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removing the unsupported VCF validator 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2909 348d0f76-0448-11de-a6fe-93d51630548a
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aaron 2010-03-02 15:45:33 +00:00
parent 1b572b192a
commit 232fcf829a
1 changed files with 0 additions and 46 deletions
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46
java/src/org/broadinstitute/sting/gatk/walkers/qc/VCFValidator.java
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@ -1,46 +0,0 @@
package org.broadinstitute.sting.gatk.walkers.qc;
import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList;
import org.broadinstitute.sting.gatk.walkers.RodWalker;
import org.broadinstitute.sting.gatk.walkers.Requires;
import org.broadinstitute.sting.gatk.walkers.RMD;
import org.broadinstitute.sting.gatk.refdata.RodVCF;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.utils.StingException;
/**
* A light-weight validator for a VCF file.
*/
@Requires(value={},referenceMetaData=@RMD(name="vcf", type=RodVCF.class))
public class VCFValidator extends RodWalker<Integer, Integer> {
/**
* It's about as simple as things come right now. We let the rod system process all of the
* entries in the file, and if no errors pop up in processing, then it validates!
*/
public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
if ( tracker != null ) {
RODRecordList rodlist = tracker.getTrackData("vcf", null);
if ( rodlist != null ) {
RodVCF rod = (RodVCF)rodlist.get(0);
if ( (rod.isSNP() || rod.isReference()) && Character.toUpperCase(rod.getReference().charAt(0)) != Character.toUpperCase(ref.getBase()) )
throw new StingException("The reference base (" + ref.getBase() + ") does not match the base from the VCF record (" + rod.getReference() + ")");
}
}
return 1;
}
public Integer reduceInit() { return 0; }
public Integer reduce(Integer value, Integer sum) {
return sum + value;
}
public void onTraversalDone(Integer result) {
out.println("The input file is a valid VCF");
}
}