From a9da9598f55c10650554cbb8fd2ab841033c5389 Mon Sep 17 00:00:00 2001 From: Khalid Shakir Date: Thu, 3 May 2012 21:57:57 -0400 Subject: [PATCH] Implemented getSamplesFromVCF. --- .../broadinstitute/sting/queue/util/VCF_BAM_utilities.scala | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/public/scala/src/org/broadinstitute/sting/queue/util/VCF_BAM_utilities.scala b/public/scala/src/org/broadinstitute/sting/queue/util/VCF_BAM_utilities.scala index 33e9adb8d..1f18858e1 100644 --- a/public/scala/src/org/broadinstitute/sting/queue/util/VCF_BAM_utilities.scala +++ b/public/scala/src/org/broadinstitute/sting/queue/util/VCF_BAM_utilities.scala @@ -7,13 +7,13 @@ import net.sf.samtools.SAMFileReader import org.broadinstitute.sting.utils.codecs.vcf.{VCFHeader, VCFCodec} import scala.collection.JavaConversions._ import org.broad.tribble.{FeatureCodec, AbstractFeatureReader} +import org.broadinstitute.sting.utils.variantcontext.VariantContext object VCF_BAM_utilities { def getSamplesFromVCF(vcfFile: File): List[String] = { - List(); - // TODO -- ask khalid for help here with type error - //return AbstractFeatureReader.getFeatureReader(vcfFile.getPath(), new VCFCodec()).getHeader().asInstanceOf[VCFHeader].getGenotypeSamples().toList + val codec: FeatureCodec[VariantContext] = new VCFCodec().asInstanceOf[FeatureCodec[VariantContext]] + AbstractFeatureReader.getFeatureReader(vcfFile.getPath, codec).getHeader.asInstanceOf[VCFHeader].getGenotypeSamples.toList } def getSamplesInBAM(bam: File): List[String] = {