From: Heng Li <lh3@live.co.uk>
Date: Fri, 10 Dec 2010 15:09:14 +0000 (+0000)
Subject: Make sure that the GT genotype field is the first
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=2a95d0bc3c8e9badd7ae09067d9b4914ed1448f7;p=samtools.git

Make sure that the GT genotype field is the first
---

diff --git a/bamtk.c b/bamtk.c
index 9dbdfde..da54ffd 100644
--- a/bamtk.c
+++ b/bamtk.c
@@ -9,7 +9,7 @@
 #endif
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.1.12-2 (r877)"
+#define PACKAGE_VERSION "0.1.12-3 (r878)"
 #endif
 
 int bam_taf2baf(int argc, char *argv[]);
diff --git a/bcftools/bcfutils.c b/bcftools/bcfutils.c
index 4d6835d..3c6ed73 100644
--- a/bcftools/bcfutils.c
+++ b/bcftools/bcfutils.c
@@ -1,3 +1,4 @@
+#include <string.h>
 #include "bcf.h"
 #include "kstring.h"
 #include "khash.h"
@@ -107,3 +108,26 @@ int bcf_gl2pl(bcf1_t *b)
 	}
 	return 0;
 }
+/* FIXME: this function will fail given AB:GTX:GT. BCFtools never
+ * produces such FMT, but others may do. */
+int bcf_fix_gt(bcf1_t *b)
+{
+	char *s;
+	int i;
+	uint32_t tmp;
+	bcf_ginfo_t gt;
+	// check the presence of the GT FMT
+	if ((s = strstr(b->fmt, ":GT")) == 0) return 0; // no GT or GT is already the first
+	if (s[3] != '\0' && s[3] != ':') return 0; // :GTX in fact
+	tmp = bcf_str2int("GT", 2);
+	for (i = 0; i < b->n_gi; ++i)
+		if (b->gi[i].fmt == tmp) break;
+	if (i == b->n_gi) return 0; // no GT in b->gi; probably a bug...
+	gt = b->gi[i];
+	// move GT to the first
+	for (; i > 0; --i) b->gi[i] = b->gi[i-1];
+	b->gi[0] = gt;
+	memmove(b->fmt + 3, b->fmt, s + 1 - b->fmt);
+	b->fmt[0] = 'G'; b->fmt[1] = 'T'; b->fmt[2] = ':';
+	return 0;
+}
diff --git a/bcftools/call1.c b/bcftools/call1.c
index 012c2b3..b913c9a 100644
--- a/bcftools/call1.c
+++ b/bcftools/call1.c
@@ -206,6 +206,7 @@ int bcfview(int argc, char *argv[])
 {
 	extern int bcf_2qcall(bcf_hdr_t *h, bcf1_t *b);
 	extern void bcf_p1_indel_prior(bcf_p1aux_t *ma, double x);
+	extern int bcf_fix_gt(bcf1_t *b);
 	bcf_t *bp, *bout = 0;
 	bcf1_t *b, *blast;
 	int c;
@@ -372,6 +373,7 @@ int bcfview(int argc, char *argv[])
 			b->n_gi = 0;
 			b->fmt[0] = '\0';
 		}
+		bcf_fix_gt(b);
 		vcf_write(bout, h, b);
 	}
 	if (vc.prior_file) free(vc.prior_file);