diff --git a/public/java/src/org/broadinstitute/sting/commandline/ArgumentSource.java b/public/java/src/org/broadinstitute/sting/commandline/ArgumentSource.java index c3402bd0a..e0e2ac378 100644 --- a/public/java/src/org/broadinstitute/sting/commandline/ArgumentSource.java +++ b/public/java/src/org/broadinstitute/sting/commandline/ArgumentSource.java @@ -185,7 +185,7 @@ public class ArgumentSource { * @return A default value for the given type. */ public Object createTypeDefault(ParsingEngine parsingEngine) { - return typeDescriptor.createTypeDefault(parsingEngine,this,field.getType()); + return typeDescriptor.createTypeDefault(parsingEngine,this,field.getGenericType()); } /** diff --git a/public/java/src/org/broadinstitute/sting/commandline/ArgumentTypeDescriptor.java b/public/java/src/org/broadinstitute/sting/commandline/ArgumentTypeDescriptor.java index 64c00a726..d1d4ff914 100644 --- a/public/java/src/org/broadinstitute/sting/commandline/ArgumentTypeDescriptor.java +++ b/public/java/src/org/broadinstitute/sting/commandline/ArgumentTypeDescriptor.java @@ -96,12 +96,13 @@ public abstract class ArgumentTypeDescriptor { /** * Generates a default for the given type. + * * @param parsingEngine the parsing engine used to validate this argument type descriptor. * @param source Source of the command-line argument. * @param type Type of value to create, in case the command-line argument system wants influence. * @return A default value for the given type. */ - public Object createTypeDefault(ParsingEngine parsingEngine,ArgumentSource source,Class type) { throw new UnsupportedOperationException("Unable to create default for type " + getClass()); } + public Object createTypeDefault(ParsingEngine parsingEngine,ArgumentSource source, Type type) { throw new UnsupportedOperationException("Unable to create default for type " + getClass()); } /** * Given the given argument source and attributes, synthesize argument definitions for command-line arguments. @@ -323,8 +324,9 @@ class RodBindingArgumentTypeDescriptor extends ArgumentTypeDescriptor { public boolean createsTypeDefault(ArgumentSource source) { return ! source.isRequired(); } @Override - public Object createTypeDefault(ParsingEngine parsingEngine, ArgumentSource source, Class type) { - return RodBinding.makeUnbound((Class)type); + public Object createTypeDefault(ParsingEngine parsingEngine, ArgumentSource source, Type type) { + Class parameterType = getParameterizedTypeClass(type); + return RodBinding.makeUnbound((Class)parameterType); } @Override @@ -646,7 +648,7 @@ class MultiplexArgumentTypeDescriptor extends ArgumentTypeDescriptor { } @Override - public Object createTypeDefault(ParsingEngine parsingEngine,ArgumentSource source,Class type) { + public Object createTypeDefault(ParsingEngine parsingEngine,ArgumentSource source, Type type) { if(multiplexer == null || multiplexedIds == null) throw new ReviewedStingException("No multiplexed ids available"); diff --git a/public/java/src/org/broadinstitute/sting/commandline/ParsingEngine.java b/public/java/src/org/broadinstitute/sting/commandline/ParsingEngine.java index 9b543142b..fbf8c6516 100755 --- a/public/java/src/org/broadinstitute/sting/commandline/ParsingEngine.java +++ b/public/java/src/org/broadinstitute/sting/commandline/ParsingEngine.java @@ -364,7 +364,7 @@ public class ParsingEngine { */ private void loadValueIntoObject( ArgumentSource source, Object instance, ArgumentMatches argumentMatches ) { // Nothing to load - if( argumentMatches.size() == 0 && !