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

Added a StandardVariantContextInputArgumentCollection that is now used for consistency by many of the core tools.

This commit is contained in:
Eric Banks 2011-08-10 12:00:56 -04:00
parent bc125f104a
commit 06cdc4d5f9
12 changed files with 124 additions and 76 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

55
public/java/src/org/broadinstitute/sting/gatk/arguments/StandardVariantContextInputArgumentCollection.java 100644
View File

@ -0,0 +1,55 @@
/*
* Copyright (c) 2010 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.arguments;
import org.broadinstitute.sting.commandline.Input;
import org.broadinstitute.sting.commandline.RodBinding;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.simpleframework.xml.Root;
/**
* @author ebanks
* @version 1.0
*/
@Root
public class StandardVariantContextInputArgumentCollection {
/**
* The VCF input file(s)
*
* The variant track can take any number of arguments on the command line. Each -V argument
* will be included as an input to the tool. If no explicit name is provided,
* the -V arguments will be named using the default algorithm: variant, variant2, variant3, etc.
* The user can override this by providing an explicit name -V:name,vcf for each -V argument,
* and each named argument will be labeled as such in the output (i.e., set=name rather than
* set=variant2). The order of arguments does not matter except for the naming.
*/
@Input(fullName="variant", shortName = "V", doc="Input VCF file", required=true)
public RodBinding<VariantContext> variants;
}

11
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java
View File

@ -27,6 +27,7 @@ package org.broadinstitute.sting.gatk.walkers.annotator;
import org.broadinstitute.sting.commandline.*; import org.broadinstitute.sting.commandline.*;
import org.broadinstitute.sting.gatk.arguments.DbsnpArgumentCollection; import org.broadinstitute.sting.gatk.arguments.DbsnpArgumentCollection;
import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils; import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
@ -35,7 +36,6 @@ import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotationType; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotationType;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedArgumentCollection;
import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.SampleUtils; import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.classloader.PluginManager; import org.broadinstitute.sting.utils.classloader.PluginManager;
@ -56,8 +56,7 @@ import java.util.*;
@By(DataSource.REFERENCE) @By(DataSource.REFERENCE)
public class VariantAnnotator extends RodWalker<Integer, Integer> { public class VariantAnnotator extends RodWalker<Integer, Integer> {
@Input(fullName="variant", shortName = "V", doc="Input VCF file", required=true) @ArgumentCollection protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection();
public RodBinding<VariantContext> variants;
@Input(fullName="snpEffFile", shortName = "snpEffFile", doc="SnpEff file", required=false) @Input(fullName="snpEffFile", shortName = "snpEffFile", doc="SnpEff file", required=false)
public RodBinding<SnpEffFeature> snpEffFile; public RodBinding<SnpEffFeature> snpEffFile;
@ -142,7 +141,7 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> {
listAnnotationsAndExit(); listAnnotationsAndExit();
// get the list of all sample names from the variant VCF input rod, if applicable // get the list of all sample names from the variant VCF input rod, if applicable
List<String> rodName = Arrays.asList(variants.getName()); List<String> rodName = Arrays.asList(variantCollection.variants.getName());
Set<String> samples = SampleUtils.getUniqueSamplesFromRods(getToolkit(), rodName); Set<String> samples = SampleUtils.getUniqueSamplesFromRods(getToolkit(), rodName);
// add the non-VCF sample from the command-line, if applicable // add the non-VCF sample from the command-line, if applicable
@ -166,7 +165,7 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> {
// note that if any of the definitions conflict with our new ones, then we want to overwrite the old ones // note that if any of the definitions conflict with our new ones, then we want to overwrite the old ones
Set<VCFHeaderLine> hInfo = new HashSet<VCFHeaderLine>(); Set<VCFHeaderLine> hInfo = new HashSet<VCFHeaderLine>();
hInfo.addAll(engine.getVCFAnnotationDescriptions()); hInfo.addAll(engine.getVCFAnnotationDescriptions());
for ( VCFHeaderLine line : VCFUtils.getHeaderFields(getToolkit(), Arrays.asList(variants.getName())) ) { for ( VCFHeaderLine line : VCFUtils.getHeaderFields(getToolkit(), Arrays.asList(variantCollection.variants.getName())) ) {
if ( isUniqueHeaderLine(line, hInfo) ) if ( isUniqueHeaderLine(line, hInfo) )
hInfo.add(line); hInfo.add(line);
} }
@ -225,7 +224,7 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> {
if ( tracker == null ) if ( tracker == null )
return 0; return 0;
Collection<VariantContext> VCs = tracker.getValues(variants, context.getLocation()); Collection<VariantContext> VCs = tracker.getValues(variantCollection.variants, context.getLocation());
if ( VCs.size() == 0 ) if ( VCs.size() == 0 )
return 0; return 0;

