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

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);
 					}

minimap.h

@@ -5,7 +5,7 @@
 #include <stdio.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_DUAL       (0x002LL) // skip pairs where query name is lexicographically larger than target name

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