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This commit is contained in:
Christopher Hartl 2012-02-02 09:11:17 -05:00
parent f8c5406084
commit 45bf2562cc
1 changed files with 14 additions and 1 deletions
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15
public/scala/qscript/org/broadinstitute/sting/queue/qscripts/lib/VcfToPed.scala
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@ -103,7 +103,20 @@ class VcfToPed extends QScript {
toPed.reference_sequence = ref toPed.reference_sequence = ref
toPed.intervals :+= new File(subListFile) toPed.intervals :+= new File(subListFile)
toPed.dbsnp = dbsnp toPed.dbsnp = dbsnp
toPed.variant = variants if ( samFile != null ) {
val base : String = bed.getName.stripSuffix(".bed")+"_%d".format(chunk)
val extract : SelectVariants = new SelectVariants
extract.reference_sequence = ref
extract.memoryLimit = 2
extract.intervals :+= subListFile
extract.variant = variants
extract.out = new File(tmpdir,base+"_extract%d.vcf".format(chunk))
extract.sample_file :+= samFile
add(extract)
toPed.variant = extract.out
} else {
toPed.variant = variants
}
toPed.metaData = meta toPed.metaData = meta
val base : String = bed.getName.stripSuffix(".bed")+"_%d".format(chunk) val base : String = bed.getName.stripSuffix(".bed")+"_%d".format(chunk)
val tBed = new File(tmpdir,base+".bed") val tBed = new File(tmpdir,base+".bed")