Fix three bugs in bam2bcf indel calling

- bam2bcf_indel.c: Initialize K=0 at declaration to avoid using an
  uninitialized variable in the max-deletion loop (line ~783) which
  runs before K is reset at line ~791.

- bam2bcf_iaux.c: Fix memset size in iaux_init_scores() to use
  n*sizeof(int) instead of n, since read_scores is int*. Without
  this, only 1/4 of the array (on most platforms) was being zeroed.

- bam2bcf_iaux.c: Fix per-sample indel fraction denominator in
  iaux_init_types() to use ntot (per-sample read count) instead of
  naux (running cross-sample indel count), which produced incorrect
  filtering thresholds.

Author: sirus20x6

bam2bcf_iaux.c

@@ -162,7 +162,7 @@ static int iaux_init_scores(indel_aux_t *iaux, int ismpl)
         iaux->mread_scores = n;
         iaux->read_scores  = tmp;
     }
-    memset(iaux->read_scores,0,n);
+    memset(iaux->read_scores,0,n*sizeof(int));
     return 0;
 }
 
@@ -287,7 +287,7 @@ static int iaux_init_types(indel_aux_t *iaux)
         nalt = naux - nalt;
         if ( iaux->bca->per_sample_flt )
         {
-            double frac = (double)nalt/naux;
+            double frac = (double)nalt/ntot;
             if ( nalt >= iaux->bca->min_support && frac >= iaux->bca->min_frac ) indel_support_ok = 1;
             if ( nalt > iaux->bca->max_support && frac > 0 ) iaux->bca->max_support = nalt, iaux->bca->max_frac = frac;
         }

bam2bcf_indel.c

@@ -702,7 +702,7 @@ int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos,
 
     int i, s, j, k, t, n_types, *types, max_rd_len, left, right, max_ins;
     int *score, max_ref2;
-    int N, K, l_run, ref_type, n_alt;
+    int N, K = 0, l_run, ref_type, n_alt;
     char *inscns = 0, *ref2, *query, **ref_sample;
 
     // determine if there is a gap