Release samtools-0.1.17

[samtools.git] / bam2bcf_indel.c

diff --git a/bam2bcf_indel.c b/bam2bcf_indel.c
index f37a7831f9625be14b416510374fd5f71150cfdd..2fdee9f75a2261266912b7fe355e9ea51892ff6d 100644 (file)
--- a/bam2bcf_indel.c
+++ b/bam2bcf_indel.c
@@ -168,6 +168,12 @@ int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_calla
                if (n_types == 1 || (double)n_alt / n_tot < bca->min_frac || n_alt < bca->min_support) { // then skip
                        free(aux); return -1;
                }
+               if (n_types >= 64) {
+                       free(aux);
+                       if (bam_verbose >= 2) 
+                               fprintf(stderr, "[%s] excessive INDEL alleles at position %d. Skip the position.\n", __func__, pos + 1);
+                       return -1;
+               }
                types = (int*)calloc(n_types, sizeof(int));
                t = 0;
                types[t++] = aux[0] - MINUS_CONST; 
@@ -178,7 +184,6 @@ int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_calla
                for (t = 0; t < n_types; ++t)
                        if (types[t] == 0) break;
                ref_type = t; // the index of the reference type (0)
-               assert(n_types < 64);
        }
        { // calculate left and right boundary
                left = pos > INDEL_WINDOW_SIZE? pos - INDEL_WINDOW_SIZE : 0;