-rainbow-2.0.4+dfsg/debian/mans/rbasm.1-5-.SH SYNOPSIS
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bio-rainbow-2.0.4+dfsg/debian/patches/rename_binary.patch-9-
bio-rainbow-2.0.4+dfsg/debian/patches/rename_binary.patch:10: #all: rainbow rbasm rbmergetag ezmsim
bio-rainbow-2.0.4+dfsg/debian/patches/rename_binary.patch-11--all: rainbow ezmsim rbasm
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bio-rainbow-2.0.4+dfsg/debian/patches/rename_binary.patch-22- clean:
bio-rainbow-2.0.4+dfsg/debian/patches/rename_binary.patch:23:- rm -f *.o *.gcda *.gcno *.gcov gmon.out rainbow rbasm ezmsim rbmergetag *.exe
bio-rainbow-2.0.4+dfsg/debian/patches/rename_binary.patch:24:+ rm -f *.o *.gcda *.gcno *.gcov gmon.out bio-rainbow rbasm ezmsim rbmergetag *.exe
bio-rainbow-2.0.4+dfsg/debian/patches/rename_binary.patch-25-
##############################################
bio-rainbow-2.0.4+dfsg/debian/patches/spelling.patch-7-@@ -93,10 +93,10 @@ NOTE: the input file format should be: <
bio-rainbow-2.0.4+dfsg/debian/patches/spelling.patch:8: Usage: rbasm [options]
bio-rainbow-2.0.4+dfsg/debian/patches/spelling.patch-9- -i <string> Input file [STDIN]
##############################################
bio-rainbow-2.0.4+dfsg/.pc/add_hardening.patch/Makefile-11-
bio-rainbow-2.0.4+dfsg/.pc/add_hardening.patch/Makefile:12:#all: rainbow rbasm rbmergetag ezmsim
bio-rainbow-2.0.4+dfsg/.pc/add_hardening.patch/Makefile-13-all: rainbow ezmsim rbasm
##############################################
bio-rainbow-2.0.4+dfsg/.pc/add_hardening.patch/Makefile-44-clean:
bio-rainbow-2.0.4+dfsg/.pc/add_hardening.patch/Makefile:45: rm -f *.o *.gcda *.gcno *.gcov gmon.out rainbow rbasm ezmsim rbmergetag *.exe
bio-rainbow-2.0.4+dfsg/.pc/add_hardening.patch/Makefile-46-
##############################################
bio-rainbow-2.0.4+dfsg/.pc/rename_binary.patch/Makefile-17-
bio-rainbow-2.0.4+dfsg/.pc/rename_binary.patch/Makefile:18:#all: rainbow rbasm rbmergetag ezmsim
bio-rainbow-2.0.4+dfsg/.pc/rename_binary.patch/Makefile-19-all: rainbow ezmsim rbasm
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bio-rainbow-2.0.4+dfsg/.pc/rename_binary.patch/Makefile-50-clean:
bio-rainbow-2.0.4+dfsg/.pc/rename_binary.patch/Makefile:51: rm -f *.o *.gcda *.gcno *.gcov gmon.out rainbow rbasm ezmsim rbmergetag *.exe
bio-rainbow-2.0.4+dfsg/.pc/rename_binary.patch/Makefile-52-
##############################################
bio-rainbow-2.0.4+dfsg/.pc/rename_binary.patch/README.txt-92-NOTE: the input file format should be: <seqid:int>\t<cluster_id:int>\t<read1:string>\t<read2:string>[\t<pre_cluster_id:int>]
bio-rainbow-2.0.4+dfsg/.pc/rename_binary.patch/README.txt:93:Usage: rbasm [options]
bio-rainbow-2.0.4+dfsg/.pc/rename_binary.patch/README.txt-94- -i <string> Input file [STDIN]
##############################################
bio-rainbow-2.0.4+dfsg/.pc/rename_binary.patch/README.txt-116-v2.0.1: README and usage infomation updated
bio-rainbow-2.0.4+dfsg/.pc/rename_binary.patch/README.txt:117:v2.0.2: 'merge' options are riched. The 'merge' assembly work can be customized like rbasm now. Thanks Ross Whetten in NCSU for advicing this.
bio-rainbow-2.0.4+dfsg/.pc/rename_binary.patch/README.txt-118-v2.0.3: changed the name of script 'select_best_rbcontig2.pl' to 'select_best_rbcontig_plus_read1.pl', and documented it.
##############################################
bio-rainbow-2.0.4+dfsg/.pc/spelling.patch/README.txt-92-NOTE: the input file format should be: <seqid:int>\t<cluster_id:int>\t<read1:string>\t<read2:string>[\t<pre_cluster_id:int>]
bio-rainbow-2.0.4+dfsg/.pc/spelling.patch/README.txt:93:Usage: rbasm [options]
bio-rainbow-2.0.4+dfsg/.pc/spelling.patch/README.txt-94- -i <string> Input file [STDIN]
##############################################
bio-rainbow-2.0.4+dfsg/.pc/spelling.patch/README.txt-116-v2.0.1: README and usage infomation updated
bio-rainbow-2.0.4+dfsg/.pc/spelling.patch/README.txt:117:v2.0.2: 'merge' options are riched. The 'merge' assembly work can be customized like rbasm now. Thanks Ross Whetten in NCSU for advicing this.
bio-rainbow-2.0.4+dfsg/.pc/spelling.patch/README.txt-118-v2.0.3: changed the name of script 'select_best_rbcontig2.pl' to 'select_best_rbcontig_plus_read1.pl', and documented it.
##############################################
bio-rainbow-2.0.4+dfsg/Makefile-17-
bio-rainbow-2.0.4+dfsg/Makefile:18:#all: rainbow rbasm rbmergetag ezmsim
bio-rainbow-2.0.4+dfsg/Makefile-19-all: bio-rainbow ezmsim rbasm
##############################################
bio-rainbow-2.0.4+dfsg/Makefile-50-clean:
bio-rainbow-2.0.4+dfsg/Makefile:51: rm -f *.o *.gcda *.gcno *.gcov gmon.out bio-rainbow rbasm ezmsim rbmergetag *.exe
bio-rainbow-2.0.4+dfsg/Makefile-52-
##############################################
bio-rainbow-2.0.4+dfsg/README.txt-92-NOTE: the input file format should be: <seqid:int>\t<cluster_id:int>\t<read1:string>\t<read2:string>[\t<pre_cluster_id:int>]
bio-rainbow-2.0.4+dfsg/README.txt:93:Usage: rbasm [options]
bio-rainbow-2.0.4+dfsg/README.txt-94- -i <string> Input file [STDIN]
##############################################
bio-rainbow-2.0.4+dfsg/README.txt-116-v2.0.1: README and usage infomation updated
bio-rainbow-2.0.4+dfsg/README.txt:117:v2.0.2: 'merge' options are riched. The 'merge' assembly work can be customized like rbasm now. Thanks Ross Whetten in NCSU for advicing this.
bio-rainbow-2.0.4+dfsg/README.txt-118-v2.0.3: changed the name of script 'select_best_rbcontig2.pl' to 'select_best_rbcontig_plus_read1.pl', and documented it.