Mercurial > repos > nick > allele_counts
diff tests/errors.vcf.in @ 5:31361191d2d2
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Version 1.1: Stranded output, slightly different handling of minor allele ties and 0 coverage sites, revised help text, added test datasets.
| author | nick |
|---|---|
| date | Thu, 12 Sep 2013 11:34:23 -0400 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tests/errors.vcf.in Thu Sep 12 11:34:23 2013 -0400 @@ -0,0 +1,25 @@ +##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 \ No newline at end of file