/dports/biology/canu/canu-2.2/src/utility/src/utility/ |
H A D | align-ksw2.H | 29 int m_cigar, n_cigar; member 105 if (*n_cigar == 0 || op != (cigar[(*n_cigar) - 1]&0xf)) { in ksw_push_cigar() 106 if (*n_cigar == *m_cigar) { in ksw_push_cigar() 110 cigar[(*n_cigar)++] = len<<4 | op; in ksw_push_cigar() 111 } else cigar[(*n_cigar)-1] += len<<4; in ksw_push_cigar() 122 int n_cigar = 0, m_cigar = *m_cigar_, i = i0, j = j0, r, state = 0; in ksw_backtrack() local 143 else cigar = ksw_push_cigar(km, &n_cigar, &m_cigar, cigar, 1, 1), --j; // insertion in ksw_backtrack() 148 for (i = 0; i < n_cigar>>1; ++i) // reverse CIGAR in ksw_backtrack() 149 tmp = cigar[i], cigar[i] = cigar[n_cigar-1-i], cigar[n_cigar-1-i] = tmp; in ksw_backtrack() 150 *m_cigar_ = m_cigar, *n_cigar_ = n_cigar, *cigar_ = cigar; in ksw_backtrack() [all …]
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/dports/biology/mmseqs2/MMseqs2-13-45111/lib/ksw2/ |
H A D | ksw2.h | 56 int m_cigar, n_cigar; member 131 if (*n_cigar == 0 || op != (cigar[(*n_cigar) - 1]&0xf)) { in ksw_push_cigar() 132 if (*n_cigar == *m_cigar) { in ksw_push_cigar() 136 cigar[(*n_cigar)++] = len<<4 | op; in ksw_push_cigar() 137 } else cigar[(*n_cigar)-1] += len<<4; in ksw_push_cigar() 148 int n_cigar = 0, m_cigar = *m_cigar_, i = i0, j = j0, r, state = 0; in ksw_backtrack() local 169 else cigar = ksw_push_cigar(km, &n_cigar, &m_cigar, cigar, 1, 1), --j; // insertion in ksw_backtrack() 174 for (i = 0; i < n_cigar>>1; ++i) // reverse CIGAR in ksw_backtrack() 175 tmp = cigar[i], cigar[i] = cigar[n_cigar-1-i], cigar[n_cigar-1-i] = tmp; in ksw_backtrack() 176 *m_cigar_ = m_cigar, *n_cigar_ = n_cigar, *cigar_ = cigar; in ksw_backtrack() [all …]
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/dports/biology/minimap2/minimap2-2.24/ |
H A D | ksw2.h | 36 int m_cigar, n_cigar; member 112 if (*n_cigar == 0 || op != (cigar[(*n_cigar) - 1]&0xf)) { in ksw_push_cigar() 113 if (*n_cigar == *m_cigar) { in ksw_push_cigar() 117 cigar[(*n_cigar)++] = len<<4 | op; in ksw_push_cigar() 118 } else cigar[(*n_cigar)-1] += len<<4; in ksw_push_cigar() 129 int n_cigar = 0, m_cigar = *m_cigar_, i = i0, j = j0, r, state = 0; in ksw_backtrack() local 150 else cigar = ksw_push_cigar(km, &n_cigar, &m_cigar, cigar, KSW_CIGAR_INS, 1), --j; in ksw_backtrack() 155 for (i = 0; i < n_cigar>>1; ++i) // reverse CIGAR in ksw_backtrack() 156 tmp = cigar[i], cigar[i] = cigar[n_cigar-1-i], cigar[n_cigar-1-i] = tmp; in ksw_backtrack() 157 *m_cigar_ = m_cigar, *n_cigar_ = n_cigar, *cigar_ = cigar; in ksw_backtrack() [all …]
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H A D | align.c | 150 p->n_cigar = l; in mm_fix_cigar() 155 p->n_cigar = l; in mm_fix_cigar() 164 --p->n_cigar; in mm_fix_cigar() 235 p->n_cigar = m; in mm_update_cigar_eqx() 300 } else if (r->p->n_cigar + n_cigar + sizeof(mm_extra_t)/4 > r->p->capacity) { in mm_append_cigar() 301 r->p->capacity = r->p->n_cigar + n_cigar + sizeof(mm_extra_t)/4; in mm_append_cigar() 308 if (n_cigar > 1) memcpy(p->cigar + p->n_cigar, cigar + 1, (n_cigar - 1) * 4); in mm_append_cigar() 309 p->n_cigar += n_cigar - 1; in mm_append_cigar() 311 memcpy(p->cigar + p->n_cigar, cigar, n_cigar * 4); in mm_append_cigar() 312 p->n_cigar += n_cigar; in mm_append_cigar() [all …]