15
public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCFWalker.java
View File

@ -25,10 +25,8 @@
package org.broadinstitute.sting.gatk.walkers.beagle; package org.broadinstitute.sting.gatk.walkers.beagle;
import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.*;
import org.broadinstitute.sting.commandline.Input; import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection;
import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.commandline.RodBinding;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource; import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
@ -54,8 +52,9 @@ import static java.lang.Math.log10;
*/ */
@Requires(value={}) @Requires(value={})
public class BeagleOutputToVCFWalker extends RodWalker<Integer, Integer> { public class BeagleOutputToVCFWalker extends RodWalker<Integer, Integer> {
@Input(fullName="variant", shortName = "V", doc="Input VCF file", required=true)
public RodBinding<VariantContext> variants; @ArgumentCollection
protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection();
@Input(fullName="comp", shortName = "comp", doc="Comparison VCF file", required=false) @Input(fullName="comp", shortName = "comp", doc="Comparison VCF file", required=false)
public RodBinding<VariantContext> comp = RodBinding.makeUnbound(VariantContext.class); public RodBinding<VariantContext> comp = RodBinding.makeUnbound(VariantContext.class);
@ -111,7 +110,7 @@ public class BeagleOutputToVCFWalker extends RodWalker<Integer, Integer> {
hInfo.add(new VCFInfoHeaderLine("AFH", 1, VCFHeaderLineType.Float, "Allele Number from Comparison ROD at this site")); hInfo.add(new VCFInfoHeaderLine("AFH", 1, VCFHeaderLineType.Float, "Allele Number from Comparison ROD at this site"));
} }
Set<String> samples = SampleUtils.getSampleListWithVCFHeader(getToolkit(), Arrays.asList(variants.getName())); Set<String> samples = SampleUtils.getSampleListWithVCFHeader(getToolkit(), Arrays.asList(variantCollection.variants.getName()));
final VCFHeader vcfHeader = new VCFHeader(hInfo, samples); final VCFHeader vcfHeader = new VCFHeader(hInfo, samples);
vcfWriter.writeHeader(vcfHeader); vcfWriter.writeHeader(vcfHeader);
@ -123,7 +122,7 @@ public class BeagleOutputToVCFWalker extends RodWalker<Integer, Integer> {
return 0; return 0;
GenomeLoc loc = context.getLocation(); GenomeLoc loc = context.getLocation();
VariantContext vc_input = tracker.getFirstValue(variants, loc); VariantContext vc_input = tracker.getFirstValue(variantCollection.variants, loc);
VariantContext vc_comp = tracker.getFirstValue(comp, loc); VariantContext vc_comp = tracker.getFirstValue(comp, loc);

9
public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInputWalker.java
View File

@ -27,6 +27,7 @@ package org.broadinstitute.sting.gatk.walkers.beagle;
import org.broadinstitute.sting.commandline.*; import org.broadinstitute.sting.commandline.*;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@ -52,8 +53,8 @@ import java.util.*;
*/ */
@Requires(value={}) @Requires(value={})
public class ProduceBeagleInputWalker extends RodWalker<Integer, Integer> { public class ProduceBeagleInputWalker extends RodWalker<Integer, Integer> {
@Input(fullName="variant", shortName = "V", doc="Input VCF file", required=true)
public RodBinding<VariantContext> variants; @ArgumentCollection protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection();
@Input(fullName="validation", shortName = "validation", doc="Input VCF file", required=false) @Input(fullName="validation", shortName = "validation", doc="Input VCF file", required=false)
public RodBinding<VariantContext> validation = RodBinding.makeUnbound(VariantContext.class); public RodBinding<VariantContext> validation = RodBinding.makeUnbound(VariantContext.class);
@ -98,7 +99,7 @@ public class ProduceBeagleInputWalker extends RodWalker<Integer, Integer> {
public void initialize() { public void initialize() {
samples = SampleUtils.getSampleListWithVCFHeader(getToolkit(), Arrays.asList(variants.getName())); samples = SampleUtils.getSampleListWithVCFHeader(getToolkit(), Arrays.asList(variantCollection.variants.getName()));
beagleWriter.print("marker alleleA alleleB"); beagleWriter.print("marker alleleA alleleB");
for ( String sample : samples ) for ( String sample : samples )
@ -120,7 +121,7 @@ public class ProduceBeagleInputWalker extends RodWalker<Integer, Integer> {
public Integer map( RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context ) { public Integer map( RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context ) {
if( tracker != null ) { if( tracker != null ) {
GenomeLoc loc = context.getLocation(); GenomeLoc loc = context.getLocation();
VariantContext variant_eval = tracker.getFirstValue(variants, loc); VariantContext variant_eval = tracker.getFirstValue(variantCollection.variants, loc);
VariantContext validation_eval = tracker.getFirstValue(validation, loc); VariantContext validation_eval = tracker.getFirstValue(validation, loc);
if ( goodSite(variant_eval,validation_eval) ) { if ( goodSite(variant_eval,validation_eval) ) {

