At chartl's superb suggestion, command line files are now all Files instead of old method of sometimes "has a File". Should be easier when reassigning them.
No longer generating deprecated GATK arguments on the Queue extensions. Emitting deprecation warnings to Queue compile to help debugging issues. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4195 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kshakir
parent
0bb05fb472
commit
fd5970fdd4
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@ -110,8 +110,9 @@ public abstract class ArgumentDefinitionField extends ArgumentField {
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public static List<? extends ArgumentField> getArgumentFields(Class<?> classType) {
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List<ArgumentField> argumentFields = new ArrayList<ArgumentField>();
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for (ArgumentSource argumentSource: ParsingEngine.extractArgumentSources(classType))
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for (ArgumentDefinition argumentDefinition: argumentSource.createArgumentDefinitions())
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argumentFields.addAll(getArgumentFields(argumentDefinition));
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if (!argumentSource.isDeprecated())
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for (ArgumentDefinition argumentDefinition: argumentSource.createArgumentDefinitions())
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argumentFields.addAll(getArgumentFields(argumentDefinition));
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return argumentFields;
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}
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@ -131,7 +132,7 @@ public abstract class ArgumentDefinitionField extends ArgumentField {
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//return Collections.<ArgumentField>emptyList();
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} else if ("input_file".equals(argumentDefinition.fullName) && argumentDefinition.ioType == ArgumentIOType.INPUT) {
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return Arrays.asList(new InputNamedFileDefinitionField(argumentDefinition), new IndexFilesField());
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return Arrays.asList(new InputTaggedFileDefinitionField(argumentDefinition), new IndexFilesField());
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} else if (argumentDefinition.ioType == ArgumentIOType.INPUT) {
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return Collections.singletonList(new InputArgumentField(argumentDefinition));
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@ -327,15 +328,15 @@ public abstract class ArgumentDefinitionField extends ArgumentField {
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/**
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* Named input_files.
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*/
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public static class InputNamedFileDefinitionField extends ArgumentDefinitionField {
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public InputNamedFileDefinitionField(ArgumentDefinition argumentDefinition) {
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public static class InputTaggedFileDefinitionField extends ArgumentDefinitionField {
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public InputTaggedFileDefinitionField(ArgumentDefinition argumentDefinition) {
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super(argumentDefinition);
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}
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@Override protected Class<?> getInnerType() { return null; } // NamedFile does not need to be imported.
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@Override protected String getFieldType() { return "List[NamedFile]"; }
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@Override protected Class<?> getInnerType() { return null; } // TaggedFile does not need to be imported.
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@Override protected String getFieldType() { return "List[File]"; }
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@Override protected String getDefaultValue() { return "Nil"; }
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@Override protected String getCommandLineTemplate() {
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return " + repeat(\"\", %3$s, format=NamedFile.formatCommandLine(\"%1$s\"))";
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return " + repeat(\"\", %3$s, format=TaggedFile.formatCommandLine(\"%1$s\"))";
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}
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}
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@ -354,8 +355,8 @@ public abstract class ArgumentDefinitionField extends ArgumentField {
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@Override protected String getRawFieldName() { return "index_files"; }
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@Override protected String getFreezeFields() {
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return String.format(
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"index_files ++= input_file.filter(bam => bam != null && bam.file.getName.endsWith(\".bam\")).map(bam => new File(bam.file.getPath + \".bai\"))%n" +
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"index_files ++= input_file.filter(sam => sam != null && sam.file.getName.endsWith(\".sam\")).map(sam => new File(sam.file.getPath + \".sai\"))%n");
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"index_files ++= input_file.filter(bam => bam != null && bam.getName.endsWith(\".bam\")).map(bam => new File(bam.getPath + \".bai\"))%n" +
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"index_files ++= input_file.filter(sam => sam != null && sam.getName.endsWith(\".sam\")).map(sam => new File(sam.getPath + \".sai\"))%n");
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}
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}
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@ -44,20 +44,20 @@ class Index(bamIn: File) extends SamtoolsIndexFunction {
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class MergeBAMs(bamList: File) extends PrintReads with UNIVERSAL_GATK_ARGS {
