Bug fixes

[samtools.git] / bam2bcf_indel.c

diff --git a/bam2bcf_indel.c b/bam2bcf_indel.c
index 87736c398415ed6b4916ea767186283e43f1d6cb..9aea5f9d669f79850fb45438fdcf1183c3e1227f 100644 (file)
--- a/bam2bcf_indel.c
+++ b/bam2bcf_indel.c
@@ -142,6 +142,7 @@ int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_calla
        if (s == n) return -1; // there is no indel at this position.
        for (s = N = 0; s < n; ++s) N += n_plp[s]; // N is the total number of reads
        { // find out how many types of indels are present
+        bca->max_support = bca->max_frac = 0;
                int m, n_alt = 0, n_tot = 0, indel_support_ok = 0;
                uint32_t *aux;
                aux = calloc(N + 1, 4);
@@ -161,8 +162,10 @@ int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_calla
                                j = bam_cigar2qlen(&p->b->core, bam1_cigar(p->b));
                                if (j > max_rd_len) max_rd_len = j;
                        }
-            if ( !indel_support_ok && na >= bca->min_support && (double)na/nt >= bca->min_frac )
+            float frac = (float)na/nt;
+            if ( !indel_support_ok && na >= bca->min_support && frac >= bca->min_frac )
                 indel_support_ok = 1;
+            if ( na > bca->max_support && frac > 0 ) bca->max_support = na, bca->max_frac = frac;
             n_alt += na; 
             n_tot += nt;
                }
@@ -175,12 +178,12 @@ int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_calla
                // squeeze out identical types
                for (i = 1, n_types = 1; i < m; ++i)
                        if (aux[i] != aux[i-1]) ++n_types;
-        // Taking totals makes hard to call rare indels
-        if ( !bca->per_sample_flt ) 
-            indel_support_ok = ( (double)n_alt / n_tot < bca->min_frac || n_alt < bca->min_support ) ? 0 : 1;
-               if ( n_types == 1 || !indel_support_ok ) { // then skip
-                       free(aux); return -1;
-               }
+        // Taking totals makes it hard to call rare indels
+        if ( !bca->per_sample_flt )
+            indel_support_ok = ( (float)n_alt / n_tot < bca->min_frac || n_alt < bca->min_support ) ? 0 : 1;
+        if ( n_types == 1 || !indel_support_ok ) { // then skip
+            free(aux); return -1;
+        }
                if (n_types >= 64) {
                        free(aux);
                        if (bam_verbose >= 2)