bcftools.1 and samtools.1 were merged in upstream release 0.1.17.

[samtools.git] / bam2bcf_indel.c

diff --git a/bam2bcf_indel.c b/bam2bcf_indel.c
index 899428f1c8c4202caaefded876e290c37f7cb6ac..2fdee9f75a2261266912b7fe355e9ea51892ff6d 100644 (file)
--- a/bam2bcf_indel.c
+++ b/bam2bcf_indel.c
@@ -3,12 +3,14 @@
 #include <string.h>
 #include "bam.h"
 #include "bam2bcf.h"
-#include "ksort.h"
 #include "kaln.h"
 #include "kprobaln.h"
 #include "khash.h"
 KHASH_SET_INIT_STR(rg)
 
+#include "ksort.h"
+KSORT_INIT_GENERIC(uint32_t)
+
 #define MINUS_CONST 0x10000000
 #define INDEL_WINDOW_SIZE 50
 
@@ -110,7 +112,6 @@ static inline int est_indelreg(int pos, const char *ref, int l, char *ins4)
 int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_callaux_t *bca, const char *ref,
                                          const void *rghash)
 {
-       extern void ks_introsort_uint32_t(int, uint32_t*);
        int i, s, j, k, t, n_types, *types, max_rd_len, left, right, max_ins, *score1, *score2, max_ref2;
        int N, K, l_run, ref_type, n_alt;
        char *inscns = 0, *ref2, *query, **ref_sample;
@@ -167,6 +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; 
@@ -177,7 +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;