Implements "bcftools view -G removes all format header lines"

Resolves samtools#248

test/test.pl

@@ -107,6 +107,7 @@
 test_vcf_view($opts,in=>'view',out=>'view.10.out',args=>q[-ne 'INDEL=1 || PV4[0]<0.006'],reg=>'');
 test_vcf_view($opts,in=>'view',out=>'view.exclude.out',args=>'-s ^NA00003',reg=>'');
 test_vcf_view($opts,in=>'view.omitgenotypes',out=>'view.omitgenotypes.out',args=>'',reg=>'');
+test_vcf_view($opts,in=>'view.omitgenotypes',out=>'view.dropgenotypes.out',args=>'-G',reg=>'');
 test_vcf_view($opts,in=>'view.vectors',out=>'view.vectors.A.out',args=>'-asA',reg=>'');
 test_vcf_view($opts,in=>'view.vectors',out=>'view.vectors.B.out',args=>'-asB',reg=>'');
 test_vcf_view($opts,in=>'view.filter',out=>'view.filter.1.out',args=>q[-H -i'FMT/FGS[0]="AAAAAA"'],reg=>'');    # test expressions

test/view.9.out

@@ -20,10 +20,6 @@
 ##INFO=<ID=QD,Number=1,Type=Float,Description="Variant confidence/quality by depth">
 ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes">
 ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
-##FORMAT=<ID=DP,Number=1,Type=Integer,Description="# high-quality bases">
-##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
-##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
-##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods">
 ##FILTER=<ID=StrandBias,Description="Min P-value for strand bias (INFO/PV4) [0.0001]">
 ##FILTER=<ID=BaseQualBias,Description="Min P-value for baseQ bias (INFO/PV4) [1e-100]">
 ##FILTER=<ID=MapQualBias,Description="Min P-value for mapQ bias (INFO/PV4) [0]">

test/view.dropgenotypes.out

@@ -0,0 +1,12 @@
+##fileformat=VCFv4.2
+##FILTER=<ID=PASS,Description="All filters passed">
+##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta
+##contig=<ID=20,length=62435964,assembly=B36,md5=f126cdf8a6e0c7f379d618ff66beb2da,species="Homo sapiens",taxonomy=x>
+##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
+20	14370	rs6054257	G	A	29	PASS	NS=3;DP=14
+20	17330	.	T	A	3	PASS	NS=3;DP=11
+20	1110696	rs6040355	A	G,T	67	PASS	NS=2;DP=10
+20	1230237	.	T	.	47	PASS	NS=3;DP=13
+20	1234567	microsat1	GTC	G,GTCT	50	PASS	NS=3;DP=9

vcfview.c

@@ -220,8 +220,10 @@ static void init_data(args_t *args)
     if ( !args->out ) error("%s: %s\n", args->fn_out,strerror(errno));
 
     // headers: hdr=full header, hsub=subset header, hnull=sites only header
-    if (args->sites_only)
+    if (args->sites_only){
         args->hnull = bcf_hdr_subset(args->hdr, 0, 0, 0);
+        bcf_hdr_remove(args->hnull, BCF_HL_FMT, NULL);
+    }
     if (args->n_samples > 0)
     {
         args->hsub = bcf_hdr_subset(args->hdr, args->n_samples, args->samples, args->imap);