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Searched refs:n_cigar (Results 1 – 25 of 198) sorted by relevance

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/dports/biology/canu/canu-2.2/src/utility/src/utility/
H A Dalign-ksw2.H29 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 …]
/dports/biology/mmseqs2/MMseqs2-13-45111/lib/ksw2/
H A Dksw2.h56 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 …]
/dports/biology/minimap2/minimap2-2.24/
H A Dksw2.h36 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 …]
H A Dalign.c150 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()
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/dports/biology/samtools/samtools-1.14/misc/
H A Dace2sam.c73 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()
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/dports/biology/rainbow/rainbow_2.0.4/
H A Daln_cigar.h47 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 …]
/dports/biology/bwa/bwa-0.7.17/
H A Dbwase.c185 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
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H A Dbamlite.h62 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)-…
/dports/biology/py-pysam/pysam-0.18.0/samtools/
H A Dbam.c74 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()
H A Dbam.c.pysam.c76 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()
H A Dpadding.c44 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 …]
H A Dpadding.c.pysam.c46 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 …]
/dports/biology/samtools/samtools-1.14/
H A Dbam.c74 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()
H A Dpadding.c44 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 …]
/dports/biology/stringtie/stringtie-2.1.1/gclib/
H A DGBam.cpp90 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 …]
/dports/biology/freebayes/freebayes-1.3.5/contrib/SeqLib/src/
H A DBamRecord.cpp58 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 …]
/dports/biology/gffread/gffread-0.12.7/gclib/
H A DGBam.cpp93 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 …]
/dports/biology/freebayes/freebayes-1.3.5/contrib/SeqLib/SeqLib/
H A DBamRecord.h507 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 …]
/dports/biology/vt/vt-0.57721/lib/htslib/
H A Dsam.c333 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 …]
/dports/biology/stacks/stacks-2.4/htslib/
H A Dsam.c333 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 …]
/dports/biology/freebayes/freebayes-1.3.5/contrib/htslib/
H A Dsam.c574 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 …]
/dports/biology/vt/vt-0.57721/lib/htslib/htslib/
H A Dsam.h166 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);
/dports/biology/bedtools/bedtools2-2.30.0/src/utils/htslib/htslib/
H A Dsam.h166 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);
/dports/biology/stacks/stacks-2.4/htslib/htslib/
H A Dsam.h166 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);
/dports/biology/kallisto/kallisto-0.46.1/ext/htslib/htslib/
H A Dsam.h159 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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