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Replace "Short" CIGAR in SA tag with "Full Length" CIGAR? #287

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Replace "Short" CIGAR in SA tag with "Full Length" CIGAR? #287

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dda9466
SA full lenght CIGAR
Archieyoung Dec 3, 2018
70bb6ed
fix SA full lenght CIGAR by repace r with q
Archieyoung Dec 3, 2018
4600430
fix SA full lenght CIGAR by restore the missing print of chr and pos
Archieyoung Dec 3, 2018
0b954ce
remove comment
Archieyoung Dec 3, 2018
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23 changes: 13 additions & 10 deletions format.c
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Original file line number Diff line number Diff line change
Expand Up @@ -506,18 +506,21 @@ void mm_write_sam2(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, int se
mm_sprintf_lite(s, "\tSA:Z:");
for (i = 0; i < n_regs; ++i) {
const mm_reg1_t *q = &regs[i];
int l_M, l_I = 0, l_D = 0, clip5 = 0, clip3 = 0;
if (r == q || q->parent != q->id || q->p == 0) continue;
if (q->qe - q->qs < q->re - q->rs) l_M = q->qe - q->qs, l_D = (q->re - q->rs) - l_M;
else l_M = q->re - q->rs, l_I = (q->qe - q->qs) - l_M;
clip5 = q->rev? t->l_seq - q->qe : q->qs;
clip3 = q->rev? q->qs : t->l_seq - q->qe;

uint32_t k, clip_len[2];

clip_len[0] = q->rev? t->l_seq - q->qe : q->qs;
clip_len[1] = q->rev? q->qs : t->l_seq - q->qe;

mm_sprintf_lite(s, "%s,%d,%c,", mi->seq[q->rid].name, q->rs+1, "+-"[q->rev]);
if (clip5) mm_sprintf_lite(s, "%dS", clip5);
if (l_M) mm_sprintf_lite(s, "%dM", l_M);
if (l_I) mm_sprintf_lite(s, "%dI", l_I);
if (l_D) mm_sprintf_lite(s, "%dD", l_D);
if (clip3) mm_sprintf_lite(s, "%dS", clip3);

int clip_char = !(opt_flag&MM_F_SOFTCLIP)? 'H' : 'S';
if (clip_len[0]) mm_sprintf_lite(s, "%d%c", clip_len[0], clip_char);
for (k = 0; k < q->p->n_cigar; ++k)
mm_sprintf_lite(s, "%d%c", q->p->cigar[k]>>4, "MIDNSHP=XB"[q->p->cigar[k]&0xf]);
if (clip_len[1]) mm_sprintf_lite(s, "%d%c", clip_len[1], clip_char);

mm_sprintf_lite(s, ",%d,%d;", q->mapq, q->blen - q->mlen + q->p->n_ambi);
}
}
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