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Implemented getSamplesFromVCF.

This commit is contained in:
Khalid Shakir 2012-05-03 21:57:57 -04:00
parent 7c11dde328
commit a9da9598f5
1 changed files with 3 additions and 3 deletions
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6
public/scala/src/org/broadinstitute/sting/queue/util/VCF_BAM_utilities.scala
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@ -7,13 +7,13 @@ import net.sf.samtools.SAMFileReader
import org.broadinstitute.sting.utils.codecs.vcf.{VCFHeader, VCFCodec} import org.broadinstitute.sting.utils.codecs.vcf.{VCFHeader, VCFCodec}
import scala.collection.JavaConversions._ import scala.collection.JavaConversions._
import org.broad.tribble.{FeatureCodec, AbstractFeatureReader} import org.broad.tribble.{FeatureCodec, AbstractFeatureReader}
import org.broadinstitute.sting.utils.variantcontext.VariantContext
object VCF_BAM_utilities { object VCF_BAM_utilities {
def getSamplesFromVCF(vcfFile: File): List[String] = { def getSamplesFromVCF(vcfFile: File): List[String] = {
List(); val codec: FeatureCodec[VariantContext] = new VCFCodec().asInstanceOf[FeatureCodec[VariantContext]]
// TODO -- ask khalid for help here with type error AbstractFeatureReader.getFeatureReader(vcfFile.getPath, codec).getHeader.asInstanceOf[VCFHeader].getGenotypeSamples.toList
//return AbstractFeatureReader.getFeatureReader(vcfFile.getPath(), new VCFCodec()).getHeader().asInstanceOf[VCFHeader].getGenotypeSamples().toList
} }
def getSamplesInBAM(bam: File): List[String] = { def getSamplesInBAM(bam: File): List[String] = {