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Searched defs:n_cigar (Results 1 – 25 of 46) sorted by relevance

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/dports/biology/rainbow/rainbow_2.0.4/
H A Daln_cigar.h42 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()
/dports/biology/canu/canu-2.2/src/utility/src/utility/
H A Dalign-ksw2.H29 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
/dports/biology/mmseqs2/MMseqs2-13-45111/lib/ksw2/
H A Dksw2.h56 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
/dports/biology/minimap2/minimap2-2.24/
H A Dksw2.h36 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
/dports/biology/bwa/bwa-0.7.17/
H A Dbwase.c169 …_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
H A Dbwa.c121 …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()
H A Dbwtaln.h60 uint32_t n_cigar:15, gap:8, mm:8, strand:1; member
83 int n_cigar; member
H A Dbwtsw2_pair.c98 int n_cigar, beg, end, len; member
H A Dbwape.c409 …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
H A Dbamlite.h62 uint32_t flag:16, n_cigar:16; member
H A Dbwtsw2.h30 int flag, nn, n_cigar, chr, pos, qual, mchr, mpos, pqual, isize, nm; member
/dports/biology/samtools/samtools-1.14/misc/
H A Dace2sam.c73 long m_cigar = 0, n_cigar = 0; in main() local
/dports/biology/ugene/ugene-40.1/src/libs_3rdparty/samtools/src/samtools/
H A Dkaln.c89 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()
/dports/biology/stringtie/stringtie-2.1.1/samtools-0.1.18/
H A Dkaln.c89 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()
/dports/biology/seqan1/seqan-1.3.1/lib/samtools/
H A Dkaln.c89 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()
/dports/biology/freebayes/freebayes-1.3.5/contrib/htslib/
H A Dsam.c475 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
/dports/biology/stacks/stacks-2.4/src/
H A DBamI.h281 uint32_t BamRecord::cig_ref_len(const uint32_t* cigar, uint32_t n_cigar) { in cig_ref_len()
/dports/www/h2o-devel/h2o-dcc7134/deps/klib/
H A Dksw.c445 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
/dports/biology/py-pysam/pysam-0.18.0/htslib/
H A Dsam.c477 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
/dports/biology/htslib/htslib-1.14/
H A Dsam.c477 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
/dports/biology/emboss/EMBOSS-6.6.0/ajax/core/
H A Dajseqbam.h322 ajushort n_cigar; member
/dports/biology/py-pysam/pysam-0.18.0/samtools/
H A Dbam2depth.c123 int n_cigar = b->core.n_cigar; in qlen_used() local
H A Dbam2depth.c.pysam.c125 int n_cigar = b->core.n_cigar; in qlen_used() local
/dports/biology/samtools/samtools-1.14/
H A Dbam2depth.c123 int n_cigar = b->core.n_cigar; in qlen_used() local
/dports/biology/vt/vt-0.57721/lib/htslib/
H A Dsam.c329 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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