--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/b_out_dev/snps.subs.vcf	Tue Mar 12 17:37:29 2019 -0400
@@ -0,0 +1,27 @@
+##fileformat=VCFv4.2
+##snippy="snippy-vcf_extract_subs snps.filt.vcf"
+##fileformat=VCFv4.2
+##FILTER=<ID=PASS,Description="All filters passed">
+##fileDate=20190312
+##source=freeBayes v1.2.0-dirty
+##reference=reference/ref.fa
+##contig=<ID=reference,length=700>
+##phasing=none
+##commandline="freebayes -p 2 -P 0 -C 2 --min-repeat-entropy 1.5 --strict-vcf -q 13 -m 60 --min-coverage 2 -F 0.05 -f reference/ref.fa snps.bam --region reference:0-700"
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total read depth at the locus">
+##INFO=<ID=RO,Number=1,Type=Integer,Description="Count of full observations of the reference haplotype.">
+##INFO=<ID=AO,Number=A,Type=Integer,Description="Count of full observations of this alternate haplotype.">
+##INFO=<ID=TYPE,Number=A,Type=String,Description="The type of allele, either snp, mnp, ins, del, or complex.">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
+##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count">
+##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of the reference observations">
+##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observation count">
+##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of the alternate observations">
+##bcftools_viewVersion=1.9+htslib-1.9
+##bcftools_viewCommand=view --include 'FMT/GT="1/1" && QUAL>=60.0 && FMT/DP>=2 && (FMT/AO)/(FMT/DP)>=0.9' snps.raw.vcf; Date=Tue Mar 12 14:35:28 2019
+##bcftools_annotateVersion=1.9+htslib-1.9
+##bcftools_annotateCommand=annotate --remove ^INFO/TYPE,^INFO/DP,^INFO/RO,^INFO/AO,^INFO/AB,^FORMAT/GT,^FORMAT/DP,^FORMAT/RO,^FORMAT/AO,^FORMAT/QR,^FORMAT/QA,^FORMAT/GL; Date=Tue Mar 12 14:35:28 2019
+##INFO=<ID=OLDVAR,Number=R,Type=String,Description="Original REF,ALT before decomposition">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	b
+reference	4	.	A	T	321.326	.	TYPE=snp;DP=10;RO=0;AO=10	GT:DP:RO:AO:QR:QA	1/1:10:0:10:0:400