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r235: optionally output tag cs in PAF

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cs encodes the query, the reference sequence and CIGAR.
This commit is contained in:
Heng Li
2017-07-31 12:06:49 -04:00
parent 46de0fbdad
commit 4c0713ee14
5 changed files with 72 additions and 7 deletions
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format.c
+60 -2
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@@ -1,7 +1,9 @@
#include <stdarg.h>
#include <stdlib.h>
#include <string.h>
#include <assert.h>
#include <stdio.h>
#include "kalloc.h"
#include "mmpriv.h"
static inline void str_enlarge(kstring_t *s, int l)
@@ -54,6 +56,60 @@ static void mm_sprintf_lite(kstring_t *s, const char *fmt, ...)
s->s[s->l] = 0;
}
static void write_cs(void *km, kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, const mm_reg1_t *r)
{
extern unsigned char seq_nt4_table[256];
int i, q_off, t_off;
uint8_t *qseq, *tseq;
char *tmp;
if (r->p == 0) return;
mm_sprintf_lite(s, "\tcs:Z:");
qseq = (uint8_t*)kmalloc(km, r->qe - r->qs);
tseq = (uint8_t*)kmalloc(km, r->re - r->rs);
tmp = (char*)kmalloc(km, r->re - r->rs > r->qe - r->qs? r->re - r->rs + 1 : r->qe - r->qs + 1);
mm_idx_getseq(mi, r->rid, r->rs, r->re, tseq);
if (!r->rev) {
for (i = r->qs; i < r->qe; ++i)
qseq[i - r->qs] = seq_nt4_table[(uint8_t)t->seq[i]];
} else {
for (i = r->qs; i < r->qe; ++i)
qseq[r->qe - i - 1] = seq_nt4_table[(uint8_t)t->seq[i]];
}
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);
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);
}
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);
}
q_off += len, t_off += len;
} else if (op == 1) {
for (j = 0, tmp[len] = 0; j < len; ++j)
tmp[j] = "ACGTN"[qseq[q_off + j]];
mm_sprintf_lite(s, "+%s", tmp);
q_off += len;
} else if (op == 2) {
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;
}
}
assert(t_off == r->re - r->rs && q_off == r->qe - r->qs);
kfree(km, qseq); kfree(km, tseq); kfree(km, tmp);
}
static inline void write_tags(kstring_t *s, const mm_reg1_t *r)
{
int type = r->inv? 'I' : r->id == r->parent? 'P' : 'S';
@@ -63,7 +119,7 @@ static inline void write_tags(kstring_t *s, const mm_reg1_t *r)
if (r->p) mm_sprintf_lite(s, "\tNM:i:%d\tms:i:%d\tAS:i:%d\tnn:i:%d", r->p->n_diff, r->p->dp_max, r->p->dp_score, r->p->n_ambi);
}
void mm_write_paf(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, const mm_reg1_t *r)
void mm_write_paf(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, const mm_reg1_t *r, void *km, int opt_flag)
{
s->l = 0;
mm_sprintf_lite(s, "%s\t%d\t%d\t%d\t%c\t", t->name, t->l_seq, r->qs, r->qe, "+-"[r->rev]);
@@ -74,12 +130,14 @@ void mm_write_paf(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, const m
else mm_sprintf_lite(s, "\t%d\t%d", r->fuzzy_mlen, r->fuzzy_blen);
mm_sprintf_lite(s, "\t%d", r->mapq);
write_tags(s, r);
if (r->p) {
if (r->p && (opt_flag & MM_F_OUT_CG)) {
uint32_t k;
mm_sprintf_lite(s, "\tcg:Z:");
for (k = 0; k < r->p->n_cigar; ++k)
mm_sprintf_lite(s, "%d%c", r->p->cigar[k]>>4, "MID"[r->p->cigar[k]&0xf]);
}
if (r->p && (opt_flag & MM_F_OUT_CS))
write_cs(km, s, mi, t, r);
}
static char comp_tab[] = {