X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bam2bcf.c;h=f7c48aa94f32e417d718371ee0c621b906ea0b85;hb=ff6d24e37138561b372621eb4b7418e6292c1494;hp=be8cf1fe529a735800947b80b2a52c7fbaadb2d4;hpb=599bea10bc3487a0cbdf505e792a21a13fee2b11;p=samtools.git

diff --git a/bam2bcf.c b/bam2bcf.c
index be8cf1f..f7c48aa 100644
--- a/bam2bcf.c
+++ b/bam2bcf.c
@@ -20,7 +20,7 @@ bcf_callaux_t *bcf_call_init(double theta, int min_baseQ)
 	if (theta <= 0.) theta = CALL_DEFTHETA;
 	bca = calloc(1, sizeof(bcf_callaux_t));
 	bca->capQ = 60;
-	bca->openQ = 40; bca->extQ = 20; bca->tandemQ = 80;
+	bca->openQ = 40; bca->extQ = 20; bca->tandemQ = 100;
 	bca->min_baseQ = min_baseQ;
 	bca->e = errmod_init(1. - theta);
 	return bca;
@@ -181,9 +181,11 @@ int bcf_call2bcf(int tid, int pos, bcf_call_t *bc, bcf1_t *b, bcf_callret1_t *bc
 		kputc(ref[pos], &s);
 		for (i = 1; i < 4; ++i) {
 			if (bc->a[i] < 0) break;
-			if (i > 1) kputc(',', &s);
+			if (i > 1) {
+				kputc(',', &s); kputc(ref[pos], &s);
+			}
 			if (bca->indel_types[bc->a[i]] < 0) { // deletion
-				for (j = -bca->indel_types[bc->a[i]]; j < bca->indelreg; ++i)
+				for (j = -bca->indel_types[bc->a[i]]; j < bca->indelreg; ++j)
 					kputc(ref[pos+1+j], &s);
 			} else { // insertion; cannot be a reference unless a bug
 				char *inscns = &bca->inscns[bc->a[i] * bca->maxins];