zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable

This commit is contained in:
Eric Banks 2011-08-11 13:39:36 -04:00
parent 265c3d744b b705d9cf15
commit e93538cdf7
18 changed files with 168 additions and 108 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

2
public/java/src/org/broadinstitute/sting/commandline/ArgumentSource.java
View File

@ -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());
}
/**

10
public/java/src/org/broadinstitute/sting/commandline/ArgumentTypeDescriptor.java
View File

@ -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<? extends Feature>)type);
public Object createTypeDefault(ParsingEngine parsingEngine, ArgumentSource source, Type type) {
Class parameterType = getParameterizedTypeClass(type);
return RodBinding.makeUnbound((Class<? extends Feature>)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");

2
public/java/src/org/broadinstitute/sting/commandline/ParsingEngine.java
View File

@ -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.

82
public/java/src/org/broadinstitute/sting/gatk/examples/GATKDocsExample.java 100644
View File

@ -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]
*
* <p>
* [Functionality of this walker]
* </p>
*
* <h2>Input</h2>
* <p>
* [Input description]
* </p>
*
* <h2>Output</h2>
* <p>
* [Output description]
* </p>
*
* <h2>Examples</h2>
* <pre>
* java
* -jar GenomeAnalysisTK.jar
* -T $WalkerName
* </pre>
*
* @author Your Name
* @since Date created
*/
public class GATKDocsExample extends RodWalker<Integer, Integer> {
/**
* 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:
* <ul>
* <li>This field can contain HTML as a normal javadoc</li>
* <li>Don't include information about the default value, as gatkdocs adds this automatically</li>
* <li>Try your best to describe in detail the behavior of the argument, as ultimately confusing
* docs here will just result in user posts on the forum</li>
* </ul>
*/
@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) { }
}

4
public/java/src/org/broadinstitute/sting/gatk/io/stubs/OutputStreamArgumentTypeDescriptor.java
View File

@ -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

2
public/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterArgumentTypeDescriptor.java
View File

@ -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);

2
public/java/src/org/broadinstitute/sting/gatk/io/stubs/VCFWriterArgumentTypeDescriptor.java
View File

@ -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);

2
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoodsCalculationModel.java
View File

@ -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;

2
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java
View File

@ -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()) {

7
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java
View File

@ -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<VariantContext> 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 )

9
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java
View File

@ -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<VariantContext> 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;

5
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
View File

@ -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;

5
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
View File

@ -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<String, AlignmentContext> 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;

63
public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CountCovariatesWalker.java
View File

