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Some minor changes to in-process functions that nobody else uses. CGL now properly ignores no-calls for external VCFs.

This commit is contained in:
Christopher Hartl 2012-01-19 00:20:49 -05:00
parent ab8f499bc3
commit cf9b1d350a
2 changed files with 2 additions and 1 deletions
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1
public/scala/src/org/broadinstitute/sting/queue/library/ipf/vcf/VCFExtractIntervals.scala
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@ -44,6 +44,7 @@ class VCFExtractIntervals(inVCF: File, outList: File, useFilterSites: Boolean) e
}
}
}
out.printf("%s%n",cur)
out.close
}

2
public/scala/src/org/broadinstitute/sting/queue/library/ipf/vcf/VCFExtractSamples.scala
View File

@ -6,7 +6,7 @@ import collection.JavaConversions._
import org.broadinstitute.sting.commandline._
import java.io.{PrintWriter, PrintStream, File}
class VCFExtractSamples(inVCF: File, outVCF: File, samples: List[String]) extends InProcessFunction {
class VCFExtractSamples(inVCF: File, outVCF: File, samples: List[String]) extends InProcessFunction {
def this(in: File, out: File, samples: File) = this(in,out, (new XReadLines(samples)).readLines.toList)
@Input(doc="VCF from which to extract samples") var inputVCF : File = inVCF