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this.memoryLimit = Some(3)
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this.input_file :+= bamList.toNamedFile
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this.input_file :+= bamList
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this.o = new File(MERGED_DIR + "/" + bamList.getName + ".bam")
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}
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class Call(@Input(doc="foo") bamList: File, n: Integer, name: String) extends UnifiedGenotyper with UNIVERSAL_GATK_ARGS {
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class Call(@Input(doc="foo") bamList: File, n: Int, name: String) extends UnifiedGenotyper with UNIVERSAL_GATK_ARGS {
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@Output(doc="foo") var outVCF: File = new File("%s.%d.%s.vcf".format(bamList.getName, n, name))
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this.memoryLimit = Some(4)
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this.input_file :+= bamList.toNamedFile
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this.input_file :+= bamList
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this.jobQueue = "gsa"
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this.stand_call_conf = Option(10.0)
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this.o = outVCF
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}
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class SliceList(n: Integer) extends CommandLineFunction {
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class SliceList(n: Int) extends CommandLineFunction {
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@Output(doc="foo") var list: File = new File("bams.%d.list".format(n))
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this.jobQueue = "gsa"
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def commandLine = "head -n %d %s > %s".format(n, FULL_BAM_LIST, list)
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@ -55,7 +55,7 @@ class ExampleCountReads extends QScript {
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singleCountReads.jarFile = gatkJar
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singleCountReads.reference_sequence = referenceFile
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// ':+' is the scala List append operator
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singleCountReads.input_file :+= bamFile.toNamedFile
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singleCountReads.input_file :+= bamFile
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add(singleCountReads)
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}
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}
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@ -58,7 +58,7 @@ class ExampleUnifiedGenotyper extends QScript {
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// If you are running this on a compute farm, make sure that the Sting/shell
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// folder is in your path to use mergeText.sh and splitIntervals.sh.
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genotyper.scatterCount = 3
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genotyper.input_file :+= qscript.bamFile.toNamedFile
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genotyper.input_file :+= qscript.bamFile
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genotyper.out = swapExt(qscript.bamFile, "bam", "unfiltered.vcf")
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evalUnfiltered.rodBind :+= RodBind("vcf", "VCF", genotyper.out)
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@ -80,7 +80,7 @@ class fullCallingPipeline extends QScript {
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val cleanedBase: String = projectBase + ".cleaned"
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val uncleanedBase: String = projectBase + ".uncleaned"
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// there are commands that use all the bam files
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var cleanBamFiles = List.empty[NamedFile]
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var cleanBamFiles = List.empty[File]
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for ( bam <- qscript.bamFiles ) {
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@ -94,7 +94,7 @@ class fullCallingPipeline extends QScript {
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// create the cleaning commands
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val targetCreator = new RealignerTargetCreator with CommandLineGATKArgs
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targetCreator.input_file :+= bam.toNamedFile
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targetCreator.input_file :+= bam
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targetCreator.out = indel_targets
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val realigner = new IndelRealigner with CommandLineGATKArgs
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@ -112,7 +112,7 @@ class fullCallingPipeline extends QScript {
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// put clean bams in clean genotypers
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cleanBamFiles :+= realigner.out.toNamedFile
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cleanBamFiles :+= realigner.out
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add(targetCreator,realigner,samtoolsindex)
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}
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@ -122,7 +122,7 @@ class fullCallingPipeline extends QScript {
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endToEnd(cleanedBase,cleanBamFiles)
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}
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def endToEnd(base: String, bamFiles: List[NamedFile]) = {
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def endToEnd(base: String, bamFiles: List[File]) = {
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// step through the un-indel-cleaned graph:
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// 1a. call snps and indels
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@ -158,7 +158,7 @@ class fullCallingPipeline extends QScript {
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var priority = ""