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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 136 if (l_M) write_cigar(cigar, n_cigar, m_cigar, l_M<<4); \ in main() 137 else write_cigar(cigar, n_cigar, m_cigar, l_D<<4 | 2); \ in main() 141 n_cigar = 0; in main() 145 for (i = 0; i < n_cigar; ++i) { in main() 203 n_cigar = 0; in main() 208 … if (end < t[2].l && n_cigar) cigar[n_cigar-1] -= (t[2].l - end)<<4; // fix the right-hand CIGAR in main() 220 write_cigar(cigar, n_cigar, m_cigar, k<<4|op); in main() 222 for (i = 2; i < n_cigar; ++i) { in main() 231 n_cigar = k; in main() [all …]
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/dports/biology/rainbow/rainbow_2.0.4/ |
H A D | aln_cigar.h | 47 for(i=0;i<n_cigar;i++){ in cigars_lengths() 70 cs[n_cigar].len = len; in _aln_cigar_add_cigar() 73 cs[n_cigar++].type = type; in _aln_cigar_add_cigar() 75 return n_cigar; in _aln_cigar_add_cigar() 87 if(n_cigar){ in cigars2string() 90 for(i=1;i<=n_cigar;i++){ in cigars2string() 102 if(i == n_cigar) break; in cigars2string() 179 for(i=0,ret=0;i<n_cigar;i++){ in select_cigars_seqlen() 197 for(i=n_cigar-1,ret=0;i>=0;i--){ in rev_select_cigars_seqlen() 215 for(i=0;i<n_cigar;i++){ in flip_cigars() [all …]
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/dports/biology/bwa/bwa-0.7.17/ |
H A D | bwase.c | 185 assert(*n_cigar > 0); in bwa_refine_gapped_core() 186 …if ((cigar32[*n_cigar - 1]&0xf) == 1) cigar32[*n_cigar - 1] = (cigar32[*n_cigar - 1]>>4<<4) | 3; /… in bwa_refine_gapped_core() 188 if ((cigar32[*n_cigar - 1]&0xf) == 2) --*n_cigar; // delete endding del in bwa_refine_gapped_core() 191 --*n_cigar; in bwa_refine_gapped_core() 195 for (k = 0; k < *n_cigar; ++k) in bwa_refine_gapped_core() 259 s->n_cigar = 2; in bwa_correct_trimmed() 263 ++s->n_cigar; in bwa_correct_trimmed() 273 s->n_cigar = 2; in bwa_correct_trimmed() 277 ++s->n_cigar; in bwa_correct_trimmed() 303 int n_cigar; in bwa_refine_gapped() local [all …]
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H A D | bamlite.h | 62 uint32_t flag:16, n_cigar:16; member 83 #define bam1_seq(b) ((b)->data + (b)->core.n_cigar*4 + (b)->core.l_qname) 84 #define bam1_qual(b) ((b)->data + (b)->core.n_cigar*4 + (b)->core.l_qname + (((b)->core.l_qseq + 1)… 86 #define bam1_aux(b) ((b)->data + (b)->core.n_cigar*4 + (b)->core.l_qname + (b)->core.l_qseq + ((b)-…
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/dports/biology/py-pysam/pysam-0.18.0/samtools/ |
