From 55a8306a0d0868f309db1696b2e551e7bd6d47ef Mon Sep 17 00:00:00 2001 From: ebanks Date: Mon, 23 Aug 2010 17:49:37 +0000 Subject: [PATCH] Update the @RMD tags to look for VariantContext.class instead of ReferenceOrderedDatum.class. Since the test for rod type is broken this won't affect anything right now. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4084 348d0f76-0448-11de-a6fe-93d51630548a --- .../org/broadinstitute/sting/gatk/walkers/VariantsToVCF.java | 2 +- .../sting/gatk/walkers/annotator/VariantAnnotator.java | 3 +-- .../sting/gatk/walkers/filters/VariantFiltrationWalker.java | 3 +-- .../sting/gatk/walkers/genotyper/BatchedCallsMerger.java | 3 +-- .../gatk/walkers/sequenom/SequenomValidationConverter.java | 4 ++-- .../gatk/walkers/variantutils/FilterLiftedVariants.java | 3 +-- .../sting/gatk/walkers/variantutils/LiftoverVariants.java | 3 +-- .../sting/gatk/walkers/variantutils/SelectVariants.java | 3 +-- .../oneoffprojects/walkers/BeagleOutputByDepthWalker.java | 5 +---- .../oneoffprojects/walkers/IndelConsistencyReadCounter.java | 2 +- .../playground/gatk/walkers/BeagleOutputToVCFWalker.java | 3 +-- .../playground/gatk/walkers/ProduceBeagleInputWalker.java | 3 +-- .../playground/gatk/walkers/annotator/GenomicAnnotator.java | 2 +- .../playground/gatk/walkers/diagnostics/SNPDensity.java | 3 +-- 14 files changed, 15 insertions(+), 27 deletions(-) diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/VariantsToVCF.java b/java/src/org/broadinstitute/sting/gatk/walkers/VariantsToVCF.java index 2e0fee651..6d16f29ef 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/VariantsToVCF.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/VariantsToVCF.java @@ -47,7 +47,7 @@ import java.io.PrintStream; /** * Converts variants from other file formats to VCF format. */ -@Requires(value={},referenceMetaData=@RMD(name=VariantsToVCF.INPUT_ROD_NAME,type= ReferenceOrderedDatum.class)) +@Requires(value={},referenceMetaData=@RMD(name=VariantsToVCF.INPUT_ROD_NAME, type=VariantContext.class)) @Reference(window=@Window(start=0,stop=40)) public class VariantsToVCF extends RodWalker { @Output diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java index 97b483c93..9b617d3d8 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java @@ -32,7 +32,6 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext; import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum; import org.broadinstitute.sting.gatk.walkers.*; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotationType; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation; @@ -52,7 +51,7 @@ import java.io.PrintStream; /** * Annotates variant calls with context information. Users can specify which of the available annotations to use. */ -@Requires(value={},referenceMetaData=@RMD(name="variant",type=ReferenceOrderedDatum.class)) +@Requires(value={},referenceMetaData=@RMD(name="variant",type=VariantContext.class)) @Allows(value={DataSource.READS, DataSource.REFERENCE}) @Reference(window=@Window(start=-50,stop=50)) @By(DataSource.REFERENCE) diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java index a150e4f38..5c0711e55 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java @@ -33,7 +33,6 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils; import org.broadinstitute.sting.gatk.datasources.simpleDataSources.ReferenceOrderedDataSource; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum; import org.broadinstitute.sting.gatk.refdata.VariantContextAdaptors; import org.broadinstitute.sting.gatk.walkers.*; import org.broadinstitute.sting.commandline.Argument; @@ -48,7 +47,7 @@ import java.io.PrintStream; /** * Filters variant calls using a number of user-selectable, parameterizable criteria. */ -@Requires(value={},referenceMetaData=@RMD(name="variant", type=ReferenceOrderedDatum.class)) +@Requires(value={},referenceMetaData=@RMD(name="variant", type=VariantContext.class)) @Reference(window=@Window(start=-50,stop=50)) public class VariantFiltrationWalker extends RodWalker { @Output diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/BatchedCallsMerger.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/BatchedCallsMerger.java index 5c3078739..0c22bb6f3 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/BatchedCallsMerger.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/BatchedCallsMerger.java @@ -29,7 +29,6 @@ import org.broad.tribble.vcf.VCFWriter; import org.broadinstitute.sting.gatk.contexts.*; import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedData; import org.broadinstitute.sting.gatk.walkers.*; import org.broadinstitute.sting.commandline.*; import org.broadinstitute.sting.utils.pileup.PileupElement; @@ -51,7 +50,7 @@ import net.sf.samtools.SAMReadGroupRecord; */ @Reference(window=@Window(start=-20,stop=20)) @By(DataSource.REFERENCE) -@Requires(value={},referenceMetaData=@RMD(name="trigger", type=ReferenceOrderedData.class)) +@Requires(value={},referenceMetaData=@RMD(name="trigger", type=VariantContext.class)) public class BatchedCallsMerger extends LocusWalker implements TreeReducible { @ArgumentCollection private UnifiedArgumentCollection UAC = new UnifiedArgumentCollection(); diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/SequenomValidationConverter.java b/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/SequenomValidationConverter.java index 9af09a540..6fc5bf124 100644 --- a/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/SequenomValidationConverter.