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Renamed ReadBackedPileup getXSampleName() functions to getXSample 

-- now that we don't have Sample objects floating around we don't have to have all of the Name extensions on our functions
This commit is contained in:
Mark DePristo 2011-09-30 10:02:57 -04:00
parent 3289a325fc
commit 30d23942b1
7 changed files with 15 additions and 17 deletions
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4
public/java/src/org/broadinstitute/sting/gatk/contexts/AlignmentContextUtils.java
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@ -88,8 +88,8 @@ public class AlignmentContextUtils {
GenomeLoc loc = context.getLocation(); GenomeLoc loc = context.getLocation();
HashMap<String, AlignmentContext> contexts = new HashMap<String, AlignmentContext>(); HashMap<String, AlignmentContext> contexts = new HashMap<String, AlignmentContext>();
for(String sample: context.getPileup().getSampleNames()) { for(String sample: context.getPileup().getSamples()) {
ReadBackedPileup pileupBySample = context.getPileup().getPileupForSampleName(sample); ReadBackedPileup pileupBySample = context.getPileup().getPileupForSample(sample);
// Don't add empty pileups to the split context. // Don't add empty pileups to the split context.
if(pileupBySample.size() == 0) if(pileupBySample.size() == 0)

5
public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java
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@ -30,7 +30,6 @@ import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection; 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.samples.Sample;
import org.broadinstitute.sting.gatk.filters.MappingQualityZeroFilter; import org.broadinstitute.sting.gatk.filters.MappingQualityZeroFilter;
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.*;
@ -1095,8 +1094,8 @@ public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, Ph
// filter the read-base pileup based on min base and mapping qualities: // filter the read-base pileup based on min base and mapping qualities:
pileup = pileup.getBaseAndMappingFilteredPileup(MIN_BASE_QUALITY_SCORE, MIN_MAPPING_QUALITY_SCORE); pileup = pileup.getBaseAndMappingFilteredPileup(MIN_BASE_QUALITY_SCORE, MIN_MAPPING_QUALITY_SCORE);
if (pileup != null) { if (pileup != null) {
for (final String sample : pileup.getSampleNames()) { for (final String sample : pileup.getSamples()) {
ReadBackedPileup samplePileup = pileup.getPileupForSampleName(sample); ReadBackedPileup samplePileup = pileup.getPileupForSample(sample);
ReadBasesAtPosition readBases = new ReadBasesAtPosition(); ReadBasesAtPosition readBases = new ReadBasesAtPosition();
for (PileupElement p : samplePileup) { for (PileupElement p : samplePileup) {
if (!p.isDeletion()) // IGNORE deletions for now if (!p.isDeletion()) // IGNORE deletions for now

6
public/java/src/org/broadinstitute/sting/utils/pileup/AbstractReadBackedPileup.java
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@ -548,7 +548,7 @@ public abstract class AbstractReadBackedPileup<RBP extends AbstractReadBackedPil
} }
} }
public Collection<String> getSampleNames() { public Collection<String> getSamples() {
if(pileupElementTracker instanceof PerSamplePileupElementTracker) { if(pileupElementTracker instanceof PerSamplePileupElementTracker) {
PerSamplePileupElementTracker<PE> tracker = (PerSamplePileupElementTracker<PE>)pileupElementTracker; PerSamplePileupElementTracker<PE> tracker = (PerSamplePileupElementTracker<PE>)pileupElementTracker;
return new HashSet<String>(tracker.getSamples()); return new HashSet<String>(tracker.getSamples());
@ -623,7 +623,7 @@ public abstract class AbstractReadBackedPileup<RBP extends AbstractReadBackedPil
} }
@Override @Override
public RBP getPileupForSampleNames(Collection<String> sampleNames) { public RBP getPileupForSamples(Collection<String> sampleNames) {
if(pileupElementTracker instanceof PerSamplePileupElementTracker) { if(pileupElementTracker instanceof PerSamplePileupElementTracker) {
PerSamplePileupElementTracker<PE> tracker = (PerSamplePileupElementTracker<PE>)pileupElementTracker; PerSamplePileupElementTracker<PE> tracker = (PerSamplePileupElementTracker<PE>)pileupElementTracker;
PileupElementTracker<PE> filteredElements = tracker.getElements(sampleNames); PileupElementTracker<PE> filteredElements = tracker.getElements(sampleNames);
@ -649,7 +649,7 @@ public abstract class AbstractReadBackedPileup<RBP extends AbstractReadBackedPil
@Override @Override
public RBP getPileupForSampleName(String sampleName) { public RBP getPileupForSample(String sampleName) {
if(pileupElementTracker instanceof PerSamplePileupElementTracker) { if(pileupElementTracker instanceof PerSamplePileupElementTracker) {
PerSamplePileupElementTracker<PE> tracker = (PerSamplePileupElementTracker<PE>)pileupElementTracker; PerSamplePileupElementTracker<PE> tracker = (PerSamplePileupElementTracker<PE>)pileupElementTracker;
PileupElementTracker<PE> filteredElements = tracker.getElements(sampleName); PileupElementTracker<PE> filteredElements = tracker.getElements(sampleName);