H A D | bam.c | 74 for (k = 0; k < b->core.n_cigar; ++k) in bam_remove_B() 76 if (k == b->core.n_cigar) return 0; // no 'B' in bam_remove_B() 79 if (b->l_data + (b->core.n_cigar + 1) * 4 > b->m_data) { // not enough memory in bam_remove_B() 80 b->m_data = b->l_data + b->core.n_cigar * 4; in bam_remove_B() 85 new_cigar = (uint32_t*)(b->data + (b->m_data - b->core.n_cigar * 4)); // from the end of b->data in bam_remove_B() 90 for (k = l = 0; k < b->core.n_cigar; ++k) { in bam_remove_B() 95 if (k == b->core.n_cigar - 1) break; // ignore 'B' at the end of CIGAR in bam_remove_B() 151 b->core.n_cigar = l, b->core.l_qseq = j; // update CIGAR length and query length in bam_remove_B()
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H A D | bam.c.pysam.c | 76 for (k = 0; k < b->core.n_cigar; ++k) in bam_remove_B() 78 if (k == b->core.n_cigar) return 0; // no 'B' in bam_remove_B() 81 if (b->l_data + (b->core.n_cigar + 1) * 4 > b->m_data) { // not enough memory in bam_remove_B() 82 b->m_data = b->l_data + b->core.n_cigar * 4; in bam_remove_B() 87 new_cigar = (uint32_t*)(b->data + (b->m_data - b->core.n_cigar * 4)); // from the end of b->data in bam_remove_B() 92 for (k = l = 0; k < b->core.n_cigar; ++k) { in bam_remove_B() 97 if (k == b->core.n_cigar - 1) break; // ignore 'B' at the end of CIGAR in bam_remove_B() 153 b->core.n_cigar = l, b->core.l_qseq = j; // update CIGAR length and query length in bam_remove_B()
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H A D | padding.c | 44 if (n != b->core.n_cigar) { in replace_cigar() 45 int o = b->core.l_qname + b->core.n_cigar * 4; in replace_cigar() 46 if (n > b->core.n_cigar) { in replace_cigar() 47 diff = (n - b->core.n_cigar) * 4; in replace_cigar() 48 if ((INT_MAX - b->l_data)/4 < (n - b->core.n_cigar)) { in replace_cigar() 63 diff = -(int)((b->core.n_cigar - n) * 4); in replace_cigar() 66 b->core.n_cigar = n; in replace_cigar() 99 length = bam_cigar2rlen(b->core.n_cigar, cigar); in unpad_seq() 101 for (k = 0, s->l = 0, j = 0; k < b->core.n_cigar; ++k) { in unpad_seq() 263 } else if (b->core.n_cigar > 0) { in bam_pad2unpad() [all …]
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H A D | padding.c.pysam.c | 46 if (n != b->core.n_cigar) { in replace_cigar() 47 int o = b->core.l_qname + b->core.n_cigar * 4; in replace_cigar() 48 if (n > b->core.n_cigar) { in replace_cigar() 49 diff = (n - b->core.n_cigar) * 4; in replace_cigar() 50 if ((INT_MAX - b->l_data)/4 < (n - b->core.n_cigar)) { in replace_cigar() 65 diff = -(int)((b->core.n_cigar - n) * 4); in replace_cigar() 68 b->core.n_cigar = n; in replace_cigar() 101 length = bam_cigar2rlen(b->core.n_cigar, cigar); in unpad_seq() 103 for (k = 0, s->l = 0, j = 0; k < b->core.n_cigar; ++k) { in unpad_seq() 265 } else if (b->core.n_cigar > 0) { in bam_pad2unpad() [all …]
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/dports/biology/samtools/samtools-1.14/ |
