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Sometimes, inputs are really outputs in disguise. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4631 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
chartl 2010-11-05 19:51:16 +00:00
parent bbb890dd6c
commit c19f567424
1 changed files with 8 additions and 4 deletions
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12
scala/qscript/chartl/private_mutations.q
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@ -153,6 +153,8 @@ class private_mutations extends QScript {
exome_single.filter = SINGLE_SAMPLE_EXPRESSION exome_single.filter = SINGLE_SAMPLE_EXPRESSION
exome_single.out_list = new File(LIST_DIR+"g1k_exome_single_sample.variants.list") exome_single.out_list = new File(LIST_DIR+"g1k_exome_single_sample.variants.list")
add(exome_single)
var exome_extract : ExtractSites = new ExtractSites(g1k_exome_calls,new File(VCF_DIR+"g1k_exome.sites.vcf")) var exome_extract : ExtractSites = new ExtractSites(g1k_exome_calls,new File(VCF_DIR+"g1k_exome.sites.vcf"))
add(exome_extract) add(exome_extract)
@ -167,7 +169,7 @@ class private_mutations extends QScript {
getVennExS.variantMergeOptions = Some(VariantContextUtils.VariantMergeType.UNION) getVennExS.variantMergeOptions = Some(VariantContextUtils.VariantMergeType.UNION)
getVennExS.out = new File(VCF_DIR + "g1k_exome_plus_lowpass.singlesample.merged.exome.sites.vcf") getVennExS.out = new File(VCF_DIR + "g1k_exome_plus_lowpass.singlesample.merged.exome.sites.vcf")
add(getVennExS) //add(getVennExS)
var getVennLPS : CombineVariants = new CombineVariants var getVennLPS : CombineVariants = new CombineVariants
getVennLPS.rodBind :+= new RodBind("lowpass","VCF",g1k_lowpass_hg19_merged); getVennLPS.rodBind :+= new RodBind("lowpass","VCF",g1k_lowpass_hg19_merged);
@ -189,7 +191,7 @@ class private_mutations extends QScript {
add(getG1KOverlap) add(getG1KOverlap)
callOverlaps(getG1KOverlap.samples,exome_single.out_list, g1k_exome_calls) //callOverlaps(getG1KOverlap.samples,exome_single.out_list, g1k_exome_calls)
} }
@ -288,7 +290,7 @@ class private_mutations extends QScript {
var inVCF: File = vcfIn var inVCF: File = vcfIn
@Argument(doc="The sample to extract") @Argument(doc="The sample to extract")
var inSample: String = sample var inSample: String = sample
@Input(doc="The VCF file to write to") @Output(doc="The VCF file to write to")
var outVCF: File = vcfOut var outVCF: File = vcfOut
def commandLine = { def commandLine = {
@ -369,7 +371,7 @@ class private_mutations extends QScript {
var waitForMe: File = _ var waitForMe: File = _
def commandLine = { def commandLine = {
"grep %s /humgen/1kg/processing/allPopulations_wholeGenome_august_release/bamLists/*.list | tr ':' '\\t' | awk '{print $2}' > %s".format( "grep %s /humgen/1kg/processing/allPopulations_wholeGenome_august_release/bamLists/*.list | tr ':' '\\t' | awk '{print $2}' | sort | uniq > %s".format(
inSample, inSample,
outList.getAbsolutePath outList.getAbsolutePath
) )
@ -395,6 +397,8 @@ class private_mutations extends QScript {
genotype.intervals :+= sites.out_list genotype.intervals :+= sites.out_list
genotype.out = new File(VCF_DIR+"g1k_lowpass.%s.exome_sites.vcf".format(s)) genotype.out = new File(VCF_DIR+"g1k_lowpass.%s.exome_sites.vcf".format(s))
genotype.input_file :+= bamList.outList genotype.input_file :+= bamList.outList
genotype.memoryLimit = Some(3)
genotype.output_all_callable_bases = true
add(genotype) add(genotype)