@ -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<CountCovariatesWalker.Cou
/////////////////////////////
@ArgumentCollection private RecalibrationArgumentCollection RAC = new RecalibrationArgumentCollection();
@Output
PrintStream out;
/////////////////////////////
// Command Line Arguments
/////////////////////////////
@Output(fullName="recal_file", shortName="recalFile", required=true, doc="Filename for the outputted covariates table recalibration file")
/**
* This algorithm treats every reference mismatch as an indication of error. However, real genetic variation is expected to mismatch the reference,
* so it is critical that a database of known polymorphic sites is given to the tool in order to skip over those sites.
*/
@Input(fullName="knownSites", shortName = "knownSites", doc="A database of known polymorphic sites to skip over in the recalibration algorithm", required=false)
public List<RodBinding<Feature>> 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<CountCovariatesWalker.Cou
/////////////////////////////
private final RecalDataManager dataManager = new RecalDataManager(); // Holds the data HashMap, mostly used by TableRecalibrationWalker to create collapsed data hashmaps
private final ArrayList<Covariate> requestedCovariates = new ArrayList<Covariate>(); // 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<CountCovariatesWalker.Cou
private long dbSNPCountsMM = 0, dbSNPCountsBases = 0; // mismatch/base counts for dbSNP loci
private long novelCountsMM = 0, novelCountsBases = 0; // mismatch/base counts for non-dbSNP loci
private int lociSinceLastDbsnpCheck = 0; // loci since last dbsnp validation
private int lociSinceLastDbsnpCheck = 0; // loci since last dbsnp validation
/**
* Adds the values of other to this, returning this
@ -190,20 +188,8 @@ public class CountCovariatesWalker extends LocusWalker<CountCovariatesWalker.Cou
}
// Warn the user if no dbSNP file or other variant mask was specified
boolean foundDBSNP = false;
for( ReferenceOrderedDataSource rod : this.getToolkit().getRodDataSources() ) {
if( rod != null ) {
if( rod.getType().equals(DbSNPCodec.class) ||
rod.getType().equals(VCFCodec.class) ||
rod.getType().equals(VCF3Codec.class) ||
rod.getType().equals(BEDCodec.class) ) {
foundDBSNP = true;
break;
}
}
}
if( !foundDBSNP && !RUN_WITHOUT_DBSNP ) {
throw new UserException.CommandLineException("This calculation is critically dependent on being able to skip over known variant sites. Please provide a dbSNP ROD or a VCF file containing known sites of genetic variation.");
if( knownSites.isEmpty() && !RUN_WITHOUT_DBSNP ) {
throw new UserException.CommandLineException("This calculation is critically dependent on being able to skip over known variant sites. Please provide a VCF file containing known sites of genetic variation.");
}
// Initialize the requested covariates by parsing the -cov argument
@ -266,12 +252,6 @@ public class CountCovariatesWalker extends LocusWalker<CountCovariatesWalker.Cou
logger.info( "\t" + cov.getClass().getSimpleName() );
cov.initialize( RAC ); // Initialize any covariate member variables using the shared argument collection
}
// try {
// stream = new PrintStream( RAC.RECAL_FILE );
// } catch ( FileNotFoundException e ) {
// throw new RuntimeException( "Couldn't open output file: ", e );
// }
}
@ -290,16 +270,13 @@ public class CountCovariatesWalker extends LocusWalker<CountCovariatesWalker.Cou
* @return Returns 1, but this value isn't used in the reduce step
*/
public CountedData map( RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context ) {
// If any ROD covers this site then we assume it is a site of known genetic variation and we skip it
boolean isSNP = tracker.getNTracksWithBoundFeatures() > 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<CountCovariatesWalker.Cou
return counter;
}
/**
* Update the mismatch / total_base counts for a given class of loci.
*

3
public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java
View File

@ -93,8 +93,7 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
@Output(doc="The output BAM file", required=true)
private StingSAMFileWriter OUTPUT_BAM = null;
@Argument(fullName="preserve_qscores_less_than", shortName="pQ",
doc="Bases with quality scores less than this threshold won't be recalibrated, default=5. In general it's unsafe to change qualities scores below < 5, since base callers use these values to indicate random or bad bases", required=false)
@Argument(fullName="preserve_qscores_less_than", shortName="pQ", doc="Bases with quality scores less than this threshold won't be recalibrated, default=5. In general it's unsafe to change qualities scores below < 5, since base callers use these values to indicate random or bad bases", required=false)
private int PRESERVE_QSCORES_LESS_THAN = 5;
@Argument(fullName="smoothing", shortName="sm", required = false, doc="Number of imaginary counts to add to each bin in order to smooth out bins with few data points, default=1")
private int SMOOTHING = 1;

28
public/java/test/org/broadinstitute/sting/commandline/ParsingEngineUnitTest.java
View File

@ -632,8 +632,8 @@ public class ParsingEngineUnitTest extends BaseTest {
// --------------------------------------------------------------------------------
private class SingleRodBindingArgProvider {
@Input(fullName="binding", shortName="V", required=false)
public RodBinding<Feature> binding = RodBinding.makeUnbound(Feature.class);
@Input(fullName="binding", shortName="V", required=true)
public RodBinding<Feature> binding;
}
@Test
@ -656,7 +656,7 @@ public class ParsingEngineUnitTest extends BaseTest {
private class ShortNameOnlyRodBindingArgProvider {
@Input(shortName="short", required=false)
public RodBinding<Feature> binding = RodBinding.makeUnbound(Feature.class);
public RodBinding<Feature> 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<Feature> binding;
@Input(fullName="bindingNull", shortName="VN", required=false)
public RodBinding<VariantContext> 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)

10
public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
View File

@ -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"));

38
public/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java
View File

@ -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<String, String> e = new HashMap<String, String>();
e.put( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "170f0c3cc4b8d72c539136effeec9a16");
for ( Map.Entry<String, String> 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<String, String> e = new HashMap<String, String>();
@ -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" +