H A D | bam.c | 74 for (k = 0; k < b->core.n_cigar; ++k) in bam_remove_B() 76 if (k == b->core.n_cigar) return 0; // no 'B' in bam_remove_B() 79 if (b->l_data + (b->core.n_cigar + 1) * 4 > b->m_data) { // not enough memory in bam_remove_B() 80 b->m_data = b->l_data + b->core.n_cigar * 4; in bam_remove_B() 85 new_cigar = (uint32_t*)(b->data + (b->m_data - b->core.n_cigar * 4)); // from the end of b->data in bam_remove_B() 90 for (k = l = 0; k < b->core.n_cigar; ++k) { in bam_remove_B() 95 if (k == b->core.n_cigar - 1) break; // ignore 'B' at the end of CIGAR in bam_remove_B() 151 b->core.n_cigar = l, b->core.l_qseq = j; // update CIGAR length and query length in bam_remove_B()
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H A D | padding.c | 44 if (n != b->core.n_cigar) { in replace_cigar() 45 int o = b->core.l_qname + b->core.n_cigar * 4; in replace_cigar() 46 if (n > b->core.n_cigar) { in replace_cigar() 47 diff = (n - b->core.n_cigar) * 4; in replace_cigar() 48 if ((INT_MAX - b->l_data)/4 < (n - b->core.n_cigar)) { in replace_cigar() 63 diff = -(int)((b->core.n_cigar - n) * 4); in replace_cigar() 66 b->core.n_cigar = n; in replace_cigar() 99 length = bam_cigar2rlen(b->core.n_cigar, cigar); in unpad_seq() 101 for (k = 0, s->l = 0, j = 0; k < b->core.n_cigar; ++k) { in unpad_seq() 263 } else if (b->core.n_cigar > 0) { in bam_pad2unpad() [all …]
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/dports/biology/stringtie/stringtie-2.1.1/gclib/ |
H A D | GBam.cpp | 90 int d=b->core.l_qname + b->core.n_cigar * 4;//offset of after-cigar data in set_cigar() 98 b->core.n_cigar = 0; in set_cigar() 101 if (isalpha(*s)) b->core.n_cigar++; in set_cigar() 112 realloc_bdata(b, doff + b->core.n_cigar * 4); in set_cigar() 114 for (i = 0, s = cigar; i != b->core.n_cigar; ++i) { in set_cigar() 144 int doff = b->core.l_qname + b->core.n_cigar * 4; in add_sequence() 325 uint32_t *cigar= new uint32_t[c->n_cigar]; in setupCoordinates() 326 memcpy(cigar, p, c->n_cigar * sizeof(uint32_t)); in setupCoordinates() 334 for (int i = 0; i < c->n_cigar; ++i) { in setupCoordinates() 436 if (b->core.n_cigar == 0) kputc('*', &str); in cigar() [all …]
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/dports/biology/freebayes/freebayes-1.3.5/contrib/SeqLib/src/ |
H A D | BamRecord.cpp | 58 uint32_t* cig_last = bam_get_cigar(b) + b->core.n_cigar - 1; in PositionEndWithSClips() 97 if (c.size() == b->core.n_cigar) { in SetCigar() 98 b->core.n_cigar = c.size(); in SetCigar() 100 for (size_t i = 0; i < b->core.n_cigar; ++i) in SetCigar() 111 int old_seqaux_spot = (b->core.n_cigar<<2) + b->core.l_qname; in SetCigar() 115 b->core.n_cigar = c.size(); in SetCigar() 137 b->core.n_cigar = c.size(); in SetCigar() 158 b->core.n_cigar = alignment.cigar.size(); in BamRecord() 603 b->core.n_cigar = cig.size(); in BamRecord() 723 for (int k = 0; k < b->core.n_cigar; ++k) { in OverlappingCoverage() [all …]
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/dports/biology/gffread/gffread-0.12.7/gclib/ |