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for ( bam <- bamFiles ) {
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val indel = new IndelGenotyperV2 with CommandLineGATKArgs
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indel.input_file :+= bam.toNamedFile
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indel.input_file :+= bam
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indel.out = swapExt(bam,".bam",".indels.vcf")
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indel.downsample_to_coverage = Some(500)
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indelCallFiles :+= RodBind("v"+loopNo.toString, "VCF", indel.out)
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@ -186,28 +186,28 @@ class fullCallingPipeline extends QScript {
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annotated.rodBind :+= RodBind("variant", "VCF", snps.out)
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annotated.rodBind :+= RodBind("refseq", "AnnotatorInputTable", qscript.refseqTable)
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annotated.rodBind :+= RodBind("dbsnp", "AnnotatorInputTable", qscript.dbsnpTable)
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annotated.vcfOutput = swapExt(snps.out,".vcf",".annotated.vcf").getAbsolutePath
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annotated.out = swapExt(snps.out,".vcf",".annotated.vcf")
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annotated.select :+= "dbsnp.name,dbsnp.refUCSC,dbsnp.strand,dbsnp.observed,dbsnp.avHet"
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annotated.rodToIntervalTrackName = "variant"
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// 2.a filter on cluster and near indels
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val masker = new VariantFiltration with CommandLineGATKArgs
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masker.rodBind :+= RodBind("variant", "VCF", new File(annotated.vcfOutput))
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masker.rodBind :+= RodBind("mask", "VCF", new File(mergeIndels.out.getAbsolutePath))
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masker.rodBind :+= RodBind("variant", "VCF", annotated.out)
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masker.rodBind :+= RodBind("mask", "VCF", mergeIndels.out)
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masker.maskName = "NearIndel"
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masker.clusterWindowSize = Some(qscript.snpClusterWindow)
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masker.clusterSize = Some(qscript.snpsInCluster)
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masker.out = swapExt(new File(annotated.vcfOutput),".vcf",".indel.masked.vcf")
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masker.out = swapExt(annotated.out,".vcf",".indel.masked.vcf")
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// 2.b hand filter with standard filter
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val handFilter = new VariantFiltration with CommandLineGATKArgs
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handFilter.rodBind :+= RodBind("variant", "VCF", new File(annotated.vcfOutput))
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handFilter.rodBind :+= RodBind("variant", "VCF", annotated.out)
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handFilter.rodBind :+= RodBind("mask", "VCF", mergeIndels.out)
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handFilter.filterName ++= List("StrandBias","AlleleBalance","QualByDepth","HomopolymerRun")
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handFilter.filterExpression ++= List("\"SB>=0.10\"","\"AB>=0.75\"","QD<5","\"HRun>=4\"")
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handFilter.out = swapExt(new File(annotated.vcfOutput),".vcf",".handfiltered.vcf")
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handFilter.out = swapExt(annotated.out,".vcf",".handfiltered.vcf")
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// 3.i generate gaussian clusters on the masked vcf
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@ -131,16 +131,12 @@ class CleanBamFile extends QScript {
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var fixedBam: File = null
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if (realigner.scatterCount > 1) {
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realigner.output = baseFile(".cleaned.bam")
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realigner.out = baseFile(".cleaned.bam")
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// While gathering run fix mates.
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realigner.setupScatterFunction = {
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case (scatter: IntervalScatterFunction, _) =>
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scatter.splitIntervalsScript = indelRealignerScatterScript
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}
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realigner.gatherClass = {
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case source if (source.field.getName=="output") =>
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classOf[BamGatherFunction]
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}
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realigner.setupGatherFunction = {
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case (gather: BamGatherFunction, _) =>
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gather.memoryLimit = Some(4)
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@ -151,9 +147,9 @@ class CleanBamFile extends QScript {
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gather.mergeTextScript = mergeTextScript
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}
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fixedBam = realigner.output
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fixedBam = realigner.out
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} else {
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realigner.output = baseFile(".unfixed.cleaned.bam")
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realigner.out = baseFile(".unfixed.cleaned.bam")
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// Explicitly run fix mates if the function won't be scattered.
