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Bugfixed to script.

This commit is contained in:
Christopher Hartl 2012-02-02 12:55:54 -05:00
parent 27ea6426a4
commit 974c2499cc
1 changed files with 7 additions and 5 deletions
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12
public/scala/qscript/org/broadinstitute/sting/queue/qscripts/lib/ChunkVCF.scala
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@ -23,7 +23,7 @@ class ChunkVCF extends QScript {
@Input(shortName="N",fullName="numEntriesInChunk",doc="The number of variants per chunk",required=true) @Input(shortName="N",fullName="numEntriesInChunk",doc="The number of variants per chunk",required=true)
var numEntries : Int = _ var numEntries : Int = _
@Input(shortName="I",fullName="Intervals",doc="The SNP interval list to chunk. If not provided, one will be created for you to provide in a second run.") @Input(shortName="I",fullName="Intervals",doc="The SNP interval list to chunk. If not provided, one will be created for you to provide in a second run.",required=false)
var intervals : File = _ var intervals : File = _
@Input(fullName="preserveChromosomes",doc="Restrict chunks to one chromosome (smaller chunk at end of chromosome)",required=false) @Input(fullName="preserveChromosomes",doc="Restrict chunks to one chromosome (smaller chunk at end of chromosome)",required=false)
@ -40,8 +40,8 @@ class ChunkVCF extends QScript {
def script = { def script = {
if ( intervals == null ) { if ( intervals == null ) {
// create an interval list from the VCF // create an interval list from the VCF
val ivals : File = swapExt(variants,".vcf",".intervals.list") val ivals : File = swapExt(inVCF,".vcf",".intervals.list")
val extract : VCFExtractIntervals = new VCFExtractIntervals(variants,ivals,false) val extract : VCFExtractIntervals = new VCFExtractIntervals(inVCF,ivals,false)
add(extract) add(extract)
} else { } else {
var chunkNum = 1 var chunkNum = 1
@ -54,11 +54,12 @@ class ChunkVCF extends QScript {
if ( ( preserve && ! int.split(":")(0).equals(chromosome) ) || numLinesInChunk > numEntries ) { if ( ( preserve && ! int.split(":")(0).equals(chromosome) ) || numLinesInChunk > numEntries ) {
chunkWriter.close() chunkWriter.close()
val chunkSelect : SelectVariants = new SelectVariants val chunkSelect : SelectVariants = new SelectVariants
chunkSelect.variant = inVCF
chunkSelect.reference_sequence = ref chunkSelect.reference_sequence = ref
chunkSelect.memoryLimit = 2 chunkSelect.memoryLimit = 2
chunkSelect.intervals :+= chunkFile chunkSelect.intervals :+= chunkFile
if ( extractSamples != null ) if ( extractSamples != null )
chunkSelect.sample_file = extractSamples chunkSelect.sample_file :+= extractSamples
chunkSelect.out = swapExt(inVCF,".vcf",".chunk%d.vcf".format(chunkNum)) chunkSelect.out = swapExt(inVCF,".vcf",".chunk%d.vcf".format(chunkNum))
add(chunkSelect) add(chunkSelect)
chunkNum += 1 chunkNum += 1
@ -74,12 +75,13 @@ class ChunkVCF extends QScript {
if ( numLinesInChunk > 0 ) { if ( numLinesInChunk > 0 ) {
// some work to do // some work to do
val chunkSelect : SelectVariants = new SelectVariants val chunkSelect : SelectVariants = new SelectVariants
chunkSelect.variant = inVCF
chunkSelect.reference_sequence = ref chunkSelect.reference_sequence = ref
chunkSelect.memoryLimit = 2 chunkSelect.memoryLimit = 2
chunkSelect.intervals :+= chunkFile chunkSelect.intervals :+= chunkFile
chunkWriter.close() chunkWriter.close()
if ( extractSamples != null ) if ( extractSamples != null )
chunkSelect.sample_file = extractSamples chunkSelect.sample_file :+= extractSamples
chunkSelect.out = swapExt(inVCF,".vcf",".chunk%d.vcf".format(chunkNum)) chunkSelect.out = swapExt(inVCF,".vcf",".chunk%d.vcf".format(chunkNum))
add(chunkSelect) add(chunkSelect)
} }