H A D | GBam.cpp | 93 int d=b->core.l_qname + b->core.n_cigar * 4;//offset of after-cigar data in set_cigar() 101 b->core.n_cigar = 0; in set_cigar() 104 if (isalpha(*s)) b->core.n_cigar++; in set_cigar() 110 prev_bdata=dupalloc_bdata(b, doff + b->core.n_cigar * 4 + after_cigar_len); in set_cigar() 115 realloc_bdata(b, doff + b->core.n_cigar * 4); in set_cigar() 117 for (i = 0, s = cigar; i != b->core.n_cigar; ++i) { in set_cigar() 147 int doff = b->core.l_qname + b->core.n_cigar * 4; in add_sequence() 164 uint8_t* p = b->data+(b->core.l_qname + b->core.n_cigar * 4 + (b->core.l_qseq+1)/2); in add_quals() 341 for (int i = 0; i < c->n_cigar; ++i) { in setupCoordinates() 477 if (b->core.n_cigar == 0) kputc('*', &str); in cigar() [all …]
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/dports/biology/freebayes/freebayes-1.3.5/contrib/SeqLib/SeqLib/ |
H A D | BamRecord.h | 507 for (size_t i = 0; i < b->core.n_cigar; i++) in NumAlignedBases() 522 for (size_t i = 0; i < b->core.n_cigar; i++) in MaxInsertionBases() 532 for (size_t i = 0; i < b->core.n_cigar; i++) in MaxDeletionBases() 542 for (size_t i = 0; i < b->core.n_cigar; i++) in NumMatchBases() 553 for (size_t k = 0; k < b->core.n_cigar; ++k) { in GetCigar() 563 for (int k = b->core.n_cigar - 1; k >= 0; --k) in GetReverseCigar() 641 for (size_t i = 0; i < b->core.n_cigar; ++i) { in AlignmentPosition() 668 for (size_t i = 0; i < b->core.n_cigar; ++i) in NumSoftClip() 678 for (size_t i = 0; i < b->core.n_cigar; ++i) in NumHardClip() 689 for (size_t i = 0; i < b->core.n_cigar; ++i) in NumClip() [all …]
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/dports/biology/vt/vt-0.57721/lib/htslib/ |
H A D | sam.c | 333 for (k = 0; k < n_cigar; ++k) { in bam_cigar2rqlens() 344 for (k = l = 0; k < n_cigar; ++k) in bam_cigar2qlen() 353 for (k = l = 0; k < n_cigar; ++k) in bam_cigar2rlen() 377 fake_bytes = c->n_cigar * 4; in bam_tag2cigar() 385 c->n_cigar = CG_len; in bam_tag2cigar() 386 n_cigar4 = c->n_cigar * 4; in bam_tag2cigar() 540 u32_to_le(c->n_cigar, buf); in bam_write1() 1230 size_t n_cigar = 0; in sam_parse1() local 1236 c->n_cigar = n_cigar; in sam_parse1() 1469 if (c->n_cigar) { // cigar in sam_format1() [all …]
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/dports/biology/stacks/stacks-2.4/htslib/ |
H A D | sam.c | 333 for (k = 0; k < n_cigar; ++k) { in bam_cigar2rqlens() 344 for (k = l = 0; k < n_cigar; ++k) in bam_cigar2qlen() 353 for (k = l = 0; k < n_cigar; ++k) in bam_cigar2rlen() 377 fake_bytes = c->n_cigar * 4; in bam_tag2cigar() 385 c->n_cigar = CG_len; in bam_tag2cigar() 386 n_cigar4 = c->n_cigar * 4; in bam_tag2cigar() 540 u32_to_le(c->n_cigar, buf); in bam_write1() 1226 size_t n_cigar = 0; in sam_parse1() local 1232 c->n_cigar = n_cigar; in sam_parse1() 1465 if (c->n_cigar) { // cigar in sam_format1() [all …]
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/dports/biology/freebayes/freebayes-1.3.5/contrib/htslib/ |
H A D | sam.c | 574 bam->core.n_cigar = (uint32_t)n_cigar; in bam_set1() 588 if (n_cigar > 0) { in bam_set1() 591 cp += n_cigar * 4; in bam_set1() 661 c->n_cigar = CG_len; in bam_tag2cigar() 2156 c->n_cigar = n_cigar; in sam_parse1() 2326 if (!n_cigar) { in read_ncigar() 2335 return n_cigar; in read_ncigar() 2374 size_t n_cigar = 0; in sam_parse_cigar() local 2403 return n_cigar; in sam_parse_cigar() 2407 size_t n_cigar = 0; in bam_parse_cigar() local [all …]
