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Partial commit for David so he can see what I want to do with the VariantAnnotator. Added a DbsnpArgumentCollection that people can use in their walkers to ensure that we have a standard syntax whenever allowing dbsnp rods. Added it to UG, but didn't hook it up. Maybe we should do the same for the 'variant' rod?

This commit is contained in:
Eric Banks 2011-08-09 23:19:40 -04:00
parent 489e5cffc1
commit 08631546c8
3 changed files with 75 additions and 0 deletions
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48
public/java/src/org/broadinstitute/sting/gatk/arguments/DbsnpArgumentCollection.java 100644
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@ -0,0 +1,48 @@
/*
* 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.*;
/**
* @author ebanks
* @version 1.0
*/
@Root
public class DbsnpArgumentCollection {
/**
* A dbSNP VCF file.
*/
@Input(fullName="dbsnp", shortName = "D", doc="dbSNP file", required=false)
public RodBinding<VariantContext> dbsnp = RodBinding.makeUnbound(VariantContext.class);
}

19
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java
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@ -26,6 +26,7 @@
package org.broadinstitute.sting.gatk.walkers.annotator;
import org.broadinstitute.sting.commandline.*;
import org.broadinstitute.sting.gatk.arguments.DbsnpArgumentCollection;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
@ -34,6 +35,7 @@ import org.broadinstitute.sting.gatk.walkers.*;
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.InfoFieldAnnotation;
import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedArgumentCollection;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.classloader.PluginManager;
@ -60,6 +62,23 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> {
@Input(fullName="snpEffFile", shortName = "snpEffFile", doc="SnpEff file", required=false)
public RodBinding<SnpEffFeature> snpEffFile;
/**
* A dbSNP VCF file from which to annotate.
*
* rsIDs from this file are used to populate the ID column of the output. Also, the DB INFO flag will be set when appropriate.
*/
@ArgumentCollection protected DbsnpArgumentCollection dbsnp = new DbsnpArgumentCollection();
/**
* A comparisons VCF file from which to annotate.
*
* If a record in the 'variant' track overlaps with a record from the provided comp track, the INFO field will be annotated
* as such in the output with the track name (e.g. -comp:FOO will have 'FOO' in the INFO field). Records that are filtered in the comp track will be ignored.
* Note that 'dbSNP' has been special-cased (see the --dbsnp argument).
*/
@Input(fullName="comp", shortName = "comp", doc="comparison VCF file", required=false)
public RodBinding<VariantContext> comps = RodBinding.makeUnbound(VariantContext.class);
@Output(doc="File to which variants should be written",required=true)
protected VCFWriter vcfWriter = null;

8
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
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@ -29,6 +29,7 @@ import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.ArgumentCollection;
import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.gatk.DownsampleType;
import org.broadinstitute.sting.gatk.arguments.DbsnpArgumentCollection;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
@ -59,6 +60,13 @@ public class UnifiedGenotyper extends LocusWalker<VariantCallContext, UnifiedGen
@ArgumentCollection private UnifiedArgumentCollection UAC = new UnifiedArgumentCollection();
/**
* A dbSNP VCF file from which to annotate.
*
* rsIDs from this file are used to populate the ID column of the output. Also, the DB INFO flag will be set when appropriate.
*/
@ArgumentCollection protected DbsnpArgumentCollection dbsnp = new DbsnpArgumentCollection();
// control the output
@Output(doc="File to which variants should be written",required=true)
protected VCFWriter writer = null;