* samtools-r836

[samtools.git] / bam2bcf_indel.c

diff --git a/bam2bcf_indel.c b/bam2bcf_indel.c
index a930cba03b57f5aee2f59e869be04c7ccb530fad..954e43e8f85a404704b48fb5a6191c247baaaf6d 100644 (file)
--- a/bam2bcf_indel.c
+++ b/bam2bcf_indel.c
@@ -480,9 +480,6 @@ int bcf_call_mnp_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_calla
                // squeeze out indentical types
                for (i = 1, n_types = 1; i < m; ++i)
                        if (aux[i] != aux[i-1]) ++n_types;
-               if (n_types == 1) { // no indels
-                       free(aux); return -1;
-               }
                // count reads for each type
                cnt = alloca(n_types * 4);
                cnt[0] = 1<<8 | aux[0];
@@ -495,6 +492,8 @@ int bcf_call_mnp_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_calla
                free(aux);
                // collect types
                ks_introsort(uint32_t, n_types, cnt);
+               if (n_types == 1 || (cnt[n_types-1]>>8) * MIN_SUPPORT_COEF < N) // no MNPs or too few supporting reads
+                       return -1;
                types = (int*)calloc(2, sizeof(int));
                types[0] = ref_seq; types[1] = cnt[n_types-1]&0xff;
                ref_type = 0; n_types = 2;