15
public/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java
View File

@ -26,13 +26,10 @@
package org.broadinstitute.sting.gatk.walkers.filters; package org.broadinstitute.sting.gatk.walkers.filters;
import org.broad.tribble.Feature; import org.broad.tribble.Feature;
import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.*;
import org.broadinstitute.sting.commandline.Input; import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection;
import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.commandline.RodBinding;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.*; import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLoc;
@ -53,8 +50,8 @@ import java.util.*;
@Reference(window=@Window(start=-50,stop=50)) @Reference(window=@Window(start=-50,stop=50))
public class VariantFiltrationWalker extends RodWalker<Integer, Integer> { public class VariantFiltrationWalker extends RodWalker<Integer, Integer> {
@Input(fullName="variant", shortName = "V", doc="Input VCF file", required=true) @ArgumentCollection
public RodBinding<VariantContext> variants; protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection();
@Input(fullName="mask", doc="Input ROD mask", required=false) @Input(fullName="mask", doc="Input ROD mask", required=false)
public RodBinding<Feature> mask = RodBinding.makeUnbound(Feature.class); public RodBinding<Feature> mask = RodBinding.makeUnbound(Feature.class);
@ -100,7 +97,7 @@ public class VariantFiltrationWalker extends RodWalker<Integer, Integer> {
private void initializeVcfWriter() { private void initializeVcfWriter() {
final List<String> inputNames = Arrays.asList(variants.getName()); final List<String> inputNames = Arrays.asList(variantCollection.variants.getName());
// setup the header fields // setup the header fields
Set<VCFHeaderLine> hInfo = new HashSet<VCFHeaderLine>(); Set<VCFHeaderLine> hInfo = new HashSet<VCFHeaderLine>();
@ -152,7 +149,7 @@ public class VariantFiltrationWalker extends RodWalker<Integer, Integer> {
if ( tracker == null ) if ( tracker == null )
return 0; return 0;
Collection<VariantContext> VCs = tracker.getValues(variants, context.getLocation()); Collection<VariantContext> VCs = tracker.getValues(variantCollection.variants, context.getLocation());
// is there a SNP mask present? // is there a SNP mask present?
boolean hasMask = tracker.hasValues(mask); boolean hasMask = tracker.hasValues(mask);