(source.createsTypeDefault() && source.isRequired())) + if( argumentMatches.size() == 0 && ! source.createsTypeDefault() ) return; // Target instance into which to inject the value. diff --git a/public/java/src/org/broadinstitute/sting/gatk/examples/GATKDocsExample.java b/public/java/src/org/broadinstitute/sting/gatk/examples/GATKDocsExample.java new file mode 100644 index 000000000..4541a0537 --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/gatk/examples/GATKDocsExample.java @@ -0,0 +1,82 @@ +/* + * Copyright (c) 2011, The Broad Institute + * + * Permission is hereby granted, free of charge, to any person + * obtaining a copy of this software and associated documentation + * files (the "Software"), to deal in the Software without + * restriction, including without limitation the rights to use, + * copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the + * Software is furnished to do so, subject to the following + * conditions: + * + * The above copyright notice and this permission notice shall be + * included in all copies or substantial portions of the Software. + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, + * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES + * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND + * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT + * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, + * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING + * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR + * OTHER DEALINGS IN THE SOFTWARE. + */ + +package org.broadinstitute.sting.gatk.examples; + +import org.broadinstitute.sting.commandline.Argument; +import org.broadinstitute.sting.commandline.ArgumentCollection; +import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection; +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.walkers.RodWalker; + +/** + * [Short one sentence description of this walker] + * + *

+ * [Functionality of this walker] + *

+ * + *

Input

+ *

+ * [Input description] + *

+ * + *

Output

+ *

+ * [Output description] + *

+ * + *

Examples

+ * 
+ *    java
+ *      -jar GenomeAnalysisTK.jar
+ *      -T $WalkerName
+ *
+ * + * @author Your Name + * @since Date created + */ +public class GATKDocsExample extends RodWalker { + /** + * Put detailed documentation about the argument here. No need to duplicate the summary information + * in doc annotation field, as that will be added before this text in the documentation page. + * + * Notes: + * + */ + @Argument(fullName="full", shortName="short", doc="Brief summary of argument [~ 80 characters of text]", required=false) + private boolean myWalkerArgument = false; + + public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { return 0; } + public Integer reduceInit() { return 0; } + public Integer reduce(Integer value, Integer sum) { return value + sum; } + public void onTraversalDone(Integer result) { } +} diff --git a/public/java/src/org/broadinstitute/sting/gatk/io/stubs/OutputStreamArgumentTypeDescriptor.java b/public/java/src/org/broadinstitute/sting/gatk/io/stubs/OutputStreamArgumentTypeDescriptor.java index b70d9eeec..da4eb3955 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/io/stubs/OutputStreamArgumentTypeDescriptor.java +++ b/public/java/src/org/broadinstitute/sting/gatk/io/stubs/OutputStreamArgumentTypeDescriptor.java @@ -75,12 +75,12 @@ public class OutputStreamArgumentTypeDescriptor extends ArgumentTypeDescriptor { } @Override - public Object createTypeDefault(ParsingEngine parsingEngine,ArgumentSource source,Class type) { + public Object createTypeDefault(ParsingEngine parsingEngine,ArgumentSource source, Type type) { if(!source.isRequired()) throw new ReviewedStingException("BUG: tried to create type default for argument type descriptor that can't support a type default."); OutputStreamStub stub = new OutputStreamStub(defaultOutputStream); engine.addOutput(stub); - return createInstanceOfClass(type,stub); + return createInstanceOfClass((Class)type,stub); } @Override diff --git a/public/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterArgumentTypeDescriptor.java b/public/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterArgumentTypeDescriptor.java index 8d67a837e..43ec934ed 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterArgumentTypeDescriptor.java +++ b/public/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterArgumentTypeDescriptor.java @@ -99,7 +99,7 @@ public class SAMFileWriterArgumentTypeDescriptor extends ArgumentTypeDescriptor } @Override - public Object createTypeDefault(ParsingEngine parsingEngine,ArgumentSource source,Class type) { + public Object createTypeDefault(ParsingEngine parsingEngine,ArgumentSource source, Type