Merge remote branch 'pd3master/master'

[samtools.git] / bam2bcf_indel.c

diff --git a/bam2bcf_indel.c b/bam2bcf_indel.c
index 9aea5f9d669f79850fb45438fdcf1183c3e1227f..30b3f46f8431a184fc50524e8f339b70363f6af5 100644 (file)
--- a/bam2bcf_indel.c
+++ b/bam2bcf_indel.c
@@ -109,6 +109,9 @@ static inline int est_indelreg(int pos, const char *ref, int l, char *ins4)
        return max_i - pos;
 }
 
+/*
+ *  @n:  number of samples
+ */
 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)
 {
@@ -215,6 +218,8 @@ int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_calla
         * reduces the power because sometimes, substitutions caused by
         * indels are not distinguishable from true mutations. Multiple
         * sequence realignment helps to increase the power.
+     *
+     * Masks mismatches present in at least 70% of the reads with 'N'.
         */
        { // construct per-sample consensus
                int L = right - left + 1, max_i, max2_i;
@@ -258,7 +263,7 @@ int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_calla
                        if ((double)(max2&0xffff) / ((max2&0xffff) + (max2>>16)) >= 0.7) max2_i = -1;
                        if (max_i >= 0) r[max_i] = 15;
                        if (max2_i >= 0) r[max2_i] = 15;
-//                     for (i = 0; i < right - left; ++i) fputc("=ACMGRSVTWYHKDBN"[(int)r[i]], stderr); fputc('\n', stderr);
+                       //for (i = 0; i < right - left; ++i) fputc("=ACMGRSVTWYHKDBN"[(int)r[i]], stderr); fputc('\n', stderr);
                }
                free(ref0); free(cns);
        }
@@ -275,9 +280,9 @@ int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_calla
                }
        }
        // construct the consensus sequence
-       max_ins = types[n_types - 1]; // max_ins is at least 0
+       max_ins = types[n_types - 1];   // max_ins is at least 0
        if (max_ins > 0) {
-               int *inscns_aux = calloc(4 * n_types * max_ins, sizeof(int));
+               int *inscns_aux = calloc(5 * n_types * max_ins, sizeof(int));
                // count the number of occurrences of each base at each position for each type of insertion
                for (t = 0; t < n_types; ++t) {
                        if (types[t] > 0) {
@@ -288,7 +293,8 @@ int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_calla
                                                        uint8_t *seq = bam1_seq(p->b);
                                                        for (k = 1; k <= p->indel; ++k) {
                                                                int c = bam_nt16_nt4_table[bam1_seqi(seq, p->qpos + k)];
-                                                               if (c < 4) ++inscns_aux[(t*max_ins+(k-1))*4 + c];
+                                assert(c<5);
+                                                               ++inscns_aux[(t*max_ins+(k-1))*5 + c];
                                                        }
                                                }
                                        }
@@ -299,11 +305,12 @@ int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_calla
                inscns = calloc(n_types * max_ins, 1);
                for (t = 0; t < n_types; ++t) {
                        for (j = 0; j < types[t]; ++j) {
-                               int max = 0, max_k = -1, *ia = &inscns_aux[(t*max_ins+j)*4];
-                               for (k = 0; k < 4; ++k)
+                               int max = 0, max_k = -1, *ia = &inscns_aux[(t*max_ins+j)*5];
+                               for (k = 0; k < 5; ++k)
                                        if (ia[k] > max)
                                                max = ia[k], max_k = k;
                                inscns[t*max_ins + j] = max? max_k : 4;
+                if ( max_k==4 ) { types[t] = 0; break; } // discard insertions which contain N's
                        }
                }
                free(inscns_aux);