/dports/biology/rainbow/rainbow_2.0.4/ |
H A D | aln_cigar.h | 42 static inline void cigars_lengths(AlnCigar *cigars, int n_cigar, int *aln_size, int *seq1_size, int… in cigars_lengths() 64 static inline int _aln_cigar_add_cigar(AlnCigar *cs, int n_cigar, int len, int type){ in _aln_cigar_add_cigar() 78 static inline char* cigars2string(AlnCigar *cigars, int n_cigar, char *str){ in cigars2string() 145 static inline int rank_cigars_seqlen(AlnCigar *cigars, int n_cigar, int len, int seq_idx){ in rank_cigars_seqlen() 161 static inline int rev_rank_cigars_seqlen(AlnCigar *cigars, int n_cigar, int len, int seq_idx){ in rev_rank_cigars_seqlen() 177 static inline int select_cigars_seqlen(AlnCigar *cigars, int n_cigar, int len, int seq_idx){ in select_cigars_seqlen() 195 static inline int rev_select_cigars_seqlen(AlnCigar *cigars, int n_cigar, int len, int seq_idx){ in rev_select_cigars_seqlen() 213 static inline void flip_cigars(AlnCigar *cigars, int n_cigar){ in flip_cigars() 220 static inline int sub_cigars(AlnCigar *dst, AlnCigar *cigars, int n_cigar, int off, int len){ in sub_cigars()
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/dports/biology/canu/canu-2.2/src/utility/src/utility/ |
H A D | align-ksw2.H | 29 int m_cigar, n_cigar; member 103 static inline uint32_t *ksw_push_cigar(void *km, int *n_cigar, int *m_cigar, uint32_t *cigar, uint3… in ksw_push_cigar() 122 int n_cigar = 0, m_cigar = *m_cigar_, i = i0, j = j0, r, state = 0; in ksw_backtrack() local
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/dports/biology/mmseqs2/MMseqs2-13-45111/lib/ksw2/ |
H A D | ksw2.h | 56 int m_cigar, n_cigar; member 129 static inline uint32_t *ksw_push_cigar(void*, int *n_cigar, int *m_cigar, uint32_t *cigar, uint32_t… in ksw_push_cigar() 148 int n_cigar = 0, m_cigar = *m_cigar_, i = i0, j = j0, r, state = 0; in ksw_backtrack() local
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/dports/biology/minimap2/minimap2-2.24/ |
H A D | ksw2.h | 36 int m_cigar, n_cigar; member 110 static inline uint32_t *ksw_push_cigar(void *km, int *n_cigar, int *m_cigar, uint32_t *cigar, uint3… in ksw_push_cigar() 129 int n_cigar = 0, m_cigar = *m_cigar_, i = i0, j = j0, r, state = 0; in ksw_backtrack() local
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/dports/biology/bwa/bwa-0.7.17/ |
H A D | bwase.c | 169 …_t l_pac, const ubyte_t *pacseq, int len, ubyte_t *seq, int ref_shift, bwtint_t *_rb, int *n_cigar) in bwa_refine_gapped_core() 201 char *bwa_cal_md1(int n_cigar, bwa_cigar_t *cigar, int len, bwtint_t pos, ubyte_t *seq, in bwa_cal_md1() 303 int n_cigar; in bwa_refine_gapped() local
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H A D | bwa.c | 121 …nt8_t *pac, int l_query, uint8_t *query, int64_t rb, int64_t re, int *score, int *n_cigar, int *NM) in bwa_gen_cigar2() 209 …nt8_t *pac, int l_query, uint8_t *query, int64_t rb, int64_t re, int *score, int *n_cigar, int *NM) in bwa_gen_cigar()
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H A D | bwtaln.h | 60 uint32_t n_cigar:15, gap:8, mm:8, strand:1; member 83 int n_cigar; member
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H A D | bwtsw2_pair.c | 98 int n_cigar, beg, end, len; member
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H A D | bwape.c | 409 …yte_t *pacseq, int len, const ubyte_t *seq, int64_t *beg, int reglen, int *n_cigar, uint32_t *_cnt) in bwa_sw_core() 516 int k, n_cigar[2], is_singleton, mapQ = 0, mq_adjust[2]; in bwa_paired_sw() local
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H A D | bamlite.h | 62 uint32_t flag:16, n_cigar:16; member
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H A D | bwtsw2.h | 30 int flag, nn, n_cigar, chr, pos, qual, mchr, mpos, pqual, isize, nm; member
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/dports/biology/samtools/samtools-1.14/misc/ |
H A D | ace2sam.c | 73 long m_cigar = 0, n_cigar = 0; in main() local
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/dports/biology/ugene/ugene-40.1/src/libs_3rdparty/samtools/src/samtools/ |
H A D | kaln.c | 89 static uint32_t *ka_path2cigar32(const path_t *path, int path_len, int *n_cigar) in ka_path2cigar32() 199 …(uint8_t *seq1, int len1, uint8_t *seq2, int len2, const ka_param_t *ap, int *_score, int *n_cigar) in ka_global_core()
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/dports/biology/stringtie/stringtie-2.1.1/samtools-0.1.18/ |