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var fixMates = new PicardBamJarFunction {
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@ -165,7 +161,7 @@ class CleanBamFile extends QScript {
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}
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fixMates.memoryLimit = Some(4)
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fixMates.jarFile = fixMatesJar
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fixMates.unfixed = realigner.output
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fixMates.unfixed = realigner.out
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fixMates.fixed = baseFile(".cleaned.bam")
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fixedBam = fixMates.fixed
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@ -64,7 +64,6 @@ class CountCovariates(bamIn: File, recalDataIn: File) extends org.broadinstitute
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this.recal_file = recalDataIn
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this.DBSNP = new File("/humgen/gsa-hpprojects/GATK/data/dbsnp_129_hg18.rod")
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this.logging_level = "INFO"
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this.max_reads_at_locus = Some(20000)
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this.covariate ++= List("ReadGroupCovariate", "QualityScoreCovariate", "CycleCovariate", "DinucCovariate")
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this.memoryLimit = Some(3)
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@ -75,7 +74,7 @@ class TableRecalibrate(bamInArg: File, recalDataIn: File, bamOutArg: File) exten
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this.jarFile = gatkJarFile
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this.input_file :+= bamInArg
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this.recal_file = recalDataIn
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this.output_bam = bamOutArg
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this.out = bamOutArg
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this.logging_level = "INFO"
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this.memoryLimit = Some(2)
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this.skipUQUpdate = skipUQUpdateArg
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@ -26,24 +26,23 @@ for (g: Int <- gList) {
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gvc.logging_level = "INFO"
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gvc.intervalsString :+= "20"
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gvc.use_annotation ++= List("QD", "SB", "HaplotypeScore", "HRun")
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gvc.path_to_resources = "/humgen/gsa-scr1/rpoplin/sting_dev_vb/R/"
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gvc.maxGaussians = Some(g)
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gvc.shrinkage = Some(s)
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gvc.shrinkageFormat = "%.6f"
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gvc.dirichlet = Some(d)
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gvc.dirichletFormat = "%.6f"
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gvc.clusterFile = "g%d_s%.6f_d%.6f_b%.2f.cluster".format(g,s,d,b)
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gvc.jobOutputFile = new File(gvc.clusterFile.stripSuffix(".cluster") + ".gvc.out")
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gvc.clusterFile = new File("g%d_s%.6f_d%.6f_b%.2f.cluster".format(g,s,d,b))
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gvc.jobOutputFile = swapExt(gvc.clusterFile, ".cluster", ".gvc.out")
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vr.jarFile = gatkJarFile
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vr.rodBind :+= RodBind("input20", "VCF", new File("/broad/shptmp/rpoplin/CEUTSI.chr20.filtered.vcf"))
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vr.logging_level = "INFO"
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vr.intervalsString :+= "20"
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vr.target_titv = Some(2.1)
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vr.target_titv = 2.1
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vr.ignore_filter :+= "HARD_TO_VALIDATE"
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vr.path_to_resources = "/humgen/gsa-scr1/rpoplin/sting_dev_vb/R/"
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vr.clusterFile = gvc.clusterFile
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vr.jobOutputFile = new File(vr.clusterFile.stripSuffix(".cluster") + ".vr.out")
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vr.jobOutputFile = swapExt(vr.clusterFile, ".cluster", ".vr.out")
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vr.backOff = Some(b)
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vr.backOffFormat = "%.2f"
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@ -49,6 +49,7 @@ object QScriptManager extends Logging {
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val settings = new Settings((error: String) => logger.error(error))
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val outdir = IOUtils.tempDir("Q-classes")
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settings.deprecation.value = true
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settings.outdir.value = outdir.getPath
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// Set the classpath to the current class path.
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@ -1,35 +0,0 @@
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package org.broadinstitute.sting.queue.extensions.gatk
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import java.io.File
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import org.broadinstitute.sting.queue.function.FileProvider
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/**
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* Used to provide -I input_file arguments to the GATK.
