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fix the script!

This commit is contained in:
Christopher Hartl 2012-02-01 12:05:29 -05:00
parent 810996cfca
commit 87a63d54d6
1 changed files with 8 additions and 8 deletions
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16
public/scala/qscript/org/broadinstitute/sting/queue/qscripts/lib/VcfToPed.scala
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@ -63,10 +63,10 @@ class VcfToPed extends QScript {
toPed.dbsnp = dbsnp toPed.dbsnp = dbsnp
toPed.variant = variants toPed.variant = variants
toPed.metaData = meta toPed.metaData = meta
lazy val base : String = bed.getName.stripSuffix(".bed")+"_%".format(chunk) val base : String = bed.getName.stripSuffix(".bed")+"_%d".format(chunk)
lazy val tBed = new File(tmpdir,base+".bed") val tBed = new File(tmpdir,base+".bed")
lazy val bim = new File(tmpdir,base+".bim") val bim = new File(tmpdir,base+".bim")
lazy val fam = new File(tmpdir,base+".fam") val fam = new File(tmpdir,base+".fam")
toPed.bed = tBed toPed.bed = tBed
toPed.bim = bim toPed.bim = bim
toPed.fam = fam toPed.fam = fam
@ -89,10 +89,10 @@ class VcfToPed extends QScript {
toPed.dbsnp = dbsnp toPed.dbsnp = dbsnp
toPed.variant = variants toPed.variant = variants
toPed.metaData = meta toPed.metaData = meta
lazy val base : String = bed.getName.stripSuffix(".bed")+"_%".format(chunk) val base : String = bed.getName.stripSuffix(".bed")+"_%d".format(chunk)
lazy val tBed = new File(tmpdir,base+".bed") val tBed = new File(tmpdir,base+".bed")
lazy val bim = new File(tmpdir,base+".bim") val bim = new File(tmpdir,base+".bim")
lazy val fam = new File(tmpdir,base+".fam") val fam = new File(tmpdir,base+".fam")
toPed.bed = tBed toPed.bed = tBed
toPed.bim = bim toPed.bim = bim
toPed.fam = fam toPed.fam = fam