Don't change indel qual when indelQ == 0.

For an alignment that doesn't have an indel but is aligned against
reads that do have an indel, the indel quality comes from the BAM
quality.  However we already have indelQ assigned, so this avoids
changing to BAM qual if indelQ is zero as that is a special case for a
read aligning to multiple indel "types" (lengths) with equal score.

This avoids excess AD numbers for poorly chosen alignments.

Fixes #2113

Author: jkbonfield

bam2bcf.c

@@ -314,7 +314,7 @@ int bcf_call_glfgen(int _n, const bam_pileup1_t *pl, int ref_base, bcf_callaux_t
             if (bca->edlib) {
                 if (indel_in_sample) {
                     seqQ = q = (p->aux & 0xff); // mp2 + builtin indel-bias
-                } else {
+                } else if (p->aux & 0xff) {
                     // An indel in another sample, but not this.  So just use
                     // basic sequence confidences.
                     q = bam_get_qual(p->b)[p->qpos];