X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bam2bcf_indel.c;h=ab9e83ca8f712ae7d7975d67b94b10c702e64908;hb=0b3418cf166ce4a58cedf0d9a2df5ec3dd4cc5fa;hp=2fdee9f75a2261266912b7fe355e9ea51892ff6d;hpb=3384f6c6c1642ada4edae9204ca1202672de7d5a;p=samtools.git

diff --git a/bam2bcf_indel.c b/bam2bcf_indel.c
index 2fdee9f..ab9e83c 100644
--- 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)
@@ -222,7 +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;