Fixed a compiling error when knetfile is not used.

[samtools.git] / bam2bcf_indel.c

diff --git a/bam2bcf_indel.c b/bam2bcf_indel.c
index 518768d4af3095d4ad178539acae0cbb0ed736bb..16241d0c0399fb7e727951f2d8f64d86798e25d1 100644 (file)
--- a/bam2bcf_indel.c
+++ b/bam2bcf_indel.c
@@ -112,7 +112,7 @@ int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_calla
                                          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;
+       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;
        khash_t(rg) *hash = (khash_t(rg)*)rghash;
@@ -236,7 +236,8 @@ int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_calla
                free(inscns_aux);
        }
        // compute the likelihood given each type of indel for each read
-       ref2  = calloc(right - left + max_ins + 2, 1);
+       max_ref2 = right - left + 2 + 2 * (max_ins > -types[0]? max_ins : -types[0]);
+       ref2  = calloc(max_ref2, 1);
        query = calloc(right - left + max_rd_len + max_ins + 2, 1);
        score1 = calloc(N * n_types, sizeof(int));
        score2 = calloc(N * n_types, sizeof(int));
@@ -264,6 +265,7 @@ int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_calla
                }
                for (; j < right && ref[j]; ++j)
                        ref2[k++] = bam_nt16_nt4_table[bam_nt16_table[(int)ref[j]]];
+               for (; k < max_ref2; ++k) ref2[k] = 4;
                if (j < right) right = j;
                // align each read to ref2
                for (s = K = 0; s < n; ++s) {
@@ -286,7 +288,7 @@ int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_calla
                                        const uint8_t *qual = bam1_qual(p->b), *bq;
                                        uint8_t *qq;
                                        qq = calloc(qend - qbeg, 1);
-                                       bq = (uint8_t*)bam_aux_get(p->b, "BQ");
+                                       bq = (uint8_t*)bam_aux_get(p->b, "ZQ");
                                        if (bq) ++bq; // skip type
                                        for (l = qbeg; l < qend; ++l) {
                                                qq[l - qbeg] = bq? qual[l] + (bq[l] - 64) : qual[l];