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/SequenomValidationConverter.java @@ -28,13 +28,13 @@ package org.broadinstitute.sting.gatk.walkers.sequenom; import org.broad.tribble.util.variantcontext.Allele; import org.broad.tribble.util.variantcontext.VariantContext; import org.broad.tribble.vcf.*; +import org.broad.tribble.Feature; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils; import org.broadinstitute.sting.gatk.refdata.PlinkRod; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.refdata.VariantContextAdaptors; -import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum; import org.broadinstitute.sting.gatk.walkers.*; import org.broadinstitute.sting.utils.QualityUtils; import org.broadinstitute.sting.utils.collections.Pair; @@ -48,7 +48,7 @@ import java.io.PrintStream; * Converts Sequenom files to a VCF annotated with QC metrics (HW-equilibrium, % failed probes) */ @Reference(window=@Window(start=0,stop=40)) -@Requires(value={},referenceMetaData=@RMD(name="sequenom",type= ReferenceOrderedDatum.class)) +@Requires(value={},referenceMetaData=@RMD(name="sequenom",type= Feature.class)) public class SequenomValidationConverter extends RodWalker,Integer> { @Output protected PrintStream out; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java index 5ef609898..4c62df4e8 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java @@ -30,7 +30,6 @@ import org.broad.tribble.vcf.VCFWriter; import org.broadinstitute.sting.utils.vcf.VCFUtils; import org.broadinstitute.sting.utils.SampleUtils; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum; import org.broadinstitute.sting.gatk.walkers.*; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; @@ -43,7 +42,7 @@ import java.io.PrintStream; /** * Filters a lifted-over VCF file for ref bases that have been changed. */ -@Requires(value={},referenceMetaData=@RMD(name="variant",type= ReferenceOrderedDatum.class)) +@Requires(value={},referenceMetaData=@RMD(name="variant",type= VariantContext.class)) public class FilterLiftedVariants extends RodWalker { @Output PrintStream out; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java index 18d1c9c37..3247c1dda 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java @@ -33,7 +33,6 @@ import org.broadinstitute.sting.utils.vcf.VCFUtils; import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.SampleUtils; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum; import org.broadinstitute.sting.gatk.walkers.*; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; @@ -52,7 +51,7 @@ import net.sf.samtools.SAMFileReader; /** * Lifts a VCF file over from one build to another. Note that the resulting VCF could be mis-sorted. */ -@Requires(value={},referenceMetaData=@RMD(name="variant", type=ReferenceOrderedDatum.class)) +@Requires(value={},referenceMetaData=@RMD(name="variant", type=VariantContext.class)) public class LiftoverVariants extends RodWalker { @Output protected PrintStream out; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java index adafffe1b..2405a448e 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java @@ -36,7 +36,6 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum; import org.broadinstitute.sting.gatk.walkers.RMD; import org.broadinstitute.sting.gatk.walkers.Requires; import org.broadinstitute.sting.gatk.walkers.RodWalker; @@ -55,7 +54,7 @@ import java.io.FileNotFoundException; * Takes a VCF file, selects variants based on sample(s) in which it was found and/or on various annotation criteria, * recompute the value of certain annotations based on the new sample set, and output a new VCF with the results. */ -@Requires(value={},referenceMetaData=@RMD(name="variant", type=ReferenceOrderedDatum.class)) +@Requires(value={},referenceMetaData=@RMD(name="variant", type=VariantContext.class)) public class SelectVariants extends RodWalker { @Output private PrintStream out; diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/BeagleOutputByDepthWalker.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/BeagleOutputByDepthWalker.java index d9e0c99ac..11a190014 100755 --- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/BeagleOutputByDepthWalker.java +++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/BeagleOutputByDepthWalker.java @@ -45,7 +45,6 @@ import java.util.*; * Produces an input file to Beagle imputation engine, listing genotype likelihoods for each sample in input VCF file * @help.summary Produces an input file to Beagle imputation engine, listing genotype likelihoods for each sample in input VCF file */ -//@Requires(value={},referenceMetaData=@RMD(name=BeagleOutputByDepthWalker.INPUT_EVAL_ROD_NAME,type= VCFRecord.class)) public class BeagleOutputByDepthWalker extends RodWalker { @@ -54,8 +53,6 @@ public class BeagleOutputByDepthWalker extends RodWalker { public static final String INPUT_HAPMAP_ROD_NAME = "hapmap"; public static final String INPUT_COMP_ROD_NAME = "comp"; - private boolean newLine = true; - @Output public PrintStream out; @@ -87,7 +84,7 @@ public class BeagleOutputByDepthWalker extends RodWalker { return 0; Map compGenotypes = vc_comp.getGenotypes(); - Integer alleleCountH = 0, chrCountH = 0, alleleCountEmp=0, chrCountEmp=0; + Integer alleleCountH = 0, chrCountH = 0, alleleCountEmp=0, chrCountEmp; // Get Hapmap AC and AF if (vc_hapmap != null) { diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/IndelConsistencyReadCounter.