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@meta
Feature: Parsing VCF meta information from the header
Take a header and parse that information as defined by the VCF standard.
Scenario: When parsing a header line
Given the VCF header lines
"""
##fileformat=VCFv4.1
##fileDate=20140121
##phasing=none
##reference=file:///data/GENOMES/human_GATK_GRCh37/GRCh37_gatk.fasta
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Total read depth">
##FORMAT=<ID=DP4,Number=4,Type=Integer,Description="# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
##INFO=<ID=PM,Number=0,Type=Flag,Description="Variant is Precious(Clinical,Pubmed Cited)">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL TUMOR
"""
When I parse the VCF header
Then I expect vcf.columns to be [CHROM','POS','ID','REF','ALT','QUAL','FILTER','INFO','FORMAT','NORMAL','TUMOR']
And I expect vcf.fileformat to be "VCFv4.1"
And I expect vcf.fileDate to be "20140121"
And I expect vcf.field['fileDate'] to be "20140121"
And I expect vcf.phasing to be "none"
And I expect vcf.reference to be "file:///data/GENOMES/human_GATK_GRCh37/GRCh37_gatk.fasta"
And I expect vcf.format['GT'] to be {"ID"=>"GT", "Number"=>"1", "Type"=>"String", "Description"=>"Genotype"}
And I expect vcf.format['DP'] to be {"ID"=>"DP", "Number"=>"1", "Type"=>"Integer", "Description"=>"Total read depth"}
And I expect vcf.format['DP4'] to be {"ID"=>"DP4", "Number"=>"4", "Type"=>"Integer", "Description"=>"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases"}
And I expect vcf.info['PM'] to be {"ID"=>"PM", "Number"=>"0", "Type"=>"Flag", "Description"=>"Variant is Precious(Clinical,Pubmed Cited)"}'
And I expect vcf.meta to contain all header meta information
Scenario: When parsing the header of somatic_sniper.vcf
Do something
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