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*/
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class NamedFile(var file: File, var name: String = null) extends FileProvider {
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require(file != null, "NamedFile file cannot be null")
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}
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/**
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* Used to provide -I input_file arguments to the GATK.
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*/
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object NamedFile {
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/**
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* Formats the rod binding on the command line.
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* Used for optional and repeat.
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* @param cmdLineParam command line parameter, ex: -I
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* @param prefix unused
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* @param value NamedFile to add.
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* @param suffix unused
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* @return The command line addition.
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*/
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def formatCommandLine(cmdLineParam: String)(prefix: String, value: Any, suffix: String) = {
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value match {
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case namedFile: NamedFile =>
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if (namedFile.name != null)
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" %s:%s %s".format(cmdLineParam, namedFile.name, namedFile.file)
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else
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" %s %s".format(cmdLineParam, namedFile.file)
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}
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}
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}
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@ -1,8 +0,0 @@
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package org.broadinstitute.sting.queue.extensions.gatk
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import java.io.File
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class NamedFileWrapper(private val file: File) {
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def toNamedFile = new NamedFile(file)
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def toNamedFile(name: String) = new NamedFile(file, name)
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}
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@ -1,21 +1,27 @@
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package org.broadinstitute.sting.queue.extensions.gatk
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import java.io.File
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import org.broadinstitute.sting.queue.function.FileProvider
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import org.broadinstitute.sting.queue.function.FileExtension
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import java.lang.String
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/**
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* Used to provide -B rodBind arguments to the GATK.
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*/
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case class RodBind(var trackName: String, var trackType: String, var file: File) extends FileProvider {
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class RodBind(var trackName: String, var trackType: String, path: String) extends File(path) with FileExtension {
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def this(trackName: String, trackType: String, file: File) =
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this(trackName, trackType, file.getPath)
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require(trackName != null, "RodBind trackName cannot be null")
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require(trackType != null, "RodBind trackType cannot be null")
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require(file != null, "RodBind file cannot be null")
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def withPath(newPath: String) = new RodBind(trackName, trackType, newPath)
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}
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/**
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* Used to provide -B rodBind arguments to the GATK.
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*/
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object RodBind {
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def apply(trackName: String, trackType: String, path: String) = new RodBind(trackName, trackType, path)
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def apply(trackName: String, trackType: String, file: File) = new RodBind(trackName, trackType, file)
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/**
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* Formats the rod binding on the command line.
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* Used for optional and repeat.
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@ -28,7 +34,7 @@ object RodBind {
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def formatCommandLine(cmdLineParam: String)(prefix: String, value: Any, suffix: String) = {
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value match {
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case rodBind: RodBind =>
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" %s:%s,%s %s".format(cmdLineParam, rodBind.trackName, rodBind.trackType, rodBind.file)
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" %s:%s,%s %s".format(cmdLineParam, rodBind.trackName, rodBind.trackType, rodBind.getPath)
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}
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}
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}
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|
|
|
|||
|
|
@ -0,0 +1,39 @@
|
|||
package org.broadinstitute.sting.queue.extensions.gatk
|
||||
|
||||
import java.io.File
|
||||
import org.broadinstitute.sting.queue.function.FileExtension
|
||||
|
||||
/**
|
||||
* Used to provide tagged -I input_file arguments to the GATK.
|
||||
*/
|
||||
class TaggedFile(path: String, val tag: String) extends File(path) with FileExtension {
|
||||
def this(file: File, tag: String) =
|
||||
this(file.getPath, tag)
|
||||
def withPath(path: String) = new TaggedFile(path, tag)
|
||||
}
|
||||
|
||||
/**
|
||||
* Used to provide -I input_file arguments to the GATK.
|
||||
*/
|
||||
object TaggedFile {
|
||||
def apply(path: String, tag: String) = new TaggedFile(path, tag)
|
||||
def apply(file: File, tag: String) = new TaggedFile(file, tag)
|
||||
|
||||
/**
|
||||
* Formats the rod binding on the command line.
