From 3330e254a94be6f360d54f9b972ae309c248de98 Mon Sep 17 00:00:00 2001 From: ebanks Date: Thu, 15 Apr 2010 19:41:57 +0000 Subject: [PATCH] Standardize the dbsnp track name in preparation for case-sensitivity git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3176 348d0f76-0448-11de-a6fe-93d51630548a --- .../broadinstitute/sting/gatk/GenomeAnalysisEngine.java | 3 ++- .../org/broadinstitute/sting/gatk/refdata/rodDbSNP.java | 3 +++ .../broadinstitute/sting/gatk/walkers/PileupWalker.java | 2 +- .../broadinstitute/sting/gatk/walkers/VariantsToVCF.java | 2 +- .../gatk/walkers/annotator/VariantAnnotatorEngine.java | 2 +- .../gatk/walkers/genotyper/GenotypeCalculationModel.java | 2 +- .../walkers/recalibration/TableRecalibrationWalker.java | 3 ++- .../sting/gatk/walkers/sequenom/PickSequenomProbes.java | 2 +- .../gatk/walkers/varianteval/ValidationDataAnalysis.java | 2 +- .../multisamplecaller/MultiSampleCaller.java | 3 ++- .../oneoffprojects/walkers/ValidateDbSNPConversion.java | 4 ++-- .../walkers/varianteval2/TiTvVariantEvaluator.java | 7 ------- .../walkers/varianteval2/VariantEval2Walker.java | 5 +++-- .../sting/playground/gatk/walkers/DeNovoSNPWalker.java | 3 ++- 14 files changed, 22 insertions(+), 21 deletions(-) diff --git a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java index 81ac1b9bb..3b941fa6a 100755 --- a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java +++ b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java @@ -47,6 +47,7 @@ import org.broadinstitute.sting.gatk.io.stubs.Stub; import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrack; import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackManager; import org.broadinstitute.sting.gatk.refdata.utils.RMDIntervalGenerator; +import org.broadinstitute.sting.gatk.refdata.rodDbSNP; import org.broadinstitute.sting.gatk.walkers.*; import org.broadinstitute.sting.utils.*; import org.broadinstitute.sting.utils.cmdLine.ArgumentException; @@ -331,7 +332,7 @@ public class GenomeAnalysisEngine { // // please don't use these in the future, use the new syntax <- if we're not using these please remove them // - if (argCollection.DBSNPFile != null) bindConvenienceRods("dbSNP", "dbsnp", argCollection.DBSNPFile); + if (argCollection.DBSNPFile != null) bindConvenienceRods(rodDbSNP.STANDARD_DBSNP_TRACK_NAME, "dbsnp", argCollection.DBSNPFile); if (argCollection.HAPMAPFile != null) bindConvenienceRods("hapmap", "HapMapAlleleFrequencies", argCollection.HAPMAPFile); if (argCollection.HAPMAPChipFile != null) diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/rodDbSNP.java b/java/src/org/broadinstitute/sting/gatk/refdata/rodDbSNP.java index 0c322efd6..5658b340f 100644 --- a/java/src/org/broadinstitute/sting/gatk/refdata/rodDbSNP.java +++ b/java/src/org/broadinstitute/sting/gatk/refdata/rodDbSNP.java @@ -19,6 +19,9 @@ import java.util.List; * To change this template use File | Settings | File Templates. */ public class rodDbSNP extends BasicReferenceOrderedDatum implements VariationRod { + + public static final String STANDARD_DBSNP_TRACK_NAME = "dbsnp"; + public GenomeLoc loc; // genome location of SNP // Reference sequence chromosome or scaffold // Start and stop positions in chrom diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java index a163bf8a7..f0c47edb8 100644 --- a/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java @@ -148,7 +148,7 @@ public class PileupWalker extends LocusWalker implements TreeR } String rodString = Utils.join(", ", rodStrings); - rodDbSNP dbsnp = tracker.lookup("dbSNP",rodDbSNP.class); + rodDbSNP dbsnp = tracker.lookup(rodDbSNP.STANDARD_DBSNP_TRACK_NAME,rodDbSNP.class); if ( dbsnp != null) rodString += dbsnp.toMediumString(); diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/VariantsToVCF.java b/java/src/org/broadinstitute/sting/gatk/walkers/VariantsToVCF.java index 5ce7c1f3f..251100634 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/VariantsToVCF.