From 6a26957b655d918ffb7ea90a8cfc95ea0d12156c Mon Sep 17 00:00:00 2001 From: chartl Date: Thu, 7 Apr 2011 20:11:28 +0000 Subject: [PATCH] Bug squashing git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5592 348d0f76-0448-11de-a6fe-93d51630548a --- .../oneoffs/chartl/Exome_VQSR_FullSearch.q | 24 +++++++++---------- 1 file changed, 12 insertions(+), 12 deletions(-) diff --git a/scala/qscript/oneoffs/chartl/Exome_VQSR_FullSearch.q b/scala/qscript/oneoffs/chartl/Exome_VQSR_FullSearch.q index 8e6c9a1b7..1600c4f96 100755 --- a/scala/qscript/oneoffs/chartl/Exome_VQSR_FullSearch.q +++ b/scala/qscript/oneoffs/chartl/Exome_VQSR_FullSearch.q @@ -8,7 +8,7 @@ import org.broadinstitute.sting.queue.library.ipf.intervals.ExpandIntervals import org.broadinstitute.sting.queue.QScript import org.broadinstitute.sting.utils.interval.IntervalSetRule import org.broadinstitute.sting.utils.text.XReadLines -import collection.JavaConversions +import collection.JavaConversions._ class Exome_VQSR_FullSearch extends QScript { qScript => @@ -24,12 +24,12 @@ class Exome_VQSR_FullSearch extends QScript { val OMNI_CHIP = new File("/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/Omni2.5_chip/1212samples.b37.vcf") val AXIOM_CHIP = new File("/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/affymetrix_axiom/Affymetrix_Axiom_DB_2010_v4_b37.noOmni.noHM3.vcf") val DBSNP_129 = new File("/humgen/gsa-hpprojects/GATK/data/dbsnp_129_b37.vcf") - val SENSITIVITY = (new Range(0,19)).map(u => 90.0 + 0.5*u).toList + val SENSITIVITY = (new Range(0,19,1)).map(u => 90.0 + 0.5*u).toList val RECALIBRATE_TOGETHER = List(true,false) val VQSR_HAPMAP_PRIOR = "15.0" val VQSR_OMNI_PRIOR = "12.0" - var VQSR_RODBINDS : Map[String,List[RodBind]] = new HashMap[String,List[RodBind]] + var VQSR_RODBINDS : HashMap[String,List[RodBind]] = new HashMap[String,List[RodBind]] val VQSR_TAG_FT = "known=false,training=true,truth=%s,prior=%s" val VQSR_DBSNP_TAG = "known=true,training=false,truth=false" @@ -42,10 +42,10 @@ class Exome_VQSR_FullSearch extends QScript { mrb :+= RodBind("dbsnp","VCF",DBSNP_129,VQSR_DBSNP_TAG) mrb :+= RodBind("HapMap3","VCF",HM3_SITES,VQSR_TAG_FT.format(hmSt,VQSR_HAPMAP_PRIOR)) mrb :+= RodBind("Omni","VCF",OMNI_CHIP,VQSR_TAG_FT.format(omSt,VQSR_OMNI_PRIOR)) - VQSR_RODBINDS :+= (ext,mrb) + VQSR_RODBINDS += (ext,mrb) } - val BAM_FILES : List[File] = (new XReadLines(new File("/humgen/gsa-hphome1/chartl/projects/oneoffs/VQSR_Exome/resources/broad.bam.list"))).readLines.map(u => new File(u)).toList + val BAM_FILES : List[File] = asScalaList((new XReadLines(new File("/humgen/gsa-hphome1/chartl/projects/oneoffs/VQSR_Exome/resources/broad.bam.list"))).readLines).map(u => new File(u)) val REF : File = new File("/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta") val INTS : File = new File("/seq/references/HybSelOligos/whole_exome_agilent_1.1_refseq_plus_3_boosters/whole_exome_agilent_1.1_refseq_plus_3_boosters.Homo_sapiens_assembly19.targets.interval_list") val EXPAND_INTS = 40 @@ -60,7 +60,7 @@ class Exome_VQSR_FullSearch extends QScript { this.memoryLimit = Some(4) } - val ei : ExpandIntervals = new ExpandIntervals(INTS,1,qscript.expandIntervals, new File("Resources", base + ".flanks.interval_list"), REF, "INTERVALS", "INTERVALS") + val ei : ExpandIntervals = new ExpandIntervals(INTS,1,EXPAND_INTSs, new File("Resources", SCRIPT_BASE_NAME + ".flanks.interval_list"), REF, "INTERVALS", "INTERVALS") ei.jobOutputFile = new File(".queue/logs/Overall/ExpandIntervals.out") if (EXPAND_INTS > 0) { @@ -74,16 +74,16 @@ class Exome_VQSR_FullSearch extends QScript { } val callSNPsAndIndels = new UnifiedGenotyper with CommandLineGATKArgs with ExpandedIntervals - callSNPsAndIndels.analysisName = base+"_calls" + callSNPsAndIndels.analysisName = SCRIPT_BASE_NAME+"_calls" callSNPsAndIndels.jobOutputFile = new File(".queue/logs/SNPCalling/UnifiedGenotyper.snps.out") callSNPsAndIndels.memoryLimit = Some(6) callSNPsAndIndels.downsample_to_coverage = Some(600) - callSNPsAndIndels.input_file = bamFiles + callSNPsAndIndels.input_file = BAM_FILES callSNPsAndIndels.rodBind :+= RodBind("dbsnp", "vcf", DBSNP_129) callSNPsAndIndels.out = new File(SCRIPT_BASE_NAME+".rawCalls.vcf") callSNPsAndIndels.stand_call_conf = Some(UG_CALL_THRESH) - callSNPsAndIndels.scatterCount = qscript.num_var_scatter_jobs + callSNPsAndIndels.scatterCount = 50 callSNPsAndIndels.setupScatterFunction = { case scatter: ScatterFunction => scatter.commandDirectory = new File("SnpCalls/ScatterGather") @@ -112,7 +112,7 @@ class Exome_VQSR_FullSearch extends QScript { def canPrint(line: String) : Boolean = { if ( line.startsWith("#") ) { true } val spline = line.split("\t",5) - if ( spline.apply(3).size() > 1 || spline.apply(4).size() > 1 ) { false } + if ( spline.apply(3).size > 1 || spline.apply(4).size > 1 ) { false } true } @@ -126,7 +126,7 @@ class Exome_VQSR_FullSearch extends QScript { } } - val extractSNPs : ExtractSNPs = new ExtractSNPs(callSNPsAndIndels.out,new File(base+".snpCalls.vcf")) + val extractSNPs : ExtractSNPs = new ExtractSNPs(callSNPsAndIndels.out,new File(SCRIPT_BASE_NAME+".snpCalls.vcf")) add(extractSNPs) def getPath(annoList: List[String], jointRecal: Boolean) : File = { @@ -138,7 +138,7 @@ class Exome_VQSR_FullSearch extends QScript { val directory = getPath(annotations,recalTogether) for ( call_thresh <- VQSR_CALL_THRESH ) { var filterQual = new VariantFiltration with CommandLineGATKArgs with ExpandedIntervals - filterQual.rodBind :+= new RodBind(extractSNPs.outputVCF) + filterQual.rodBind :+= new RodBind("variant","VCF",extractSNPs.outputVCF) filterQual.filterExpression :+= "QUAL < %.1f".format(VQSR_CALL_THRESH) filterQual.filterName :+= "LowQual" filterQual.commandDirectory = directory