zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

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
This commit is contained in:
chartl 2011-02-03 05:03:48 +00:00
parent 9515f94242
commit a9d0921529
1 changed files with 2 additions and 2 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

4
scala/src/org/broadinstitute/sting/queue/library/ipf/vcf/VCFSimpleMerge.scala
View File

@ -10,7 +10,7 @@ import org.broadinstitute.sting.utils.{GenomeLocParser, GenomeLoc}
class VCFSimpleMerge extends InProcessFunction { class VCFSimpleMerge extends InProcessFunction {
@Input(doc="VCFs to be merged") var vcfs: List[File] = Nil @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 = _ @Output(doc="The final VCF to write to") var outVCF : File = _
class PeekableXRL(f : File ) { class PeekableXRL(f : File ) {
@ -49,7 +49,7 @@ class VCFSimpleMerge extends InProcessFunction {
def run = { def run = {
var ssd : SAMSequenceDictionary = new SAMSequenceDictionary var ssd : SAMSequenceDictionary = new SAMSequenceDictionary
for ( line <- (new XReadLines(fasta)).readLines ) { for ( line <- (new XReadLines(fai)).readLines ) {
val spl = line.split("\\s+") val spl = line.split("\\s+")
val ctig = spl(0) val ctig = spl(0)
val pos = Integer.parseInt(spl(1)) val pos = Integer.parseInt(spl(1))