|
||||
* Used for optional and repeat.
|
||||
* @param cmdLineParam command line parameter, ex: -I
|
||||
* @param prefix unused
|
||||
* @param value TaggedFile to add.
|
||||
* @param suffix unused
|
||||
* @return The command line addition.
|
||||
*/
|
||||
def formatCommandLine(cmdLineParam: String)(prefix: String, value: Any, suffix: String) = {
|
||||
value match {
|
||||
case taggedFile: TaggedFile if (taggedFile.tag != null) =>
|
||||
" %s:%s %s".format(cmdLineParam, taggedFile.tag, taggedFile.getPath)
|
||||
case file: File =>
|
||||
" %s %s".format(cmdLineParam, file.getPath)
|
||||
}
|
||||
}
|
||||
}
|
||||
|
|
@ -1,13 +0,0 @@
|
|||
package org.broadinstitute.sting.queue.extensions
|
||||
|
||||
import java.io.File
|
||||
import org.broadinstitute.sting.queue.extensions.gatk.NamedFile
|
||||
import org.broadinstitute.sting.queue.extensions.gatk.NamedFileWrapper
|
||||
|
||||
package object gatk {
|
||||
implicit def fileToNamedFileWrapper(file: File) = new NamedFileWrapper(file)
|
||||
// TODO: Get the syntax right so that the implicits kick in for a generic type, ex: Travesable[File], Traversable[_ <: File], etc.
|
||||
// but need to return the same outter type, so T <: Traversable[File] : T[NamedFile], T <: Traversable[_ <: File]: T[NamedFile], etc.
|
||||
implicit def filesToNamedFilesWrapper(files: List[File]) = files.map(file => if (file == null) null else new NamedFile(file))
|
||||
implicit def filesToNamedFilesWrapper(files: Set[File]) = files.map(file => if (file == null) null else new NamedFile(file))
|
||||
}
|
||||
|
|
@ -94,7 +94,7 @@ trait CommandLineFunction extends QFunction with Logging {
|
|||
def outputs = getFieldFiles(outputFields)
|
||||
|
||||
/**
|
||||
* Gets the files from the fields. The fields must be a File, a FileProvider, or a List or Set of either.
|
||||
* Gets the files from the fields. The fields must be a File, a FileExtension, or a List or Set of either.
|
||||
* @param fields Fields to get files.
|
||||
* @return Set[File] for the fields.
|
||||
*/
|
||||
|
|
@ -121,7 +121,7 @@ trait CommandLineFunction extends QFunction with Logging {
|
|||
}
|
||||
|
||||
/**
|
||||
* Gets the files from the field. The field must be a File, a FileProvider, or a List or Set of either.
|
||||
* Gets the files from the field. The field must be a File, a FileExtension, or a List or Set of either.
|
||||
* @param fields Field to get files.
|
||||
* @return Set[File] for the field.
|
||||
*/
|
||||
|
|
@ -136,7 +136,7 @@ trait CommandLineFunction extends QFunction with Logging {
|
|||
}
|
||||
|
||||
/**
|
||||
* Gets the file from the field. The field must be a File or a FileProvider and not a List or Set.
|
||||
* Gets the file from the field. The field must be a File or a FileExtension and not a List or Set.
|
||||
* @param field Field to get the file.
|
||||
* @return File for the field.
|
||||
*/
|
||||
|
|
@ -144,17 +144,16 @@ trait CommandLineFunction extends QFunction with Logging {
|
|||
fieldValueToFile(field, getFieldValue(field))
|
||||
|
||||
/**
|
||||
* Converts the field value to a file. The field must be a File or a FileProvider.
|
||||
* Converts the field value to a file. The field must be a File or a FileExtension.
|
||||
* @param field Field to get the file.
|
||||
* @param value Value of the File or FileProvider or null.
|
||||
* @param value Value of the File or FileExtension or null.