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/VariantsToVCF.java @@ -33,7 +33,7 @@ public class VariantsToVCF extends RodWalker { if ( tracker == null || !BaseUtils.isRegularBase(ref.getBase()) ) return 0; - rodDbSNP dbsnp = rodDbSNP.getFirstRealSNP(tracker.getReferenceMetaData("dbsnp")); + rodDbSNP dbsnp = rodDbSNP.getFirstRealSNP(tracker.getReferenceMetaData(rodDbSNP.STANDARD_DBSNP_TRACK_NAME)); Allele refAllele = new Allele(Character.toString(ref.getBase()), true); Collection contexts = tracker.getVariantContexts(INPUT_ROD_NAME, ALLOWED_VARIANT_CONTEXT_TYPES, context.getLocation(), refAllele, true, false); diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java index 620b081a0..26dcf5ff2 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java @@ -156,7 +156,7 @@ public class VariantAnnotatorEngine { // annotate dbsnp occurrence if ( annotateDbsnp ) { - rodDbSNP dbsnp = rodDbSNP.getFirstRealSNP(tracker.getReferenceMetaData("dbsnp")); + rodDbSNP dbsnp = rodDbSNP.getFirstRealSNP(tracker.getReferenceMetaData(rodDbSNP.STANDARD_DBSNP_TRACK_NAME)); infoAnnotations.put(VCFRecord.DBSNP_KEY, dbsnp == null ? "0" : "1"); // annotate dbsnp id if available and not already there if ( dbsnp != null && !vc.hasAttribute("ID") ) diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeCalculationModel.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeCalculationModel.java index fe6159b7e..8f61de56c 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeCalculationModel.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeCalculationModel.java @@ -112,6 +112,6 @@ public abstract class GenotypeCalculationModel implements Cloneable { * @return the dbsnp rod if there is one at this position */ public static rodDbSNP getDbSNP(RefMetaDataTracker tracker) { - return rodDbSNP.getFirstRealSNP(tracker.getReferenceMetaData("dbsnp")); + return rodDbSNP.getFirstRealSNP(tracker.getReferenceMetaData(rodDbSNP.STANDARD_DBSNP_TRACK_NAME)); } } \ No newline at end of file diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java index b599dede5..8a7d7cbaf 100644 --- a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java @@ -19,6 +19,7 @@ import net.sf.samtools.util.SequenceUtil; import org.broadinstitute.sting.gatk.datasources.simpleDataSources.ReferenceOrderedDataSource; import org.broadinstitute.sting.gatk.io.StingSAMFileWriter; import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker; +import org.broadinstitute.sting.gatk.refdata.rodDbSNP; import org.broadinstitute.sting.gatk.walkers.DataSource; import org.broadinstitute.sting.gatk.walkers.ReadWalker; import org.broadinstitute.sting.gatk.walkers.Requires; @@ -152,7 +153,7 @@ public class TableRecalibrationWalker extends ReadWalker { if ( SNP_MASK != null ) { logger.info("Loading SNP mask... "); ReferenceOrderedData snp_mask; - if ( SNP_MASK.contains("dbsnp")) { + if ( SNP_MASK.contains(rodDbSNP.STANDARD_DBSNP_TRACK_NAME)) { snp_mask = new ReferenceOrderedData("snp_mask",new java.io.File(SNP_MASK),rodDbSNP.class); } else { snp_mask = new ReferenceOrderedData("snp_mask", diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/ValidationDataAnalysis.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/ValidationDataAnalysis.java index a8213428c..6eabe813b 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/ValidationDataAnalysis.