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/dports/biology/vt/vt-0.57721/lib/htslib/htslib/ |
H A D | sam.h | 166 uint32_t n_cigar; member 238 #define bam_get_seq(b) ((b)->data + ((b)->core.n_cigar<<2) + (b)->core.l_qname) 244 #define bam_get_qual(b) ((b)->data + ((b)->core.n_cigar<<2) + (b)->core.l_qname + (((b)->core.l_qs… 250 #define bam_get_aux(b) ((b)->data + ((b)->core.n_cigar<<2) + (b)->core.l_qname + (((b)->core.l_qs… 256 #define bam_get_l_aux(b) ((b)->l_data - ((b)->core.n_cigar<<2) - (b)->core.l_qname - (b)->core.l_qs… 287 int bam_cigar2qlen(int n_cigar, const uint32_t *cigar); 288 int bam_cigar2rlen(int n_cigar, const uint32_t *cigar);
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/dports/biology/bedtools/bedtools2-2.30.0/src/utils/htslib/htslib/ |
H A D | sam.h | 166 uint32_t n_cigar; member 238 #define bam_get_seq(b) ((b)->data + ((b)->core.n_cigar<<2) + (b)->core.l_qname) 244 #define bam_get_qual(b) ((b)->data + ((b)->core.n_cigar<<2) + (b)->core.l_qname + (((b)->core.l_qs… 250 #define bam_get_aux(b) ((b)->data + ((b)->core.n_cigar<<2) + (b)->core.l_qname + (((b)->core.l_qs… 256 #define bam_get_l_aux(b) ((b)->l_data - ((b)->core.n_cigar<<2) - (b)->core.l_qname - (b)->core.l_qs… 287 int bam_cigar2qlen(int n_cigar, const uint32_t *cigar); 288 int bam_cigar2rlen(int n_cigar, const uint32_t *cigar);
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/dports/biology/stacks/stacks-2.4/htslib/htslib/ |
H A D | sam.h | 166 uint32_t n_cigar; member 238 #define bam_get_seq(b) ((b)->data + ((b)->core.n_cigar<<2) + (b)->core.l_qname) 244 #define bam_get_qual(b) ((b)->data + ((b)->core.n_cigar<<2) + (b)->core.l_qname + (((b)->core.l_qs… 250 #define bam_get_aux(b) ((b)->data + ((b)->core.n_cigar<<2) + (b)->core.l_qname + (((b)->core.l_qs… 256 #define bam_get_l_aux(b) ((b)->l_data - ((b)->core.n_cigar<<2) - (b)->core.l_qname - (b)->core.l_qs… 287 int bam_cigar2qlen(int n_cigar, const uint32_t *cigar); 288 int bam_cigar2rlen(int n_cigar, const uint32_t *cigar);
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/dports/biology/kallisto/kallisto-0.46.1/ext/htslib/htslib/ |
H A D | sam.h | 159 uint32_t n_cigar; member 231 #define bam_get_seq(b) ((b)->data + ((b)->core.n_cigar<<2) + (b)->core.l_qname) 237 #define bam_get_qual(b) ((b)->data + ((b)->core.n_cigar<<2) + (b)->core.l_qname + (((b)->core.l_qs… 243 #define bam_get_aux(b) ((b)->data + ((b)->core.n_cigar<<2) + (b)->core.l_qname + (((b)->core.l_qs… 249 #define bam_get_l_aux(b) ((b)->l_data - ((b)->core.n_cigar<<2) - (b)->core.l_qname - (b)->core.l_qs… 280 int bam_cigar2qlen(int n_cigar, const uint32_t *cigar); 281 int bam_cigar2rlen(int n_cigar, const uint32_t *cigar);
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