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Forgot to commit this long ago, change so the tables are correctly propagated 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4174 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
chartl 2010-08-31 19:06:52 +00:00
parent db4ff7317f
commit 63c7cbd89b
1 changed files with 17 additions and 5 deletions
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22
java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/VariantEvaluatorBySample.java
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@ -53,8 +53,8 @@ public abstract class VariantEvaluatorBySample extends VariantEvaluator {
public String update1(VariantContext vc1, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
for ( String sample : vc1.getSampleNames() ) {
if ( includeGenotype(vc1.getGenotype(sample)) ) {
if ( ! evalBySample.sampleAndEvalResults.containsKey(sample) ) {
evalBySample.sampleAndEvalResults.put(sample,getDataPoints());
if ( ! evalBySample.containsKey(sample) ) {
evalBySample.put(sample,getDataPoints());
}
for ( SampleDataPoint dp : evalBySample.sampleAndEvalResults.get(sample) ) {
@ -72,8 +72,8 @@ public abstract class VariantEvaluatorBySample extends VariantEvaluator {
}
for ( String sample : vc1.getSampleNames() ) {
if ( includeGenotype(vc1.getGenotype(sample)) ) {
if ( ! evalBySample.sampleAndEvalResults.containsKey(sample) ) {
evalBySample.sampleAndEvalResults.put(sample,getDataPoints());
if ( ! evalBySample.containsKey(sample) ) {
evalBySample.put(sample,getDataPoints());
}
for ( SampleDataPoint dp : evalBySample.sampleAndEvalResults.get(sample) ) {
@ -94,6 +94,7 @@ public abstract class VariantEvaluatorBySample extends VariantEvaluator {
abstract class SampleDataPoint {
public String name;
public String sampleName;
public SampleDataPoint(String name) {
this.name = name;
@ -103,6 +104,10 @@ abstract class SampleDataPoint {
return name;
}
public void setSampleName(String sName) {
sampleName = sName;
}
public abstract String toString();
public void update0(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {}
@ -180,8 +185,15 @@ class EvalBySample implements TableType {
}
}
public boolean hasSample(String sample) {
public boolean containsKey(String sample) {
return sampleAndEvalResults.containsKey(sample);
}
public void put(String sample, List<SampleDataPoint> dataPoints) {
for ( SampleDataPoint dp : dataPoints ) {
dp.setSampleName(sample);
}
sampleAndEvalResults.put(sample,dataPoints);
}
}