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Fixed example unified genotyper pipeline to wrap filter expressions with quotes and use rod binding name "variant" instead of "vcf".

This commit is contained in:
Khalid Shakir 2011-08-03 02:21:01 -04:00
parent 2d94037ad0
commit a587f38808
1 changed files with 2 additions and 2 deletions
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4
public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleUnifiedGenotyper.scala
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@ -59,10 +59,10 @@ class ExampleUnifiedGenotyper extends QScript {
evalUnfiltered.rodBind :+= RodBind("eval", "VCF", genotyper.out)
evalUnfiltered.out = swapExt(genotyper.out, "vcf", "eval")
variantFilter.rodBind :+= RodBind("vcf", "VCF", genotyper.out)
variantFilter.rodBind :+= RodBind("variant", "VCF", genotyper.out)
variantFilter.out = swapExt(qscript.bamFile, "bam", "filtered.vcf")
variantFilter.filterName = filterNames
variantFilter.filterExpression = filterExpressions
variantFilter.filterExpression = filterExpressions.map("\"" + _ + "\"")
evalFiltered.rodBind :+= RodBind("eval", "VCF", variantFilter.out)
evalFiltered.out = swapExt(variantFilter.out, "vcf", "eval")