H A D | kaln.c | 89 static uint32_t *ka_path2cigar32(const path_t *path, int path_len, int *n_cigar) in ka_path2cigar32() 199 …(uint8_t *seq1, int len1, uint8_t *seq2, int len2, const ka_param_t *ap, int *_score, int *n_cigar) in ka_global_core()
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/dports/biology/seqan1/seqan-1.3.1/lib/samtools/ |
H A D | kaln.c | 89 static uint32_t *ka_path2cigar32(const path_t *path, int path_len, int *n_cigar) in ka_path2cigar32() 199 …(uint8_t *seq1, int len1, uint8_t *seq2, int len2, const ka_param_t *ap, int *_score, int *n_cigar) in ka_global_core()
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/dports/biology/freebayes/freebayes-1.3.5/contrib/htslib/ |
H A D | sam.c | 475 static void bam_cigar2rqlens(int n_cigar, const uint32_t *cigar, in bam_cigar2rqlens() 501 size_t n_cigar, const uint32_t *cigar, in bam_set1() 610 hts_pos_t bam_cigar2qlen(int n_cigar, const uint32_t *cigar) in bam_cigar2qlen() 620 hts_pos_t bam_cigar2rlen(int n_cigar, const uint32_t *cigar) in bam_cigar2rlen() 2153 int n_cigar = bam_parse_cigar(p, &p, b); in sam_parse1() local 2323 uint32_t n_cigar = 0; in read_ncigar() local 2344 static int parse_cigar(const char *in, uint32_t *a_cigar, uint32_t n_cigar) { in parse_cigar() 2374 size_t n_cigar = 0; in sam_parse_cigar() local 2407 size_t n_cigar = 0; in bam_parse_cigar() local
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/dports/biology/stacks/stacks-2.4/src/ |
H A D | BamI.h | 281 uint32_t BamRecord::cig_ref_len(const uint32_t* cigar, uint32_t n_cigar) { in cig_ref_len()
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/dports/www/h2o-devel/h2o-dcc7134/deps/klib/ |
H A D | ksw.c | 445 static inline uint32_t *push_cigar(int *n_cigar, int *m_cigar, uint32_t *cigar, int op, int len) in push_cigar() 514 int n_cigar = 0, m_cigar = 0, which = 0; in ksw_global() local
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/dports/biology/py-pysam/pysam-0.18.0/htslib/ |
H A D | sam.c | 477 static void bam_cigar2rqlens(int n_cigar, const uint32_t *cigar, in bam_cigar2rqlens() 503 size_t n_cigar, const uint32_t *cigar, in bam_set1() 612 hts_pos_t bam_cigar2qlen(int n_cigar, const uint32_t *cigar) in bam_cigar2qlen() 622 hts_pos_t bam_cigar2rlen(int n_cigar, const uint32_t *cigar) in bam_cigar2rlen() 2707 int n_cigar = bam_parse_cigar(p, &p, b); in sam_parse1() local 2793 uint32_t n_cigar = 0; in read_ncigar() local 2814 static int parse_cigar(const char *in, uint32_t *a_cigar, uint32_t n_cigar) { in parse_cigar() 2844 size_t n_cigar = 0; in sam_parse_cigar() local 2877 size_t n_cigar = 0; in bam_parse_cigar() local
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/dports/biology/htslib/htslib-1.14/ |
H A D | sam.c | 477 static void bam_cigar2rqlens(int n_cigar, const uint32_t *cigar, in bam_cigar2rqlens() 503 size_t n_cigar, const uint32_t *cigar, in bam_set1() 612 hts_pos_t bam_cigar2qlen(int n_cigar, const uint32_t *cigar) in bam_cigar2qlen() 622 hts_pos_t bam_cigar2rlen(int n_cigar, const uint32_t *cigar) in bam_cigar2rlen() 2707 int n_cigar = bam_parse_cigar(p, &p, b); in sam_parse1() local 2793 uint32_t n_cigar = 0; in read_ncigar() local 2814 static int parse_cigar(const char *in, uint32_t *a_cigar, uint32_t n_cigar) { in parse_cigar() 2844 size_t n_cigar = 0; in sam_parse_cigar() local 2877 size_t n_cigar = 0; in bam_parse_cigar() local
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/dports/biology/emboss/EMBOSS-6.6.0/ajax/core/ |
H A D | ajseqbam.h | 322 ajushort n_cigar; member
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/dports/biology/py-pysam/pysam-0.18.0/samtools/ |
H A D | bam2depth.c | 123 int n_cigar = b->core.n_cigar; in qlen_used() local
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H A D | bam2depth.c.pysam.c | 125 int n_cigar = b->core.n_cigar; in qlen_used() local
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/dports/biology/samtools/samtools-1.14/ |
H A D | bam2depth.c | 123 int n_cigar = b->core.n_cigar; in qlen_used() local
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/dports/biology/vt/vt-0.57721/lib/htslib/ |
H A D | sam.c | 329 void bam_cigar2rqlens(int n_cigar, const uint32_t *cigar, int *rlen, int *qlen) in bam_cigar2rqlens() 341 int bam_cigar2qlen(int n_cigar, const uint32_t *cigar) in bam_cigar2qlen() 350 int bam_cigar2rlen(int n_cigar, const uint32_t *cigar) in bam_cigar2rlen() 1230 size_t n_cigar = 0; in sam_parse1() local
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