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Adding Het/Hom ratio to the temp per sample metrics. Because I'm in a generous mood tonight, I'm going ahead and fixing the paths for the classes I'm touching... 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4713 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-11-21 04:24:42 +00:00
parent cff7c6ddce
commit b9a59ea54f
4 changed files with 38 additions and 16 deletions
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10
java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvaluator.java
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@ -14,15 +14,13 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
* This software is supplied without any warranty or guaranteed support whatsoever. Neither
* the Broad Institute nor MIT can be responsible for its use, misuse, or functionality.
*/
abstract class VariantEvaluator {
public abstract class VariantEvaluator {
// protected boolean accumulateInterestingSites = false, printInterestingSites = false;
// protected String interestingSitePrefix = null;
protected boolean processedASite = false;
// protected boolean processedASite = false;
// protected List<VariantContext> interestingSites = new ArrayList<VariantContext>();
public abstract String getName();
// do we want to keep track of things that are interesting
// do we want to keep track of things that are interesting
// public void accumulateInterestingSites(boolean enable) { accumulateInterestingSites = enable; }
// public void printInterestingSites(String prefix) { printInterestingSites = true; interestingSitePrefix = prefix; }
// public boolean isAccumulatingInterestingSites() { return accumulateInterestingSites; }
@ -35,6 +33,8 @@ abstract class VariantEvaluator {
// System.out.printf("%40s %s%n", interestingSitePrefix, why);
// }
public abstract String getName();
protected VariantEvalWalker veWalker = null;
public VariantEvaluator(VariantEvalWalker parent) {
veWalker = parent;

8
java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/FunctionalClassBySample.java
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@ -1,16 +1,12 @@
package org.broadinstitute.sting.gatk.walkers.varianteval;
package org.broadinstitute.sting.oneoffprojects.walkers.varianteval;
import org.broad.tribble.util.variantcontext.Genotype;
import org.broad.tribble.util.variantcontext.VariantContext;
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.varianteval.VariantEvaluatorBySample;
import org.broadinstitute.sting.gatk.walkers.varianteval.*;
import org.broadinstitute.sting.utils.report.tags.Analysis;
import org.broadinstitute.sting.gatk.walkers.varianteval.SampleDataPoint;
import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEvaluatorBySample;
import org.broadinstitute.sting.utils.report.tags.Analysis;
import org.broadinstitute.sting.utils.report.tags.DataPoint;
import java.util.ArrayList;
import java.util.List;

33
java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/SimpleMetricsBySample.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.gatk.walkers.varianteval;
package org.broadinstitute.sting.oneoffprojects.walkers.varianteval;
import org.broad.tribble.util.variantcontext.Genotype;
import org.broad.tribble.util.variantcontext.VariantContext;
@ -6,10 +6,8 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.varianteval.SampleDataPoint;
import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEvaluatorBySample;
import org.broadinstitute.sting.gatk.walkers.varianteval.*;
import org.broadinstitute.sting.utils.report.tags.Analysis;
import org.broadinstitute.sting.utils.report.tags.DataPoint;
import java.util.ArrayList;
import java.util.List;
@ -26,6 +24,7 @@ public class SimpleMetricsBySample extends VariantEvaluatorBySample {
List<SampleDataPoint> points = new ArrayList(3);
points.add(new CountSNPsSample());
points.add(new TiTvRatioSample());
points.add(new HetHomRatioSample());
points.add(new CompOverlapSample());
return points;
@ -92,6 +91,32 @@ class TiTvRatioSample extends SampleDataPoint {
}
}
class HetHomRatioSample extends SampleDataPoint {
int nHet = 0;
int nHomVar = 0;
public HetHomRatioSample() {
super("HetHomRatio");
}
public void update2(VariantContext vc, VariantContext comp, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
if ( vc != null ) {
Genotype g = vc.getGenotype(sampleName);
if ( g != null ) {
if ( g.isHet() ) {
nHet++;
} else if (g.isHomVar()) {
nHomVar++;
}
}
}
}
public String toString() {
return String.format("%.2f", ( ((double) nHet )/ nHomVar));
}
}
class CompOverlapSample extends SampleDataPoint {
int nOverlap = 0;

3
java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/VariantEvaluatorBySample.java
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@ -1,10 +1,11 @@
package org.broadinstitute.sting.gatk.walkers.varianteval;
package org.broadinstitute.sting.oneoffprojects.walkers.varianteval;
import org.broad.tribble.util.variantcontext.Genotype;
import org.broad.tribble.util.variantcontext.VariantContext;
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.varianteval.*;
import org.broadinstitute.sting.utils.report.tags.DataPoint;
import org.broadinstitute.sting.utils.report.utils.TableType;