13
public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java
View File

@ -24,12 +24,12 @@
package org.broadinstitute.sting.gatk.walkers.phasing; package org.broadinstitute.sting.gatk.walkers.phasing;
import org.broadinstitute.sting.commandline.*; import org.broadinstitute.sting.commandline.*;
import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.datasources.sample.Sample; import org.broadinstitute.sting.gatk.datasources.sample.Sample;
import org.broadinstitute.sting.gatk.filters.MappingQualityZeroReadFilter; import org.broadinstitute.sting.gatk.filters.MappingQualityZeroReadFilter;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; 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.*;
import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.DisjointSet; import org.broadinstitute.sting.utils.DisjointSet;
@ -67,8 +67,8 @@ public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, Ph
* *
* All heterozygous variants found in this VCF file will be phased, where possible * All heterozygous variants found in this VCF file will be phased, where possible
*/ */
@Input(fullName="variant", shortName = "V", doc="Phase variants from this VCF file", required=true) @ArgumentCollection
public RodBinding<VariantContext> variants; protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection();
@Output(doc = "File to which variants should be written", required = true) @Output(doc = "File to which variants should be written", required = true)
protected VCFWriter writer = null; protected VCFWriter writer = null;
@ -175,8 +175,9 @@ public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, Ph
hInfo.add(new VCFInfoHeaderLine(PHASING_INCONSISTENT_KEY, 0, VCFHeaderLineType.Flag, "Are the reads significantly haplotype-inconsistent?")); hInfo.add(new VCFInfoHeaderLine(PHASING_INCONSISTENT_KEY, 0, VCFHeaderLineType.Flag, "Are the reads significantly haplotype-inconsistent?"));
// todo -- fix samplesToPhase // todo -- fix samplesToPhase
Map<String, VCFHeader> rodNameToHeader = getVCFHeadersFromRods(getToolkit(), Arrays.asList(variants.getName())); String trackName = variantCollection.variants.getName();
Set<String> samples = new TreeSet<String>(samplesToPhase == null ? rodNameToHeader.get(variants.getName()).getGenotypeSamples() : samplesToPhase); Map<String, VCFHeader> rodNameToHeader = getVCFHeadersFromRods(getToolkit(), Arrays.asList(trackName));
Set<String> samples = new TreeSet<String>(samplesToPhase == null ? rodNameToHeader.get(trackName).getGenotypeSamples() : samplesToPhase);
writer.writeHeader(new VCFHeader(hInfo, samples)); writer.writeHeader(new VCFHeader(hInfo, samples));
} }
@ -207,7 +208,7 @@ public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, Ph
PhasingStats phaseStats = new PhasingStats(); PhasingStats phaseStats = new PhasingStats();
List<VariantContext> unprocessedList = new LinkedList<VariantContext>(); List<VariantContext> unprocessedList = new LinkedList<VariantContext>();
for (VariantContext vc : tracker.getValues(variants, context.getLocation())) { for (VariantContext vc : tracker.getValues(variantCollection.variants, context.getLocation())) {
if (samplesToPhase != null) vc = reduceVCToSamples(vc, samplesToPhase); if (samplesToPhase != null) vc = reduceVCToSamples(vc, samplesToPhase);
if (ReadBackedPhasingWalker.processVariantInPhasing(vc)) { if (ReadBackedPhasingWalker.processVariantInPhasing(vc)) {

7
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java
View File

@ -31,7 +31,6 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub; import org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.Reference; import org.broadinstitute.sting.gatk.walkers.Reference;
import org.broadinstitute.sting.gatk.walkers.Requires;
import org.broadinstitute.sting.gatk.walkers.RodWalker; import org.broadinstitute.sting.gatk.walkers.RodWalker;
import org.broadinstitute.sting.gatk.walkers.Window; import org.broadinstitute.sting.gatk.walkers.Window;
import org.broadinstitute.sting.utils.SampleUtils; import org.broadinstitute.sting.utils.SampleUtils;
@ -64,8 +63,8 @@ public class CombineVariants extends RodWalker<Integer, Integer> {
* are techincally order dependent. It is strongly recommended to provide explicit names when * are techincally order dependent. It is strongly recommended to provide explicit names when
* a rod priority list is provided. * a rod priority list is provided.
*/ */
@Input(fullName = "variant", shortName = "V", doc="The VCF files to merge together", required=true) @Input(fullName="variant", shortName = "V", doc="Input VCF file", required=true)
public List<RodBinding<VariantContext>> variantsToMerge; public List<RodBinding<VariantContext>> variants;
@Output(doc="File to which variants should be written",required=true) @Output(doc="File to which variants should be written",required=true)
protected VCFWriter vcfWriter = null; protected VCFWriter vcfWriter = null;
@ -157,7 +156,7 @@ public class CombineVariants extends RodWalker<Integer, Integer> {
// get all of the vcf rods at this locus // get all of the vcf rods at this locus
// Need to provide reference bases to simpleMerge starting at current locus // Need to provide reference bases to simpleMerge starting at current locus
Collection<VariantContext> vcs = tracker.getValues(variantsToMerge, context.getLocation()); Collection<VariantContext> vcs = tracker.getValues(variants, context.getLocation());
if ( sitesOnlyVCF ) { if ( sitesOnlyVCF ) {
vcs = VariantContextUtils.sitesOnlyVariantContexts(vcs); vcs = VariantContextUtils.sitesOnlyVariantContexts(vcs);