|
||||
* @return Null if value is null, otherwise the File.
|
||||
* @throws QException if the value is not a File or FileProvider.
|
||||
* @throws QException if the value is not a File or FileExtension.
|
||||
*/
|
||||
private def fieldValueToFile(field: ArgumentSource, value: Any): File = value match {
|
||||
case file: File => file
|
||||
case fileProvider: FileProvider => fileProvider.file
|
||||
case null => null
|
||||
case unknown => throw new QException("Non-file found. Try removing the annotation, change the annotation to @Argument, or implement FileProvider: %s: %s".format(field.field, unknown))
|
||||
case unknown => throw new QException("Non-file found. Try removing the annotation, change the annotation to @Argument, or extend File with FileExtension: %s: %s".format(field.field, unknown))
|
||||
}
|
||||
|
||||
/**
|
||||
|
|
@ -164,15 +163,19 @@ trait CommandLineFunction extends QFunction with Logging {
|
|||
*/
|
||||
def resetFieldFile(field: ArgumentSource, tempDir: File): File = {
|
||||
getFieldValue(field) match {
|
||||
case fileExtension: FileExtension => {
|
||||
val newFile = IOUtils.resetParent(tempDir, fileExtension)
|
||||
val newFileExtension = fileExtension.withPath(newFile.getPath)
|
||||
setFieldValue(field, newFileExtension)
|
||||
newFileExtension
|
||||
}
|
||||
case file: File => {
|
||||
if (file.getClass == classOf[File])
|
||||
throw new QException("Extensions of file must also extend with FileExtension so that the path can be modified.");
|
||||
val newFile = IOUtils.resetParent(tempDir, file)
|
||||
setFieldValue(field, newFile)
|
||||
newFile
|
||||
}
|
||||
case fileProvider: FileProvider => {
|
||||
fileProvider.file = IOUtils.resetParent(tempDir, fileProvider.file)
|
||||
fileProvider.file
|
||||
}
|
||||
case null => null
|
||||
case unknown =>
|
||||
throw new QException("Unable to set file from %s: %s".format(field, unknown))
|
||||
|
|
@ -242,8 +245,14 @@ trait CommandLineFunction extends QFunction with Logging {
|
|||
*/
|
||||
protected def canon(value: Any) = {
|
||||
value match {
|
||||
case file: File => absolute(file)
|
||||
case fileProvider: FileProvider => fileProvider.file = absolute(fileProvider.file); fileProvider
|
||||
case fileExtension: FileExtension =>
|
||||
val newFile = absolute(fileExtension);
|
||||
val newFileExtension = fileExtension.withPath(newFile.getPath)
|
||||
newFileExtension
|
||||
case file: File =>
|
||||
if (file.getClass != classOf[File])
|
||||
throw new QException("Extensions of file must also extend with FileExtension so that the path can be modified.");
|
||||
absolute(file)
|
||||
case x => x
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -0,0 +1,15 @@
|
|||
package org.broadinstitute.sting.queue.function
|
||||
|
||||
import java.io.File
|
||||
|
||||
/**
|
||||
* An trait for @Input or @Output CommandLineFunction fields that are extensions of files.
|
||||
*/
|
||||
trait FileExtension extends File {
|
||||
/**
|
||||
* Returns a clone of the FileExtension with the new path.
|
||||
* @param newPath new path for the clone of this FileExtension
|
||||
* @return a clone of the FileExtension with the new path.
|
||||
*/
|
||||
def withPath(newPath: String): File
|
||||
}
|
||||
|
|
@ -1,11 +0,0 @@
|
|||
package org.broadinstitute.sting.queue.function
|
||||
|
||||
import java.io.File
|
||||
|
||||
/**
|
||||
* An trait for @Input or @Output CommandLineFunction fields that are not files, but have a File that can be get/set.
|
||||
*/
|
||||
trait FileProvider {
|
||||
/** Gets/Sets the file. */
|
||||
var file: File
|
||||
}
|
||||
Loading…
Reference in New Issue