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/ValidationDataAnalysis.java @@ -15,7 +15,7 @@ import java.util.List; * To change this template use File | Settings | File Templates. */ -// @Allows(value={DataSource.REFERENCE},referenceMetaData = {@RMD(name="eval",type=VariationRod.class), @RMD(name="dbsnp",type= rodDbSNP.class),@RMD(name="hapmap-chip",type=RodGenotypeChipAsGFF.class), @RMD(name="interval",type=IntervalRod.class), @RMD(name="validation",type=RodGenotypeChipAsGFF.class)}) +// @Allows(value={DataSource.REFERENCE},referenceMetaData = {@RMD(name="eval",type=VariationRod.class), @RMD(name=rodDbSNP.STANDARD_DBSNP_TRACK_NAME,type= rodDbSNP.class),@RMD(name="hapmap-chip",type=RodGenotypeChipAsGFF.class), @RMD(name="interval",type=IntervalRod.class), @RMD(name="validation",type=RodGenotypeChipAsGFF.class)}) public class ValidationDataAnalysis extends BasicVariantAnalysis implements GenotypeAnalysis, PopulationAnalysis { private int calls_at_validated_sites = 0; diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/multisamplecaller/MultiSampleCaller.java b/java/src/org/broadinstitute/sting/oneoffprojects/multisamplecaller/MultiSampleCaller.java index 9af91a009..24dd143a8 100644 --- a/java/src/org/broadinstitute/sting/oneoffprojects/multisamplecaller/MultiSampleCaller.java +++ b/java/src/org/broadinstitute/sting/oneoffprojects/multisamplecaller/MultiSampleCaller.java @@ -8,6 +8,7 @@ import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; 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.rodDbSNP; import org.broadinstitute.sting.gatk.walkers.LocusWalker; import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.GenomeLoc; @@ -881,7 +882,7 @@ public class MultiSampleCaller extends LocusWalker sample_names) { String in_dbsnp; - if (tracker.getReferenceMetaData("DBSNP").size() > 0) { in_dbsnp = "known"; } else { in_dbsnp = "novel"; } + if (tracker.getReferenceMetaData(rodDbSNP.STANDARD_DBSNP_TRACK_NAME).size() > 0) { in_dbsnp = "known"; } else { in_dbsnp = "novel"; } AlignmentContext[] contexts = filterAlignmentContext(context, sample_names, 0); glCache.clear(); // reset the cache diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/ValidateDbSNPConversion.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/ValidateDbSNPConversion.java index 1e142c13a..dbcf79649 100644 --- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/ValidateDbSNPConversion.java +++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/ValidateDbSNPConversion.java @@ -20,8 +20,8 @@ import java.io.PrintStream; public class ValidateDbSNPConversion extends RefWalker, Matrix> { @Override public Pair map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { - if (!tracker.hasROD("dbsnp")) return null; - rodDbSNP rod = tracker.lookup("dbSNP",rodDbSNP.class); + if (!tracker.hasROD(rodDbSNP.STANDARD_DBSNP_TRACK_NAME)) return null; + rodDbSNP rod = tracker.lookup(rodDbSNP.STANDARD_DBSNP_TRACK_NAME,rodDbSNP.class); if (rod != null && rod.isSNP() && rod.isBiallelic()) { return new Pair(Matrix.BASE.toBase((byte) ref.getBase()), Matrix.BASE.toBase((byte) rod.getAlternativeBaseForSNP())); } diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/TiTvVariantEvaluator.