18
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java
View File

@ -28,9 +28,9 @@ package org.broadinstitute.sting.gatk.walkers.variantutils;
import net.sf.samtools.Cigar; import net.sf.samtools.Cigar;
import net.sf.samtools.CigarElement; import net.sf.samtools.CigarElement;
import net.sf.samtools.CigarOperator; import net.sf.samtools.CigarOperator;
import org.broadinstitute.sting.commandline.Input; import org.broadinstitute.sting.commandline.ArgumentCollection;
import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.commandline.RodBinding; import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@ -50,8 +50,9 @@ import java.util.*;
@Reference(window=@Window(start=-200,stop=200)) @Reference(window=@Window(start=-200,stop=200))
@Requires(value={}) @Requires(value={})
public class LeftAlignVariants extends RodWalker<Integer, Integer> { public class LeftAlignVariants extends RodWalker<Integer, Integer> {
@Input(fullName="variant", shortName = "V", doc="Input VCF file", required=true)
public RodBinding<VariantContext> variants; @ArgumentCollection
protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection();
@Output(doc="File to which variants should be written",required=true) @Output(doc="File to which variants should be written",required=true)
protected VCFWriter baseWriter = null; protected VCFWriter baseWriter = null;
@ -59,10 +60,11 @@ public class LeftAlignVariants extends RodWalker<Integer, Integer> {
private SortingVCFWriter writer; private SortingVCFWriter writer;
public void initialize() { public void initialize() {
Set<String> samples = SampleUtils.getSampleListWithVCFHeader(getToolkit(), Arrays.asList(variants.getName())); String trackName = variantCollection.variants.getName();
Map<String, VCFHeader> vcfHeaders = VCFUtils.getVCFHeadersFromRods(getToolkit(), Arrays.asList(variants.getName())); Set<String> samples = SampleUtils.getSampleListWithVCFHeader(getToolkit(), Arrays.asList(trackName));
Map<String, VCFHeader> vcfHeaders = VCFUtils.getVCFHeadersFromRods(getToolkit(), Arrays.asList(trackName));
Set<VCFHeaderLine> headerLines = vcfHeaders.get(variants.getName()).getMetaData(); Set<VCFHeaderLine> headerLines = vcfHeaders.get(trackName).getMetaData();
baseWriter.writeHeader(new VCFHeader(headerLines, samples)); baseWriter.writeHeader(new VCFHeader(headerLines, samples));
writer = new SortingVCFWriter(baseWriter, 200); writer = new SortingVCFWriter(baseWriter, 200);
@ -72,7 +74,7 @@ public class LeftAlignVariants extends RodWalker<Integer, Integer> {
if ( tracker == null ) if ( tracker == null )
return 0; return 0;
Collection<VariantContext> VCs = tracker.getValues(variants, context.getLocation()); Collection<VariantContext> VCs = tracker.getValues(variantCollection.variants, context.getLocation());
int changedSites = 0; int changedSites = 0;
for ( VariantContext vc : VCs ) for ( VariantContext vc : VCs )

