From: Petr Danecek <pd3@sanger.ac.uk>
Date: Tue, 26 Mar 2013 10:47:06 +0000 (+0000)
Subject: The indel stats (IS) annotation splitted into two: IDV and IMF
X-Git-Url: https://git.donarmstrong.com/?p=samtools.git;a=commitdiff_plain;h=4b7090735c74dfb91ab6cb59c588250c0eeea974

The indel stats (IS) annotation splitted into two: IDV and IMF
---

diff --git a/bam2bcf.c b/bam2bcf.c
index 340b10b..7947a31 100644
--- a/bam2bcf.c
+++ b/bam2bcf.c
@@ -415,7 +415,7 @@ int bcf_call2bcf(int tid, int pos, bcf_call_t *bc, bcf1_t *b, bcf_callret1_t *bc
 	}
 	kputc('\0', &s);
 	// INFO
-	if (bc->ori_ref < 0) ksprintf(&s,"INDEL;IS=%d,%f;", bca->max_support, bca->max_frac);
+	if (bc->ori_ref < 0) ksprintf(&s,"INDEL;IDV=%d;IMF=%f;", bca->max_support, bca->max_frac);
 	kputs("DP=", &s); kputw(bc->ori_depth, &s); kputs(";I16=", &s);
 	for (i = 0; i < 16; ++i) {
 		if (i) kputc(',', &s);
diff --git a/bcftools/call1.c b/bcftools/call1.c
index e6373d3..2008301 100644
--- a/bcftools/call1.c
+++ b/bcftools/call1.c
@@ -258,8 +258,10 @@ static void write_header(bcf_hdr_t *h)
 		kputs("##INFO=<ID=AC1,Number=1,Type=Float,Description=\"Max-likelihood estimate of the first ALT allele count (no HWE assumption)\">\n", &str);
 	if (!strstr(str.s, "##INFO=<ID=AN,"))
 		kputs("##INFO=<ID=AN,Number=1,Type=Integer,Description=\"Total number of alleles in called genotypes\">\n", &str);
-	if (!strstr(str.s, "##INFO=<ID=IS,"))
-		kputs("##INFO=<ID=IS,Number=2,Type=Float,Description=\"Maximum number of reads supporting an indel and fraction of indel reads\">\n", &str);
+	if (!strstr(str.s, "##INFO=<ID=IDV,"))
+		kputs("##INFO=<ID=IDV,Number=1,Type=Integer,Description=\"Maximum number of reads supporting an indel\">\n", &str);
+	if (!strstr(str.s, "##INFO=<ID=IMF,"))
+		kputs("##INFO=<ID=IMF,Number=1,Type=Float,Description=\"Maximum fraction of reads supporting an indel\">\n", &str);
 	if (!strstr(str.s, "##INFO=<ID=AC,"))
 		kputs("##INFO=<ID=AC,Number=A,Type=Integer,Description=\"Allele count in genotypes for each ALT allele, in the same order as listed\">\n", &str);
 	if (!strstr(str.s, "##INFO=<ID=G3,"))