From b58b97423a703c6a051dbf88efabe0d0e58fa683 Mon Sep 17 00:00:00 2001 From: Heng Li Date: Thu, 17 Apr 2025 21:46:54 -0400 Subject: [PATCH] r1281: with --write-junc, ignore aln with low mapQ --- map.c | 2 +- minimap.h | 2 +- minimap2.1 | 1 + 3 files changed, 3 insertions(+), 2 deletions(-) diff --git a/map.c b/map.c index 85b812c..54f78a4 100644 --- a/map.c +++ b/map.c @@ -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 for (j = 0; j < s->n_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); if (p->str.l > 0) mm_err_puts(p->str.s); } diff --git a/minimap.h b/minimap.h index e67f2e7..24ed903 100644 --- a/minimap.h +++ b/minimap.h @@ -5,7 +5,7 @@ #include #include -#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_DUAL (0x002LL) // skip pairs where query name is lexicographically larger than target name diff --git a/minimap2.1 b/minimap2.1 index d4001d8..4158010 100644 --- a/minimap2.1 +++ b/minimap2.1 @@ -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, 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. +Alignments with mapping quality below 10 are ignored. .TP .BI --pass1 \ FILE Junctions BED file outputted by