Test only increasing AD but leaving the default calling

Author: pd3

bam2bcf.c

@@ -216,7 +216,17 @@ int bcf_call_glfgen(int _n, const bam_pileup1_t *pl, int ref_base, bcf_callaux_t
         {
             b = p->aux>>16&0x3f;
             seqQ = q = (p->aux & 0xff); // mp2 + builtin indel-bias
-            if (p->indel && q < bca->min_baseQ) continue;
+            if (q < bca->min_baseQ)
+            {
+                if (!p->indel && r->ADF)
+                {
+                    if ( bam_is_rev(p->b) )
+                        r->ADR[b]++;
+                    else
+                        r->ADF[b]++;
+                }
+                continue;
+            }
             if (p->indel == 0 && (q < _n/2 || _n > 20)) {
                 // high quality indel calls without p->indel set aren't
                 // particularly indicative of being a good REF match either,

mpileup.c

@@ -1161,6 +1161,7 @@ static void print_usage(FILE *fp, const mplp_conf_t *mplp)
         "  -P, --platforms STR     comma separated list of platforms for indels [all]\n");
     fprintf(fp,
         "      --indel-bias FLOAT  Raise to favour recall over precision [%.2f]\n"
+        "      --ambiguous-reads FLAGS  Count ambiguous indel reads as: alt,ref,drop [drop]\n"
         "\n", mplp->indel_bias);
     fprintf(fp,
         "Configuration profiles activated with -X, --config:\n"