2
public/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedExtendedEventPileup.java
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@ -120,7 +120,7 @@ public interface ReadBackedExtendedEventPileup extends ReadBackedPileup {
* Gets a list of all the samples stored in this pileup. * Gets a list of all the samples stored in this pileup.
* @return List of samples in this pileup. * @return List of samples in this pileup.
*/ */
public Collection<String> getSampleNames(); public Collection<String> getSamples();
public Iterable<ExtendedEventPileupElement> toExtendedIterable(); public Iterable<ExtendedEventPileupElement> toExtendedIterable();

6
public/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedPileup.java
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@ -140,7 +140,7 @@ public interface ReadBackedPileup extends Iterable<PileupElement>, HasGenomeLoca
* Gets a collection of *names* of all the samples stored in this pileup. * Gets a collection of *names* of all the samples stored in this pileup.
* @return Collection of names * @return Collection of names
*/ */
public Collection<String> getSampleNames(); public Collection<String> getSamples();
/** /**
@ -148,7 +148,7 @@ public interface ReadBackedPileup extends Iterable<PileupElement>, HasGenomeLoca
* @param sampleNames Name of the sample to use. * @param sampleNames Name of the sample to use.
* @return A subset of this pileup containing only reads with the given sample. * @return A subset of this pileup containing only reads with the given sample.
*/ */
public ReadBackedPileup getPileupForSampleNames(Collection<String> sampleNames); public ReadBackedPileup getPileupForSamples(Collection<String> sampleNames);
/** /**
@ -156,7 +156,7 @@ public interface ReadBackedPileup extends Iterable<PileupElement>, HasGenomeLoca
* @param sampleName Name of the sample to use. * @param sampleName Name of the sample to use.
* @return A subset of this pileup containing only reads with the given sample. * @return A subset of this pileup containing only reads with the given sample.
*/ */
public ReadBackedPileup getPileupForSampleName(String sampleName); public ReadBackedPileup getPileupForSample(String sampleName);
/** /**
* Simple useful routine to count the number of deletion bases in this pileup * Simple useful routine to count the number of deletion bases in this pileup

2
public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java
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@ -132,7 +132,7 @@ import java.util.*;
* vc.hasGenotypes() * vc.hasGenotypes()
* vc.isMonomorphic() * vc.isMonomorphic()
* vc.isPolymorphic() * vc.isPolymorphic()
* vc.getSampleNames().size() * vc.getSamples().size()
* *
* vc.getGenotypes() * vc.getGenotypes()
* vc.getGenotypes().get("g1") * vc.getGenotypes().get("g1")

7
public/java/test/org/broadinstitute/sting/utils/pileup/ReadBackedPileupUnitTest.java
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@ -28,7 +28,6 @@ import net.sf.samtools.SAMFileHeader;
import net.sf.samtools.SAMReadGroupRecord; import net.sf.samtools.SAMReadGroupRecord;
import net.sf.samtools.SAMRecord; import net.sf.samtools.SAMRecord;
import org.testng.Assert; import org.testng.Assert;
import org.broadinstitute.sting.gatk.samples.Sample;
import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils; import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
import org.testng.annotations.Test; import org.testng.annotations.Test;
@ -187,14 +186,14 @@ public class ReadBackedPileupUnitTest {
ReadBackedPileup pileup = new ReadBackedPileupImpl(null,sampleToPileupMap); ReadBackedPileup pileup = new ReadBackedPileupImpl(null,sampleToPileupMap);
ReadBackedPileup sample2Pileup = pileup.getPileupForSampleName(sample2); ReadBackedPileup sample2Pileup = pileup.getPileupForSample(sample2);
Assert.assertEquals(sample2Pileup.size(),1,"Sample 2 pileup has wrong number of elements"); Assert.assertEquals(sample2Pileup.size(),1,"Sample 2 pileup has wrong number of elements");
Assert.assertEquals(sample2Pileup.getReads().get(0),read2,"Sample 2 pileup has incorrect read"); Assert.assertEquals(sample2Pileup.getReads().get(0),read2,"Sample 2 pileup has incorrect read");
ReadBackedPileup missingSamplePileup = pileup.getPileupForSampleName("missing"); ReadBackedPileup missingSamplePileup = pileup.getPileupForSample("missing");
Assert.assertNull(missingSamplePileup,"Pileup for sample 'missing' should be null but isn't"); Assert.assertNull(missingSamplePileup,"Pileup for sample 'missing' should be null but isn't");
missingSamplePileup = pileup.getPileupForSampleName("not here"); missingSamplePileup = pileup.getPileupForSample("not here");
Assert.assertNull(missingSamplePileup,"Pileup for sample 'not here' should be null but isn't"); Assert.assertNull(missingSamplePileup,"Pileup for sample 'not here' should be null but isn't");
} }
} }