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r467: added : (equal length) and ^ (intron) ops

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This commit is contained in:
Heng Li
2017-10-04 21:55:37 -04:00
parent 7d50e646dd
commit 9aba11769c
3 changed files with 19 additions and 8 deletions
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format.c
+16 -8
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@@ -127,7 +127,7 @@ void mm_write_sam_hdr(const mm_idx_t *idx, const char *rg, const char *ver, int
free(str.s);
}
static void write_cs(void *km, kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, const mm_reg1_t *r)
static void write_cs(void *km, kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, const mm_reg1_t *r, int no_iden)
{
extern unsigned char seq_nt4_table[256];
int i, q_off, t_off;
@@ -150,22 +150,26 @@ static void write_cs(void *km, kstring_t *s, const mm_idx_t *mi, const mm_bseq1_
}
for (i = q_off = t_off = 0; i < r->p->n_cigar; ++i) {
int j, op = r->p->cigar[i]&0xf, len = r->p->cigar[i]>>4;
assert(op >= 0 && op <= 2);
assert(op >= 0 && op <= 3);
if (op == 0) {
int l_tmp = 0;
for (j = 0; j < len; ++j) {
if (qseq[q_off + j] != tseq[t_off + j]) {
if (l_tmp > 0) {
tmp[l_tmp] = 0;
mm_sprintf_lite(s, "=%s", tmp);
if (!no_iden) {
tmp[l_tmp] = 0;
mm_sprintf_lite(s, "=%s", tmp);
} else mm_sprintf_lite(s, ":%d", l_tmp);
l_tmp = 0;
}
mm_sprintf_lite(s, "*%c%c", "acgtn"[tseq[t_off + j]], "acgtn"[qseq[q_off + j]]);
} else tmp[l_tmp++] = "ACGTN"[qseq[q_off + j]];
}
if (l_tmp > 0) {
tmp[l_tmp] = 0;
mm_sprintf_lite(s, "=%s", tmp);
if (!no_iden) {
tmp[l_tmp] = 0;
mm_sprintf_lite(s, "=%s", tmp);
} else mm_sprintf_lite(s, ":%d", l_tmp);
}
q_off += len, t_off += len;
} else if (op == 1) {
@@ -173,11 +177,15 @@ static void write_cs(void *km, kstring_t *s, const mm_idx_t *mi, const mm_bseq1_
tmp[j] = "acgtn"[qseq[q_off + j]];
mm_sprintf_lite(s, "+%s", tmp);
q_off += len;
} else if (op == 2) {
} else if (op == 2 || (op == 3 && len < 4)) {
for (j = 0, tmp[len] = 0; j < len; ++j)
tmp[j] = "acgtn"[tseq[t_off + j]];
mm_sprintf_lite(s, "-%s", tmp);
t_off += len;
} else { // op == 3 && len >= 4
mm_sprintf_lite(s, "^%c%c%d%c%c", "acgtn"[tseq[t_off]], "acgtn"[tseq[t_off+1]],
len, "acgtn"[tseq[t_off+len-2]], "acgtn"[tseq[t_off+len-1]]);
t_off += len;
}
}
assert(t_off == r->re - r->rs && q_off == r->qe - r->qs);
@@ -215,7 +223,7 @@ void mm_write_paf(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, const m
mm_sprintf_lite(s, "%d%c", r->p->cigar[k]>>4, "MIDN"[r->p->cigar[k]&0xf]);
}
if (r->p && (opt_flag & MM_F_OUT_CS))
write_cs(km, s, mi, t, r);
write_cs(km, s, mi, t, r, opt_flag&MM_F_CS_NO_EQUAL);
}
static void sam_write_sq(kstring_t *s, char *seq, int l, int rev, int comp)