22
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java
View File

@ -29,10 +29,8 @@ import net.sf.picard.liftover.LiftOver;
import net.sf.picard.util.Interval; import net.sf.picard.util.Interval;
import net.sf.samtools.SAMFileHeader; import net.sf.samtools.SAMFileHeader;
import net.sf.samtools.SAMFileReader; import net.sf.samtools.SAMFileReader;
import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.*;
import org.broadinstitute.sting.commandline.Input; import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection;
import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.commandline.RodBinding;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@ -52,8 +50,9 @@ import java.util.*;
*/ */
@Requires(value={}) @Requires(value={})
public class LiftoverVariants extends RodWalker<Integer, Integer> { public class LiftoverVariants extends RodWalker<Integer, Integer> {
@Input(fullName="variant", shortName = "V", doc="Input VCF file", required=true)
public RodBinding<VariantContext> variants; @ArgumentCollection
protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection();
@Output(doc="File to which variants should be written",required=true) @Output(doc="File to which variants should be written",required=true)
protected File file = null; protected File file = null;
@ -88,12 +87,13 @@ public class LiftoverVariants extends RodWalker<Integer, Integer> {
throw new UserException.BadInput("the chain file you are using is not compatible with the reference you are trying to lift over to; please use the appropriate chain file for the given reference"); throw new UserException.BadInput("the chain file you are using is not compatible with the reference you are trying to lift over to; please use the appropriate chain file for the given reference");
} }
Set<String> samples = SampleUtils.getSampleListWithVCFHeader(getToolkit(), Arrays.asList(variants.getName())); String trackName = variantCollection.variants.getName();
Map<String, VCFHeader> vcfHeaders = VCFUtils.getVCFHeadersFromRods(getToolkit(), Arrays.asList(variants.getName())); Set<String> samples = SampleUtils.getSampleListWithVCFHeader(getToolkit(), Arrays.asList(trackName));
Map<String, VCFHeader> vcfHeaders = VCFUtils.getVCFHeadersFromRods(getToolkit(), Arrays.asList(trackName));
Set<VCFHeaderLine> metaData = new HashSet<VCFHeaderLine>(); Set<VCFHeaderLine> metaData = new HashSet<VCFHeaderLine>();
if ( vcfHeaders.containsKey(variants.getName()) ) if ( vcfHeaders.containsKey(trackName) )
metaData.addAll(vcfHeaders.get(variants.getName()).getMetaData()); metaData.addAll(vcfHeaders.get(trackName).getMetaData());
if ( RECORD_ORIGINAL_LOCATION ) { if ( RECORD_ORIGINAL_LOCATION ) {
metaData.add(new VCFInfoHeaderLine("OriginalChr", 1, VCFHeaderLineType.String, "Original contig name for the record")); metaData.add(new VCFInfoHeaderLine("OriginalChr", 1, VCFHeaderLineType.String, "Original contig name for the record"));
metaData.add(new VCFInfoHeaderLine("OriginalStart", 1, VCFHeaderLineType.Integer, "Original start position for the record")); metaData.add(new VCFInfoHeaderLine("OriginalStart", 1, VCFHeaderLineType.Integer, "Original start position for the record"));
@ -146,7 +146,7 @@ public class LiftoverVariants extends RodWalker<Integer, Integer> {
if ( tracker == null ) if ( tracker == null )
return 0; return 0;
Collection<VariantContext> VCs = tracker.getValues(variants, context.getLocation()); Collection<VariantContext> VCs = tracker.getValues(variantCollection.variants, context.getLocation());
for ( VariantContext vc : VCs ) for ( VariantContext vc : VCs )
convertAndWrite(vc, ref); convertAndWrite(vc, ref);

8
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
View File

@ -25,6 +25,7 @@
package org.broadinstitute.sting.gatk.walkers.variantutils; package org.broadinstitute.sting.gatk.walkers.variantutils;
import org.broadinstitute.sting.commandline.*; import org.broadinstitute.sting.commandline.*;
import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection;
import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.codecs.vcf.*; import org.broadinstitute.sting.utils.codecs.vcf.*;
import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.exceptions.UserException;
@ -61,8 +62,7 @@ public class SelectVariants extends RodWalker<Integer, Integer> {
* Variants from this file are sent through the filtering and modifying routines as directed * Variants from this file are sent through the filtering and modifying routines as directed
* by the arguments to SelectVariants, and finally are emitted. * by the arguments to SelectVariants, and finally are emitted.
*/ */
@Input(fullName="variant", shortName = "V", doc="Select variants from this VCF file", required=true) @ArgumentCollection protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection();
public RodBinding<VariantContext> variants;
/** /**
* If provided, we will filter out variants that are "discordant" to the variants in this file * If provided, we will filter out variants that are "discordant" to the variants in this file
@ -194,7 +194,7 @@ public class SelectVariants extends RodWalker<Integer, Integer> {
*/ */
public void initialize() { public void initialize() {
// Get list of samples to include in the output // Get list of samples to include in the output
List<String> rodNames = Arrays.asList(variants.getName()); List<String> rodNames = Arrays.asList(variantCollection.variants.getName());
Map<String, VCFHeader> vcfRods = VCFUtils.getVCFHeadersFromRods(getToolkit(), rodNames); Map<String, VCFHeader> vcfRods = VCFUtils.getVCFHeadersFromRods(getToolkit(), rodNames);
TreeSet<String> vcfSamples = new TreeSet<String>(SampleUtils.getSampleList(vcfRods, VariantContextUtils.GenotypeMergeType.REQUIRE_UNIQUE)); TreeSet<String> vcfSamples = new TreeSet<String>(SampleUtils.getSampleList(vcfRods, VariantContextUtils.GenotypeMergeType.REQUIRE_UNIQUE));
@ -318,7 +318,7 @@ public class SelectVariants extends RodWalker<Integer, Integer> {
if ( tracker == null ) if ( tracker == null )
return 0; return 0;
Collection<VariantContext> vcs = tracker.getValues(variants, context.getLocation()); Collection<VariantContext> vcs = tracker.getValues(variantCollection.variants, context.getLocation());
if ( vcs == null || vcs.size() == 0) { if ( vcs == null || vcs.size() == 0) {
return 0; return 0;