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/IndelConsistencyReadCounter.java index 168c3870b..66c150ca0 100755 --- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/IndelConsistencyReadCounter.java +++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/IndelConsistencyReadCounter.java @@ -36,7 +36,7 @@ import org.broad.tribble.util.variantcontext.VariantContext; import java.util.*; @By(DataSource.READS) -@Requires(value={},referenceMetaData=@RMD(name="indels", type=ReferenceOrderedDatum.class)) +@Requires(value={},referenceMetaData=@RMD(name="indels", type=VariantContext.class)) // walker to count reads that are and are not consistent with homozygous indels public class IndelConsistencyReadCounter extends ReadWalker { diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/BeagleOutputToVCFWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/BeagleOutputToVCFWalker.java index c1e7708b4..c3aa67e41 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/BeagleOutputToVCFWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/BeagleOutputToVCFWalker.java @@ -36,7 +36,6 @@ import org.broadinstitute.sting.gatk.contexts.variantcontext.*; import org.broadinstitute.sting.gatk.datasources.simpleDataSources.ReferenceOrderedDataSource; import org.broadinstitute.sting.gatk.refdata.features.beagle.BeagleFeature; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum; import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrack; import org.broadinstitute.sting.gatk.walkers.RodWalker; import org.broadinstitute.sting.gatk.walkers.RMD; @@ -54,7 +53,7 @@ import static java.lang.Math.log10; /** * Takes files produced by Beagle imputation engine and creates a vcf with modified annotations. */ -@Requires(value={},referenceMetaData=@RMD(name=BeagleOutputToVCFWalker.INPUT_ROD_NAME, type=ReferenceOrderedDatum.class)) +@Requires(value={},referenceMetaData=@RMD(name=BeagleOutputToVCFWalker.INPUT_ROD_NAME, type=VariantContext.class)) public class BeagleOutputToVCFWalker extends RodWalker { diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/ProduceBeagleInputWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/ProduceBeagleInputWalker.java index 8a7876cfa..89961ec08 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/ProduceBeagleInputWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/ProduceBeagleInputWalker.java @@ -34,7 +34,6 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum; import org.broadinstitute.sting.gatk.walkers.RodWalker; import org.broadinstitute.sting.gatk.walkers.RMD; import org.broadinstitute.sting.gatk.walkers.Requires; @@ -48,7 +47,7 @@ import java.util.*; /** * Produces an input file to Beagle imputation engine, listing genotype likelihoods for each sample in input variant file */ -@Requires(value={},referenceMetaData=@RMD(name=ProduceBeagleInputWalker.ROD_NAME, type=ReferenceOrderedDatum.class)) +@Requires(value={},referenceMetaData=@RMD(name=ProduceBeagleInputWalker.ROD_NAME, type=VariantContext.class)) public class ProduceBeagleInputWalker extends RodWalker { public static final String ROD_NAME = "variant"; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/annotator/GenomicAnnotator.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/annotator/GenomicAnnotator.java index 031127473..514c01aa7 100644 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/annotator/GenomicAnnotator.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/annotator/GenomicAnnotator.java @@ -72,7 +72,7 @@ import org.broadinstitute.sting.utils.vcf.VCFUtils; * * For details, see: http://www.broadinstitute.org/gsa/wiki/index.php/GenomicAnnotator */ -//@Requires(value={DataSource.READS, DataSource.REFERENCE},referenceMetaData=@RMD(name="variant",type=VariationRod.class)) +//@Requires(value={DataSource.READS, DataSource.REFERENCE},referenceMetaData=@RMD(name="variant",type=VariantContext.class)) //@Allows(value={DataSource.READS, DataSource.REFERENCE}) //@Reference(window=@Window(start=-50,stop=50)) @By(DataSource.REFERENCE) diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/diagnostics/SNPDensity.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/diagnostics/SNPDensity.java index 4947bf988..06632766c 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/diagnostics/SNPDensity.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/diagnostics/SNPDensity.java @@ -29,7 +29,6 @@ import org.broad.tribble.util.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum; import org.broadinstitute.sting.gatk.walkers.*; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.collections.Pair; @@ -43,7 +42,7 @@ import java.io.PrintStream; * Computes the density of SNPs passing and failing filters in intervals on the genome and emits a table for display */ @By(DataSource.REFERENCE) -@Requires(value={},referenceMetaData=@RMD(name="eval",type=ReferenceOrderedDatum.class)) +@Requires(value={},referenceMetaData=@RMD(name="eval",type=VariantContext.class)) public class SNPDensity extends RefWalker, SNPDensity.Counter> { @Output private PrintStream out;