From a9d092152904eba2424ff35c438751b187f0486b Mon Sep 17 00:00:00 2001 From: chartl Date: Thu, 3 Feb 2011 05:03:48 +0000 Subject: [PATCH] That variable name could only lead to trouble. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5180 348d0f76-0448-11de-a6fe-93d51630548a --- .../sting/queue/library/ipf/vcf/VCFSimpleMerge.scala | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/scala/src/org/broadinstitute/sting/queue/library/ipf/vcf/VCFSimpleMerge.scala b/scala/src/org/broadinstitute/sting/queue/library/ipf/vcf/VCFSimpleMerge.scala index c82f3ad96..94b79454f 100755 --- a/scala/src/org/broadinstitute/sting/queue/library/ipf/vcf/VCFSimpleMerge.scala +++ b/scala/src/org/broadinstitute/sting/queue/library/ipf/vcf/VCFSimpleMerge.scala @@ -10,7 +10,7 @@ import org.broadinstitute.sting.utils.{GenomeLocParser, GenomeLoc} class VCFSimpleMerge extends InProcessFunction { @Input(doc="VCFs to be merged") var vcfs: List[File] = Nil - @Input(doc="The reference fasta index") var fasta: File = _ + @Input(doc="The reference fasta index") var fai: File = _ @Output(doc="The final VCF to write to") var outVCF : File = _ class PeekableXRL(f : File ) { @@ -49,7 +49,7 @@ class VCFSimpleMerge extends InProcessFunction { def run = { var ssd : SAMSequenceDictionary = new SAMSequenceDictionary - for ( line <- (new XReadLines(fasta)).readLines ) { + for ( line <- (new XReadLines(fai)).readLines ) { val spl = line.split("\\s+") val ctig = spl(0) val pos = Integer.parseInt(spl(1))