From a9a8e7769267e5a39a10004f2e0a10bee9e33aaf Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@live.co.uk>
Date: Thu, 16 Feb 2012 14:33:07 +0000
Subject: [PATCH] bugfix: wrong SP; missing DV in the VCF header

---
 bam.h            | 2 +-
 bam2bcf.c        | 2 +-
 bcftools/call1.c | 7 ++++++-
 3 files changed, 8 insertions(+), 3 deletions(-)

diff --git a/bam.h b/bam.h
index df345b6..11f8028 100644
--- a/bam.h
+++ b/bam.h
@@ -40,7 +40,7 @@
   @copyright Genome Research Ltd.
  */
 
-#define BAM_VERSION "0.1.18-dev (r982:310)"
+#define BAM_VERSION "0.1.18-dev (r982:313)"
 
 #include <stdint.h>
 #include <stdlib.h>
diff --git a/bam2bcf.c b/bam2bcf.c
index 83f2e56..6ac5dce 100644
--- a/bam2bcf.c
+++ b/bam2bcf.c
@@ -328,7 +328,7 @@ int bcf_call2bcf(int tid, int pos, bcf_call_t *bc, bcf1_t *b, bcf_callret1_t *bc
 	if (bcr && fmt_flag) {
 		uint16_t *dp = (fmt_flag & B2B_FMT_DP)? b->gi[1].data : 0;
 		uint16_t *dv = (fmt_flag & B2B_FMT_DV)? b->gi[1 + ((fmt_flag & B2B_FMT_DP) != 0)].data : 0;
-		int32_t  *sp = (fmt_flag & B2B_FMT_DV)? b->gi[1 + ((fmt_flag & B2B_FMT_DP) != 0) + ((fmt_flag & B2B_FMT_DV) != 0)].data : 0;
+		int32_t  *sp = (fmt_flag & B2B_FMT_SP)? b->gi[1 + ((fmt_flag & B2B_FMT_DP) != 0) + ((fmt_flag & B2B_FMT_DV) != 0)].data : 0;
 		for (i = 0; i < bc->n; ++i) {
 			bcf_callret1_t *p = bcr + i;
 			if (dp) dp[i] = p->depth  < 0xffff? p->depth  : 0xffff;
diff --git a/bcftools/call1.c b/bcftools/call1.c
index 3cc4649..f6717b3 100644
--- a/bcftools/call1.c
+++ b/bcftools/call1.c
@@ -33,6 +33,7 @@ KSTREAM_INIT(gzFile, gzread, 16384)
 #define VC_EM       0x10000
 #define VC_PAIRCALL 0x20000
 #define VC_QCNT     0x40000
+#define VC_INDEL_ONLY 0x80000
 
 typedef struct {
 	int flag, prior_type, n1, n_sub, *sublist, n_perm;
@@ -283,6 +284,8 @@ static void write_header(bcf_hdr_t *h)
         kputs("##FORMAT=<ID=GL,Number=3,Type=Float,Description=\"Likelihoods for RR,RA,AA genotypes (R=ref,A=alt)\">\n", &str);
 	if (!strstr(str.s, "##FORMAT=<ID=DP,"))
 		kputs("##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"# high-quality bases\">\n", &str);
+	if (!strstr(str.s, "##FORMAT=<ID=DV,"))
+		kputs("##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"# high-quality non-reference bases\">\n", &str);
 	if (!strstr(str.s, "##FORMAT=<ID=SP,"))
 		kputs("##FORMAT=<ID=SP,Number=1,Type=Integer,Description=\"Phred-scaled strand bias P-value\">\n", &str);
 	if (!strstr(str.s, "##FORMAT=<ID=PL,"))
@@ -318,7 +321,7 @@ int bcfview(int argc, char *argv[])
 	memset(&vc, 0, sizeof(viewconf_t));
 	vc.prior_type = vc.n1 = -1; vc.theta = 1e-3; vc.pref = 0.5; vc.indel_frac = -1.; vc.n_perm = 0; vc.min_perm_p = 0.01; vc.min_smpl_frac = 0; vc.min_lrt = 1;
 	memset(qcnt, 0, 8 * 256);
-	while ((c = getopt(argc, argv, "FN1:l:cC:eHAGvbSuP:t:p:QgLi:IMs:D:U:X:d:T:Y")) >= 0) {
+	while ((c = getopt(argc, argv, "FN1:l:cC:eHAGvbSuP:t:p:QgLi:IMs:D:U:X:d:T:Yw")) >= 0) {
 		switch (c) {
 		case '1': vc.n1 = atoi(optarg); break;
 		case 'l': vc.bed = bed_read(optarg); break;
@@ -335,6 +338,7 @@ int bcfview(int argc, char *argv[])
 		case 'u': vc.flag |= VC_UNCOMP | VC_BCFOUT; break;
 		case 'g': vc.flag |= VC_CALL_GT | VC_CALL; break;
 		case 'I': vc.flag |= VC_NO_INDEL; break;
+		case 'w': vc.flag |= VC_INDEL_ONLY; break;
 		case 'M': vc.flag |= VC_ANNO_MAX; break;
 		case 'Y': vc.flag |= VC_QCNT; break;
 		case 't': vc.theta = atof(optarg); break;
@@ -482,6 +486,7 @@ int bcfview(int argc, char *argv[])
 		if (vc.flag & VC_FIX_PL) bcf_fix_pl(b);
 		is_indel = bcf_is_indel(b);
 		if ((vc.flag & VC_NO_INDEL) && is_indel) continue;
+		if ((vc.flag & VC_INDEL_ONLY) && !is_indel) continue;
 		if ((vc.flag & VC_ACGT_ONLY) && !is_indel) {
 			int x;
 			if (b->ref[0] == 0 || b->ref[1] != 0) continue;
-- 
2.39.2