type) { if(!source.isRequired()) throw new ReviewedStingException("BUG: tried to create type default for argument type descriptor that can't support a type default."); SAMFileWriterStub stub = new SAMFileWriterStub(engine,defaultOutputStream); diff --git a/public/java/src/org/broadinstitute/sting/gatk/io/stubs/VCFWriterArgumentTypeDescriptor.java b/public/java/src/org/broadinstitute/sting/gatk/io/stubs/VCFWriterArgumentTypeDescriptor.java index 6e5499339..98026554b 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/io/stubs/VCFWriterArgumentTypeDescriptor.java +++ b/public/java/src/org/broadinstitute/sting/gatk/io/stubs/VCFWriterArgumentTypeDescriptor.java @@ -114,7 +114,7 @@ public class VCFWriterArgumentTypeDescriptor extends ArgumentTypeDescriptor { } @Override - public Object createTypeDefault(ParsingEngine parsingEngine,ArgumentSource source,Class type) { + public Object createTypeDefault(ParsingEngine parsingEngine,ArgumentSource source, Type type) { if(!source.isRequired()) throw new ReviewedStingException("BUG: tried to create type default for argument type descriptor that can't support a type default."); VCFWriterStub stub = new VCFWriterStub(engine, defaultOutputStream, false, argumentSources, false, false); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoodsCalculationModel.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoodsCalculationModel.java index 8261cd588..594c1dd28 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoodsCalculationModel.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoodsCalculationModel.java @@ -26,6 +26,7 @@ package org.broadinstitute.sting.gatk.walkers.genotyper; import org.apache.log4j.Logger; +import org.broadinstitute.sting.commandline.RodBinding; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; @@ -35,6 +36,7 @@ import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import org.broadinstitute.sting.utils.variantcontext.Allele; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import java.util.Map; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java index 897e1a668..41b340058 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java @@ -321,7 +321,7 @@ public class IndelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihood haplotypeMap.clear(); if (getAlleleListFromVCF) { - for( final VariantContext vc_input : tracker.getValues(VariantContext.class, "alleles") ) { + for( final VariantContext vc_input : tracker.getValues(UAC.alleles) ) { if( vc_input != null && allowableTypes.contains(vc_input.getType()) && ref.getLocus().getStart() == vc_input.getStart()) { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java index 9205e33a0..477155241 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java @@ -26,6 +26,7 @@ package org.broadinstitute.sting.gatk.walkers.genotyper; import org.apache.log4j.Logger; +import org.broadinstitute.sting.commandline.RodBinding; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; @@ -57,13 +58,13 @@ public class SNPGenotypeLikelihoodsCalculationModel extends GenotypeLikelihoodsC useAlleleFromVCF = UAC.GenotypingMode == GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES; } - public static VariantContext getSNPVCFromAllelesRod(RefMetaDataTracker tracker, ReferenceContext ref, boolean requireSNP, Logger logger) { + public static VariantContext getSNPVCFromAllelesRod(RefMetaDataTracker tracker, ReferenceContext ref, boolean requireSNP, Logger logger, final RodBinding allelesBinding) { if ( tracker == null || ref == null || logger == null ) throw new ReviewedStingException("Bad arguments: tracker=" + tracker + " ref=" + ref + " logger=" + logger); VariantContext vc = null; // search for usable record - for( final VariantContext vc_input : tracker.getValues(VariantContext.class, "alleles", ref.getLocus()) ) { + for( final VariantContext vc_input : tracker.getValues(allelesBinding) ) { if ( vc_input != null && ! vc_input.isFiltered() && (! requireSNP || vc_input.isSNP() )) { if ( vc == null ) { vc = vc_input; @@ -95,7 +96,7 @@ public class SNPGenotypeLikelihoodsCalculationModel extends GenotypeLikelihoodsC if ( alternateAlleleToUse != null ) { bestAlternateAllele = alternateAlleleToUse.getBases()[0]; } else if ( useAlleleFromVCF ) { - VariantContext vc = getSNPVCFromAllelesRod(tracker, ref, true, logger); + VariantContext vc = getSNPVCFromAllelesRod(tracker, ref, true, logger, UAC.alleles); // ignore places where we don't have a variant if ( vc == null ) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java index 52bf3f715..1a76bfd07 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java @@ -27,6 +27,9 @@ package org.broadinstitute.sting.gatk.walkers.genotyper; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Hidden; +import org.broadinstitute.sting.commandline.Input; +import org.broadinstitute.sting.commandline.RodBinding; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import java.io.File; @@ -61,6 +64,11 @@ public class UnifiedArgumentCollection { @Argument(fullName = "computeSLOD", shortName = "sl", doc = "If provided, we will calculate the SLOD", required = false) public boolean COMPUTE_SLOD = false; + /** + * When the UnifiedGenotyper is put into GENOTYPE_GIVEN_ALLELES mode it will genotype the samples using only the alleles provide in this rod binding + */ + @Input(fullName="alleles", shortName = "alleles", doc="The set of alleles at which to genotype when in GENOTYPE_MODE = GENOTYPE_GIVEN_ALLELES", required=false) + public RodBinding alleles; // control the error modes @Hidden @@ -168,6 +176,7 @@ public class UnifiedArgumentCollection { uac.OUTPUT_DEBUG_INDEL_INFO = OUTPUT_DEBUG_INDEL_INFO; uac.INDEL_HAPLOTYPE_SIZE = INDEL_HAPLOTYPE_SIZE; uac.DO_CONTEXT_DEPENDENT_PENALTIES = DO_CONTEXT_DEPENDENT_PENALTIES; + uac.alleles = alleles; uac.GET_GAP_PENALTIES_FROM_DATA = GET_GAP_PENALTIES_FROM_DATA; uac.INDEL_RECAL_FILE = INDEL_RECAL_FILE; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java index f5092f5cd..d31bb6fb9 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java @@ -25,10 +25,7 @@ package org.broadinstitute.sting.gatk.walkers.genotyper; -import org.broadinstitute.sting.commandline.Argument; -import org.broadinstitute.sting.commandline.ArgumentCollection; -import org.broadinstitute.sting.commandline.Output; -import org.broadinstitute.sting.commandline.RodBinding; +import org.broadinstitute.sting.commandline.*; import org.broadinstitute.sting.gatk.DownsampleType; import org.broadinstitute.sting.gatk.arguments.DbsnpArgumentCollection; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java index 77f1c5e25..dc728ff6b 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java @@ -58,6 +58,7 @@ public class UnifiedGenotyperEngine { // the unified argument collection private final UnifiedArgumentCollection UAC; + public UnifiedArgumentCollection getUAC() { return UAC; } // the annotation engine private final VariantAnnotatorEngine annotationEngine; @@ -232,7 +233,7 @@ public class UnifiedGenotyperEngine { private VariantCallContext generateEmptyContext(RefMetaDataTracker tracker, ReferenceContext ref, Map stratifiedContexts, AlignmentContext rawContext) { VariantContext vc; if ( UAC.GenotypingMode == GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES ) { - VariantContext vcInput = SNPGenotypeLikelihoodsCalculationModel.getSNPVCFromAllelesRod(tracker, ref, false, logger); + VariantContext vcInput = SNPGenotypeLikelihoodsCalculationModel.getSNPVCFromAllelesRod(tracker, ref, false, logger, UAC.alleles); if ( vcInput == null ) return null; vc = new VariantContext("UG_call", vcInput.getChr(), vcInput.getStart(), vcInput.getEnd(), vcInput.getAlleles()); @@ -630,7 +631,7 @@ public class UnifiedGenotyperEngine { // no extended event pileup // if we're genotyping given alleles and we have a requested SNP at this position, do SNP if (UAC.GenotypingMode == GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES) { - VariantContext vcInput = SNPGenotypeLikelihoodsCalculationModel.getSNPVCFromAllelesRod(tracker, refContext, false, logger); + VariantContext vcInput = SNPGenotypeLikelihoodsCalculationModel.getSNPVCFromAllelesRod(tracker, refContext, false, logger, UAC.alleles); if (vcInput == null) return null; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CountCovariatesWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CountCovariatesWalker.java index 914f54363..b4739f366 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CountCovariatesWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CountCovariatesWalker.java @@ -25,15 +25,10 @@ package org.broadinstitute.sting.gatk.walkers.recalibration; -import org.broad.tribble.bed.BEDCodec; -import org.broad.tribble.dbsnp.DbSNPCodec; -import org.broadinstitute.sting.commandline.Argument; -import org.broadinstitute.sting.commandline.ArgumentCollection; -import org.broadinstitute.sting.commandline.Gather; -import org.broadinstitute.sting.commandline.Output; +import org.broad.tribble.Feature; +import org.broadinstitute.sting.commandline.*; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource; import org.broadinstitute.sting.gatk.filters.MappingQualityUnavailableReadFilter; import org.broadinstitute.sting.gatk.filters.MappingQualityZeroReadFilter; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; @@ -42,8 +37,6 @@ import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.baq.BAQ; import org.broadinstitute.sting.utils.classloader.PluginManager; -import org.broadinstitute.sting.utils.codecs.vcf.VCF3Codec; -import org.broadinstitute.sting.utils.codecs.vcf.VCFCodec; import org.broadinstitute.sting.utils.collections.NestedHashMap; import org.broadinstitute.sting.utils.exceptions.DynamicClassResolutionException; import org.broadinstitute.sting.utils.exceptions.UserException; @@ -94,13 +87,18 @@ public class CountCovariatesWalker extends LocusWalker> knownSites = Collections.emptyList(); + @Output + PrintStream out; + @Output(fullName="recal_file", shortName="recalFile", required=true, doc="Filename for the output covariates table recalibration file") @Gather(CountCovariatesGatherer.class) public PrintStream RECAL_FILE; @@ -124,8 +122,8 @@ public class CountCovariatesWalker extends LocusWalker requestedCovariates = new ArrayList(); // A list to hold the covariate objects that were requested - private static final double DBSNP_VS_NOVEL_MISMATCH_RATE = 2.0; // rate at which dbSNP sites (on an individual level) mismatch relative to novel sites (determined by looking at NA12878) - private static int DBSNP_VALIDATION_CHECK_FREQUENCY = 1000000; // how often to validate dbsnp mismatch rate (in terms of loci seen) + private static final double DBSNP_VS_NOVEL_MISMATCH_RATE = 2.0; // rate at which dbSNP sites (on an individual level) mismatch relative to novel sites (determined by looking at NA12878) + private static int DBSNP_VALIDATION_CHECK_FREQUENCY = 1000000; // how often to validate dbsnp mismatch rate (in terms of loci seen) public static class CountedData { private long countedSites = 0; // Number of loci used in the calculations, used for reporting in the output file @@ -136,7 +134,7 @@ public class CountCovariatesWalker extends LocusWalker 0; - // Only use data from non-dbsnp sites // Assume every mismatch at a non-dbsnp site is indicative of poor quality CountedData counter = new CountedData(); - if( !isSNP ) { + if( tracker.getValues(knownSites).size() == 0 ) { // If something here is in one of the knownSites tracks then skip over it, otherwise proceed // For each read at this locus - for( PileupElement p : context.getBasePileup() ) { - GATKSAMRecord gatkRead = (GATKSAMRecord) p.getRead(); + for( final PileupElement p : context.getBasePileup() ) { + final GATKSAMRecord gatkRead = (GATKSAMRecord) p.getRead(); int offset = p.getOffset(); if( gatkRead.containsTemporaryAttribute( SKIP_RECORD_ATTRIBUTE ) ) { @@ -358,8 +335,6 @@ public class CountCovariatesWalker extends LocusWalker binding = RodBinding.makeUnbound(Feature.class); + @Input(fullName="binding", shortName="V", required=true) + public RodBinding binding; } @Test @@ -656,7 +656,7 @@ public class ParsingEngineUnitTest extends BaseTest { private class ShortNameOnlyRodBindingArgProvider { @Input(shortName="short", required=false) - public RodBinding binding = RodBinding.makeUnbound(Feature.class); + public RodBinding binding; // = RodBinding.makeUnbound(Feature.class); } @Test @@ -677,22 +677,38 @@ public class