15
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java
View File

@ -28,13 +28,10 @@ package org.broadinstitute.sting.gatk.walkers.variantutils;
import org.broad.tribble.Feature; import org.broad.tribble.Feature;
import org.broad.tribble.TribbleException; import org.broad.tribble.TribbleException;
import org.broad.tribble.dbsnp.DbSNPFeature; import org.broad.tribble.dbsnp.DbSNPFeature;
import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.*;
import org.broadinstitute.sting.commandline.Hidden; import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection;
import org.broadinstitute.sting.commandline.Input;
import org.broadinstitute.sting.commandline.RodBinding;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.refdata.features.DbSNPHelper; import org.broadinstitute.sting.gatk.refdata.features.DbSNPHelper;
import org.broadinstitute.sting.gatk.walkers.*; import org.broadinstitute.sting.gatk.walkers.*;
@ -56,8 +53,8 @@ import java.util.Set;
@Requires(value={}) @Requires(value={})
public class ValidateVariants extends RodWalker<Integer, Integer> { public class ValidateVariants extends RodWalker<Integer, Integer> {
@Input(fullName="variant", shortName = "V", doc="Input VCF file", required=true) @ArgumentCollection
public RodBinding<VariantContext> variants; protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection();
public enum ValidationType { public enum ValidationType {
ALL, REF, IDS, ALLELES, CHR_COUNTS ALL, REF, IDS, ALLELES, CHR_COUNTS
@ -78,14 +75,14 @@ public class ValidateVariants extends RodWalker<Integer, Integer> {
private File file = null; private File file = null;
public void initialize() { public void initialize() {
file = new File(variants.getSource()); file = new File(variantCollection.variants.getSource());
} }
public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
if ( tracker == null ) if ( tracker == null )
return 0; return 0;
Collection<VariantContext> VCs = tracker.getValues(variants, context.getLocation()); Collection<VariantContext> VCs = tracker.getValues(variantCollection.variants, context.getLocation());
for ( VariantContext vc : VCs ) for ( VariantContext vc : VCs )
validate(vc, tracker, ref); validate(vc, tracker, ref);

12
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java
View File

@ -24,12 +24,10 @@
package org.broadinstitute.sting.gatk.walkers.variantutils; package org.broadinstitute.sting.gatk.walkers.variantutils;
import org.broadinstitute.sting.commandline.Input; import org.broadinstitute.sting.commandline.*;
import org.broadinstitute.sting.commandline.RodBinding; import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection;
import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@ -48,8 +46,8 @@ import java.util.*;
@Requires(value={}) @Requires(value={})
public class VariantsToTable extends RodWalker<Integer, Integer> { public class VariantsToTable extends RodWalker<Integer, Integer> {
@Input(fullName="variant", shortName = "V", doc="Input VCF file", required=true) @ArgumentCollection
public RodBinding<VariantContext> variants; protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection();
@Output(doc="File to which results should be written",required=true) @Output(doc="File to which results should be written",required=true)
protected PrintStream out; protected PrintStream out;
@ -138,7 +136,7 @@ public class VariantsToTable extends RodWalker<Integer, Integer> {
return 0; return 0;
if ( ++nRecords < MAX_RECORDS || MAX_RECORDS == -1 ) { if ( ++nRecords < MAX_RECORDS || MAX_RECORDS == -1 ) {
for ( VariantContext vc : tracker.getValues(variants, context.getLocation())) { for ( VariantContext vc : tracker.getValues(variantCollection.variants, context.getLocation())) {
if ( (keepMultiAllelic || vc.isBiallelic()) && ( showFiltered || vc.isNotFiltered() ) ) { if ( (keepMultiAllelic || vc.isBiallelic()) && ( showFiltered || vc.isNotFiltered() ) ) {
List<String> vals = extractFields(vc, fieldsToTake, ALLOW_MISSING_DATA); List<String> vals = extractFields(vc, fieldsToTake, ALLOW_MISSING_DATA);
out.println(Utils.join("\t", vals)); out.println(Utils.join("\t", vals));