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optionally output unmapped query in PAF

This commit is contained in:
Heng Li 2018-07-07 10:26:08 -05:00
parent bcf92b3c46
commit a609a07f8c
4 changed files with 16 additions and 0 deletions
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4
format.c
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@ -259,6 +259,10 @@ static inline void write_tags(kstring_t *s, 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;
if (r == 0) {
mm_sprintf_lite(s, "%s\t%d", t->name, t->l_seq);
return;
}
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]);
if (mi->seq[r->rid].name) mm_sprintf_lite(s, "%s", mi->seq[r->rid].name);
else mm_sprintf_lite(s, "%d", r->rid);

2
main.c
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@ -60,6 +60,7 @@ static struct option long_options[] = {
{ "lj-min-ratio", required_argument, 0, 0 }, // 30
{ "score-N", required_argument, 0, 0 }, // 31
{ "eqx", no_argument, 0, 0 }, // 32
{ "paf-no-hit", no_argument, 0, 0 }, // 33
{ "help", no_argument, 0, 'h' },
{ "max-intron-len", required_argument, 0, 'G' },
{ "version", no_argument, 0, 'V' },
@ -179,6 +180,7 @@ int main(int argc, char *argv[])
else if (c == 0 && long_idx ==30) opt.min_join_flank_ratio = atof(optarg); // --lj-min-ratio
else if (c == 0 && long_idx ==31) opt.sc_ambi = atoi(optarg); // --score-N
else if (c == 0 && long_idx ==32) opt.flag |= MM_F_EQX; // --eqx
else if (c == 0 && long_idx ==33) opt.flag |= MM_F_PAF_NO_HIT; // --paf-no-hit
else if (c == 0 && long_idx == 14) { // --frag
yes_or_no(&opt, MM_F_FRAG_MODE, long_idx, optarg, 1);
} else if (c == 0 && long_idx == 15) { // --secondary

9
map.c
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@ -496,6 +496,15 @@ static void *worker_pipeline(void *shared, int step, void *in)
mm_write_paf(&p->str, mi, t, r, km, p->opt->flag);
mm_err_puts(p->str.s);
}
if (s->n_reg[i] == 0) {
if (p->opt->flag & MM_F_OUT_SAM) {
mm_write_sam2(&p->str, mi, t, i - seg_st, -1, s->n_seg[k], &s->n_reg[seg_st], (const mm_reg1_t*const*)&s->reg[seg_st], km, p->opt->flag);
mm_err_puts(p->str.s);
} else if (p->opt->flag & MM_F_PAF_NO_HIT) {
mm_write_paf(&p->str, mi, t, 0, 0, p->opt->flag);
mm_err_puts(p->str.s);
}
}
if (s->n_reg[i] == 0 && (p->opt->flag & MM_F_OUT_SAM)) { // write an unmapped record
mm_write_sam2(&p->str, mi, t, i - seg_st, -1, s->n_seg[k], &s->n_reg[seg_st], (const mm_reg1_t*const*)&s->reg[seg_st], km, p->opt->flag);
mm_err_puts(p->str.s);

1
minimap.h
View File

@ -32,6 +32,7 @@
#define MM_F_OUT_MD 0x1000000
#define MM_F_COPY_COMMENT 0x2000000
#define MM_F_EQX 0x4000000 // use =/X instead of M
#define MM_F_PAF_NO_HIT 0x8000000 // output unmapped reads to PAF
#define MM_I_HPC 0x1
#define MM_I_NO_SEQ 0x2