view tests/errors.vcf.in @ 10:db6f217dc45a

Uploaded tarball. Version 1.1. - Added stranded output. - Added, tested no-filter mode. - now prints all sites. - Changed handling of minor allele ties. - Added test datasets. - Revised help text.

##fileformat=VCFv4.1
##comment="ARGS=-f 10 -c 10"
##comment="This is a test set of made-up sites, each created in order to test a certain type of error handling. It's meant to be run with -f 10 -c 10"
##fileDate=19700101
##source=Dan
##reference=file:///scratch/dan/galaxy/galaxy-central/database/files/002/dataset_0000.dat
##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=AC,Number=.,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
##FORMAT=<ID=AF,Number=.,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
##FORMAT=<ID=NC,Number=.,Type=String,Description="Nucleotide and indel counts">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	THYROID
# A correct control
chr1	0	.	A	.	.	.	AC=;AF=	GT:AC:AF:NC	0/0:1:1:+A=15,-A=15,
# List some bases more than once
chr1	0	.	A	.	.	.	AC=;AF=	GT:AC:AF:NC	0/0:1:1:+A=15,-A=15,+A=12,
# Comma omissions
chr1	0	.	A	.	.	.	AC=;AF=	GT:AC:AF:NC	0/0:1:1:+A=15,-A=15
chr1	0	.	A	.	.	.	AC=;AF=	GT:AC:AF:NC	0/0:1:1:+A=15-A=15,
chr1	0	.	A	.	.	.	AC=;AF=	GT:AC:AF:NC	0/0:1:1:+A=15,+G=1,+C=1,-A=15,-G=1,
chr1	0	.	A	.	.	.	AC=;AF=	GT:AC:AF:NC	0/0:1:1:+A=15,+G=1+C=1,-A=15,-G=1,
# Wrong number of sample columns
chr1	0	.	A	.	.	.	AC=;AF=	GT:AC:AF:NC	0/0:1:1:+A=15,-A=15,	0/0:1:1:+A=15,-A=15,
chr1	0	.	A	.	.	.	AC=;AF=	GT:AC:AF:NC