X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bcftools%2Fcall1.c;fp=bcftools%2Fcall1.c;h=3cc464949eb69e630ee7905c96d4f8050b1b569c;hb=cb5f44947629a68d16a48d32eef6e42a66e482fe;hp=b0baee2ea1b346e24eadd2d9bccea0ed6e886f6a;hpb=2c05c1d8da65572e6587702ba13ad8a26b2200c2;p=samtools.git

diff --git a/bcftools/call1.c b/bcftools/call1.c
index b0baee2..3cc4649 100644
--- a/bcftools/call1.c
+++ b/bcftools/call1.c
@@ -131,7 +131,6 @@ static int update_bcf1(bcf1_t *b, const bcf_p1aux_t *pa, const bcf_p1rst_t *pr,
 		if (em[5] >= 0 && em[6] >= 0) ksprintf(&s, ";AF2=%.4g,%.4g", 1 - em[5], 1 - em[6]);
 		if (em[7] >= 0) ksprintf(&s, ";LRT=%.3g", em[7]);
 		if (em[8] >= 0) ksprintf(&s, ";LRT2=%.3g", em[8]);
-		//if (em[9] >= 0) ksprintf(&s, ";LRT1=%.3g", em[9]);
 	}
 	if (cons_llr > 0) {
 		ksprintf(&s, ";CLR=%d", cons_llr);
@@ -274,6 +273,8 @@ static void write_header(bcf_hdr_t *h)
         kputs("##INFO=<ID=QCHI2,Number=1,Type=Integer,Description=\"Phred scaled PCHI2.\">\n", &str);
     if (!strstr(str.s, "##INFO=<ID=RP,"))
         kputs("##INFO=<ID=PR,Number=1,Type=Integer,Description=\"# permutations yielding a smaller PCHI2.\">\n", &str);
+    if (!strstr(str.s, "##INFO=<ID=VDB,"))
+        kputs("##INFO=<ID=VDB,Number=1,Type=Float,Description=\"Variant Distance Bias\">\n", &str);
     if (!strstr(str.s, "##FORMAT=<ID=GT,"))
         kputs("##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\n", &str);
     if (!strstr(str.s, "##FORMAT=<ID=GQ,"))
@@ -285,7 +286,7 @@ static void write_header(bcf_hdr_t *h)
 	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,"))
-		kputs("##FORMAT=<ID=PL,Number=-1,Type=Integer,Description=\"List of Phred-scaled genotype likelihoods, number of values is (#ALT+1)*(#ALT+2)/2\">\n", &str);
+		kputs("##FORMAT=<ID=PL,Number=G,Type=Integer,Description=\"List of Phred-scaled genotype likelihoods\">\n", &str);
 	h->l_txt = str.l + 1; h->txt = str.s;
 }