ParsingEngineUnitTest extends BaseTest { Assert.assertEquals(argProvider.binding.getTags().getPositionalTags().size(), 1, "Tags aren't correctly set"); } + private class OptionalRodBindingArgProvider { + @Input(fullName="binding", shortName="V", required=false) + public RodBinding binding; + + @Input(fullName="bindingNull", shortName="VN", required=false) + public RodBinding bindingNull = null; + } + @Test - public void unbasicRodBindingArgumentTest() { + public void optionalRodBindingArgumentTest() { final String[] commandLine = new String[] {}; - parsingEngine.addArgumentSource( SingleRodBindingArgProvider.class ); + parsingEngine.addArgumentSource( OptionalRodBindingArgProvider.class ); parsingEngine.parse( commandLine ); parsingEngine.validate(); - SingleRodBindingArgProvider argProvider = new SingleRodBindingArgProvider(); + OptionalRodBindingArgProvider argProvider = new OptionalRodBindingArgProvider(); parsingEngine.loadArgumentsIntoObject( argProvider ); + Assert.assertNotNull(argProvider.binding, "Default value not applied corrected to RodBinding"); Assert.assertEquals(argProvider.binding.getName(), RodBinding.UNBOUND_VARIABLE_NAME, "Name isn't set properly"); Assert.assertEquals(argProvider.binding.getSource(), RodBinding.UNBOUND_SOURCE, "Source isn't set to its expected value"); Assert.assertEquals(argProvider.binding.getType(), Feature.class, "Type isn't set to its expected value"); Assert.assertEquals(argProvider.binding.isBound(), false, "Bound() isn't returning its expected value"); Assert.assertEquals(argProvider.binding.getTags().getPositionalTags().size(), 0, "Tags aren't correctly set"); + + Assert.assertNotNull(argProvider.bindingNull, "Default value not applied corrected to RodBinding"); + Assert.assertEquals(argProvider.bindingNull.getName(), RodBinding.UNBOUND_VARIABLE_NAME, "Name isn't set properly"); + Assert.assertEquals(argProvider.bindingNull.getSource(), RodBinding.UNBOUND_SOURCE, "Source isn't set to its expected value"); + Assert.assertEquals(argProvider.bindingNull.getType(), VariantContext.class, "Type isn't set to its expected value"); + Assert.assertEquals(argProvider.bindingNull.isBound(), false, "Bound() isn't returning its expected value"); + Assert.assertEquals(argProvider.bindingNull.getTags().getPositionalTags().size(), 0, "Tags aren't correctly set"); } @Test(expectedExceptions = UserException.class) diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java index 88c5116b1..d11fb7e29 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java @@ -45,7 +45,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { GenomeAnalysisEngine.resetRandomGenerator(); WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec( - baseCommand + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -B:alleles,vcf " + result.get(0).getAbsolutePath() + " -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,050,000", 1, + baseCommand + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + result.get(0).getAbsolutePath() + " -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,050,000", 1, Arrays.asList(md5)); executeTest("test MultiSample Pilot2 with alleles passed in", spec2); } @@ -53,12 +53,12 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { @Test public void testWithAllelesPassedIn() { WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec( - baseCommand + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -B:alleles,vcf " + validationDataLocation + "allelesForUG.vcf -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,025,000", 1, + baseCommand + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "allelesForUG.vcf -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,025,000", 1, Arrays.asList("811ddc0bd8322b14f14f58df8c627aa9")); executeTest("test MultiSample Pilot2 with alleles passed in", spec1); WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec( - baseCommand + " --output_mode EMIT_ALL_SITES --genotyping_mode GENOTYPE_GIVEN_ALLELES -B:alleles,vcf " + validationDataLocation + "allelesForUG.vcf -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,025,000", 1, + baseCommand + " --output_mode EMIT_ALL_SITES --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "allelesForUG.vcf -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,025,000", 1, Arrays.asList("5cf08dd7ac3d218082f7be3915ce0b15")); executeTest("test MultiSample Pilot2 with alleles passed in and emitting all sites", spec2); } @@ -286,13 +286,13 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { @Test public void testWithIndelAllelesPassedIn() { WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec( - baseCommandIndels + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -B:alleles,vcf " + validationDataLocation + "indelAllelesForUG.vcf -I " + validationDataLocation + + baseCommandIndels + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "indelAllelesForUG.vcf -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,100,000", 1, Arrays.asList("69b0b3f089c80b9864294d838a061336")); executeTest("test MultiSample Pilot2 indels with alleles passed in", spec1); WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec( - baseCommandIndels + " --output_mode EMIT_ALL_SITES --genotyping_mode GENOTYPE_GIVEN_ALLELES -B:alleles,vcf " + baseCommandIndels + " --output_mode EMIT_ALL_SITES --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "indelAllelesForUG.vcf -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,100,000", 1, Arrays.asList("c90174cfd7dd68bdef36fe2c60145e10")); diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java index 74f803ac6..b2833b935 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java @@ -54,7 +54,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-R " + b36KGReference + - " -B:dbsnp,vcf " + b36dbSNP129 + + " -knownSites " + b36dbSNP129 + " -T CountCovariates" + " -I " + bam + ( bam.equals( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam" ) @@ -135,7 +135,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest { " -standard" + " -OQ" + " -recalFile %s" + - " -B:dbsnp,vcf " + b36dbSNP129, + " -knownSites " + b36dbSNP129, 1, // just one output file Arrays.asList(md5)); executeTest("testCountCovariatesUseOriginalQuals", spec); @@ -182,7 +182,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-R " + b36KGReference + - " -B:dbsnp,vcf " + b36dbSNP129 + + " -knownSites " + b36dbSNP129 + " -T CountCovariates" + " -I " + bam + " -standard" + @@ -225,30 +225,6 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest { } } - @Test - public void testCountCovariatesVCF() { - HashMap e = new HashMap(); - e.put( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "170f0c3cc4b8d72c539136effeec9a16"); - - for ( Map.Entry entry : e.entrySet() ) { - String bam = entry.getKey(); - String md5 = entry.getValue(); - - WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( - "-R " + b36KGReference + - " -B:dbsnp,VCF3 " + validationDataLocation + "vcfexample3.vcf" + - " -T CountCovariates" + - " -I " + bam + - " -L 1:10,000,000-10,200,000" + - " -standard" + - " --solid_recal_mode SET_Q_ZERO" + - " -recalFile %s", - 1, // just one output file - Arrays.asList(md5)); - executeTest("testCountCovariatesVCF", spec); - } - } - @Test public void testCountCovariatesBED() { HashMap e = new HashMap(); @@ -260,7 +236,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-R " + b36KGReference + - " -B:bed,bed " + validationDataLocation + "recalibrationTest.bed" + + " -knownSites:bed " + validationDataLocation + "recalibrationTest.bed" + " -T CountCovariates" + " -I " + bam + " -L 1:10,000,000-10,200,000" + @@ -284,10 +260,10 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-R " + b36KGReference + - " -B:anyNameABCD,VCF3 " + validationDataLocation + "vcfexample3.vcf" + + " -knownSites:anyNameABCD,VCF3 " + validationDataLocation + "vcfexample3.vcf" + " -T CountCovariates" + " -I " + bam + - " -B:dbsnp,vcf " + b36dbSNP129 + + " -knownSites " + b36dbSNP129 + " -L 1:10,000,000-10,200,000" + " -cov ReadGroupCovariate" + " -cov QualityScoreCovariate" + @@ -312,7 +288,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-R " + b36KGReference + - " -B:dbsnp,vcf " + b36dbSNP129 + + " -knownSites " + b36dbSNP129 + " -T CountCovariates" + " -I " + bam + " -cov ReadGroupCovariate" +