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r1281: with --write-junc, ignore aln with low mapQ

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Heng Li
2025-04-17 21:46:54 -04:00
parent df9e650346
commit b58b97423a
3 changed files with 3 additions and 2 deletions
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map.c
+1 -1
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@@ -601,7 +601,7 @@ static void *worker_pipeline(void *shared, int step, void *in)
} else if (p->opt->flag & MM_F_OUT_JUNC) { // extra logic for --write-junc } else if (p->opt->flag & MM_F_OUT_JUNC) { // extra logic for --write-junc
for (j = 0; j < s->n_reg[i]; ++j) { for (j = 0; j < s->n_reg[i]; ++j) {
const mm_reg1_t *r = &s->reg[i][j]; const mm_reg1_t *r = &s->reg[i][j];
if (r->id != r->parent) continue; if (r->id != r->parent || r->mapq < 10) continue;
mm_write_junc(&p->str, mi, t, r); mm_write_junc(&p->str, mi, t, r);
if (p->str.l > 0) mm_err_puts(p->str.s); if (p->str.l > 0) mm_err_puts(p->str.s);
} }
minimap.h
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@@ -5,7 +5,7 @@
#include <stdio.h> #include <stdio.h>
#include <sys/types.h> #include <sys/types.h>
#define MM_VERSION "2.28-r1280-dirty" #define MM_VERSION "2.28-r1281-dirty"
#define MM_F_NO_DIAG (0x001LL) // no exact diagonal hit #define MM_F_NO_DIAG (0x001LL) // no exact diagonal hit
#define MM_F_NO_DUAL (0x002LL) // skip pairs where query name is lexicographically larger than target name #define MM_F_NO_DUAL (0x002LL) // skip pairs where query name is lexicographically larger than target name
minimap2.1
+1
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@@ -552,6 +552,7 @@ Output splice junctions in 6-column BED: contig name, start, end,
read name, score and strand. Score is the sum of donor and acceptor scores, read name, score and strand. Score is the sum of donor and acceptor scores,
where GT gets 3, GC gets 2 and AT gets 1 at donor sites, where GT gets 3, GC gets 2 and AT gets 1 at donor sites,
while AG gets 3 and AC gets 1 at acceptor sites. while AG gets 3 and AC gets 1 at acceptor sites.
Alignments with mapping quality below 10 are ignored.
.TP .TP
.BI --pass1 \ FILE .BI --pass1 \ FILE
Junctions BED file outputted by Junctions BED file outputted by