Fix missing declaration for getopt on Mac OS X

[samtools.git] / bam2bcf_indel.c

diff --git a/bam2bcf_indel.c b/bam2bcf_indel.c
index f37a7831f9625be14b416510374fd5f71150cfdd..ab9e83ca8f712ae7d7975d67b94b10c702e64908 100644 (file)
--- a/bam2bcf_indel.c
+++ b/bam2bcf_indel.c
@@ -66,7 +66,7 @@ static int tpos2qpos(const bam1_core_t *c, const uint32_t *cigar, int32_t tpos,
        for (k = 0; k < c->n_cigar; ++k) {
                int op = cigar[k] & BAM_CIGAR_MASK;
                int l = cigar[k] >> BAM_CIGAR_SHIFT;
-               if (op == BAM_CMATCH) {
+               if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF) {
                        if (c->pos > tpos) return y;
                        if (x + l > tpos) {
                                *_tpos = tpos;
@@ -161,6 +161,11 @@ int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_calla
                                if (j > max_rd_len) max_rd_len = j;
                        }
                }
+        // To prevent long stretches of N's to be mistaken for indels (sometimes thousands of bases),
+        //  check the number of N's in the sequence and skip places where half or more reference bases are Ns.
+        int nN=0; for (i=pos; i-pos<max_rd_len && ref[i]; i++) if ( ref[i]=='N' ) nN++;
+        if ( nN*2>i ) return -1;
+
                ks_introsort(uint32_t, m, aux);
                // squeeze out identical types
                for (i = 1, n_types = 1; i < m; ++i)
@@ -168,6 +173,12 @@ 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; 
@@ -178,7 +189,6 @@ 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;
@@ -217,7 +227,7 @@ int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_calla
                                for (k = 0; k < b->core.n_cigar; ++k) {
                                        int op = cigar[k]&0xf;
                                        int j, l = cigar[k]>>4;
-                                       if (op == BAM_CMATCH) {
+                                       if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF) {
                                                for (j = 0; j < l; ++j)
                                                        if (x + j >= left && x + j < right)
                                                                cns[x+j-left] += (bam1_seqi(seq, y+j) == ref0[x+j-left])? 1 : 0x10000;