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/TiTvVariantEvaluator.java index 794cea7ad..1737b8471 100755 --- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/TiTvVariantEvaluator.java +++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/TiTvVariantEvaluator.java @@ -7,9 +7,6 @@ import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext; import org.broadinstitute.sting.playground.utils.report.tags.Analysis; import org.broadinstitute.sting.playground.utils.report.tags.DataPoint; -import java.util.List; -import java.util.Arrays; - @Analysis(name = "Ti/Tv Variant Evaluator", description = "Ti/Tv Variant Evaluator") public class TiTvVariantEvaluator extends VariantEvaluator { @@ -58,10 +55,6 @@ public class TiTvVariantEvaluator extends VariantEvaluator { if (vc1 != null) updateTiTv(vc1, false); if (vc2 != null) updateTiTv(vc2, true); - //if ( vc1 == null && vc2 != null && vc2.isSNP() && vc2.isBiallelic() ) - // System.out.printf("VC2 = %s%n", vc2); - //if ( vc2 != null && vc2.getName().equals("dbsnp") ) - return null; // we don't capture any intersting sites } diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/VariantEval2Walker.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/VariantEval2Walker.java index bcd4af2e4..282023b4f 100755 --- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/VariantEval2Walker.java +++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/VariantEval2Walker.java @@ -9,6 +9,7 @@ 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.VariantContextAdaptors; +import org.broadinstitute.sting.gatk.refdata.rodDbSNP; import org.broadinstitute.sting.gatk.walkers.RodWalker; import org.broadinstitute.sting.playground.utils.report.ReportMarshaller; import org.broadinstitute.sting.playground.utils.report.VE2ReportFactory; @@ -95,7 +96,7 @@ public class VariantEval2Walker extends RodWalker { protected String[] SELECT_NAMES = {}; @Argument(shortName="known", doc="Name of ROD bindings containing variant sites that should be treated as known when splitting eval rods into known and novel subsets", required=false) - protected String[] KNOWN_NAMES = {"dbsnp"}; + protected String[] KNOWN_NAMES = {rodDbSNP.STANDARD_DBSNP_TRACK_NAME}; @Argument(shortName="sample", doc="Derive eval and comp contexts using only these sample genotypes, when genotypes are available in the original context", required=false) protected String[] SAMPLES = {}; @@ -238,7 +239,7 @@ public class VariantEval2Walker extends RodWalker { for ( ReferenceOrderedDataSource d : this.getToolkit().getRodDataSources() ) { if ( d.getName().startsWith("eval") ) { evalNames.add(d.getName()); - } else if ( d.getName().startsWith("dbsnp") || d.getName().startsWith("hapmap") || d.getName().startsWith("comp") ) { + } else if ( d.getName().startsWith(rodDbSNP.STANDARD_DBSNP_TRACK_NAME) || d.getName().startsWith("hapmap") || d.getName().startsWith("comp") ) { compNames.add(d.getName()); } else { logger.info("Not evaluating ROD binding " + d.getName()); diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/DeNovoSNPWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/DeNovoSNPWalker.java index efd8332fb..561e9711e 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/DeNovoSNPWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/DeNovoSNPWalker.java @@ -7,6 +7,7 @@ import org.broadinstitute.sting.gatk.contexts.variantcontext.Genotype; import org.broadinstitute.sting.gatk.filters.ZeroMappingQualityReadFilter; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.refdata.VariationRod; +import org.broadinstitute.sting.gatk.refdata.rodDbSNP; import org.broadinstitute.sting.gatk.walkers.*; import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyper; import org.broadinstitute.sting.gatk.walkers.genotyper.VariantCallContext; @@ -45,7 +46,7 @@ public class DeNovoSNPWalker extends RefWalker{ public String map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { VariationRod child = tracker.lookup("child",VariationRod.class); - VariationRod dbsnp = tracker.lookup("dbSNP",VariationRod.class); + VariationRod dbsnp = tracker.lookup(rodDbSNP.STANDARD_DBSNP_TRACK_NAME,VariationRod.class); if (child != null) { if (child.isSNP() && child.getNegLog10PError() > 5) { // BTR > 5