From 30d23942b1f481568ca95fd6ff82a0b1099ad237 Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Fri, 30 Sep 2011 10:02:57 -0400 Subject: [PATCH] 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 --- .../sting/gatk/contexts/AlignmentContextUtils.java | 4 ++-- .../gatk/walkers/phasing/ReadBackedPhasingWalker.java | 5 ++--- .../sting/utils/pileup/AbstractReadBackedPileup.java | 6 +++--- .../sting/utils/pileup/ReadBackedExtendedEventPileup.java | 2 +- .../sting/utils/pileup/ReadBackedPileup.java | 6 +++--- .../sting/utils/variantcontext/VariantContext.java | 2 +- .../sting/utils/pileup/ReadBackedPileupUnitTest.java | 7 +++---- 7 files changed, 15 insertions(+), 17 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/contexts/AlignmentContextUtils.java b/public/java/src/org/broadinstitute/sting/gatk/contexts/AlignmentContextUtils.java index f77fbe4e9..c9506ec4c 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/contexts/AlignmentContextUtils.java +++ b/public/java/src/org/broadinstitute/sting/gatk/contexts/AlignmentContextUtils.java @@ -88,8 +88,8 @@ public class AlignmentContextUtils { GenomeLoc loc = context.getLocation(); HashMap contexts = new HashMap(); - for(String sample: context.getPileup().getSampleNames()) { - ReadBackedPileup pileupBySample = context.getPileup().getPileupForSampleName(sample); + for(String sample: context.getPileup().getSamples()) { + ReadBackedPileup pileupBySample = context.getPileup().getPileupForSample(sample); // Don't add empty pileups to the split context. if(pileupBySample.size() == 0) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java index bbbdf5f1a..998cfa654 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java @@ -30,7 +30,6 @@ import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; 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.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.*; @@ -1095,8 +1094,8 @@ public class ReadBackedPhasingWalker extends RodWalker getSampleNames() { + public Collection getSamples() { if(pileupElementTracker instanceof PerSamplePileupElementTracker) { PerSamplePileupElementTracker tracker = (PerSamplePileupElementTracker)pileupElementTracker; return new HashSet(tracker.getSamples()); @@ -623,7 +623,7 @@ public abstract class AbstractReadBackedPileup sampleNames) { + public RBP getPileupForSamples(Collection sampleNames) { if(pileupElementTracker instanceof PerSamplePileupElementTracker) { PerSamplePileupElementTracker tracker = (PerSamplePileupElementTracker)pileupElementTracker; PileupElementTracker filteredElements = tracker.getElements(sampleNames); @@ -649,7 +649,7 @@ public abstract class AbstractReadBackedPileup tracker = (PerSamplePileupElementTracker)pileupElementTracker; PileupElementTracker filteredElements = tracker.getElements(sampleName); diff --git a/public/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedExtendedEventPileup.java b/public/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedExtendedEventPileup.java index afed68177..e7c0bc18f 100644 --- a/public/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedExtendedEventPileup.java +++ b/public/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedExtendedEventPileup.java @@ -120,7 +120,7 @@ public interface ReadBackedExtendedEventPileup extends ReadBackedPileup { * Gets a list of all the samples stored in this pileup. * @return List of samples in this pileup. */ - public Collection getSampleNames(); + public Collection getSamples(); public Iterable toExtendedIterable(); diff --git a/public/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedPileup.java b/public/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedPileup.java index 32ab50695..3d30aa11b 100644 --- a/public/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedPileup.java +++ b/public/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedPileup.java @@ -140,7 +140,7 @@ public interface ReadBackedPileup extends Iterable, HasGenomeLoca * Gets a collection of *names* of all the samples stored in this pileup. * @return Collection of names */ - public Collection getSampleNames(); + public Collection getSamples(); /** @@ -148,7 +148,7 @@ public interface ReadBackedPileup extends Iterable, HasGenomeLoca * @param sampleNames Name of the sample to use. * @return A subset of this pileup containing only reads with the given sample. */ - public ReadBackedPileup getPileupForSampleNames(Collection sampleNames); + public ReadBackedPileup getPileupForSamples(Collection sampleNames); /** @@ -156,7 +156,7 @@ public interface ReadBackedPileup extends Iterable, HasGenomeLoca * @param sampleName Name of the sample to use. * @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 diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java index 412cbd90b..05e21c8b8 100755 --- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java +++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java @@ -132,7 +132,7 @@ import java.util.*; * vc.hasGenotypes() * vc.isMonomorphic() * vc.isPolymorphic() - * vc.getSampleNames().size() + * vc.getSamples().size() * * vc.getGenotypes() * vc.getGenotypes().get("g1") diff --git a/public/java/test/org/broadinstitute/sting/utils/pileup/ReadBackedPileupUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/pileup/ReadBackedPileupUnitTest.java index 4e0541522..b07da7cc8 100644 --- a/public/java/test/org/broadinstitute/sting/utils/pileup/ReadBackedPileupUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/utils/pileup/ReadBackedPileupUnitTest.java @@ -28,7 +28,6 @@ import net.sf.samtools.SAMFileHeader; import net.sf.samtools.SAMReadGroupRecord; import net.sf.samtools.SAMRecord; import org.testng.Assert; -import org.broadinstitute.sting.gatk.samples.Sample; import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils; import org.testng.annotations.Test; @@ -187,14 +186,14 @@ public class ReadBackedPileupUnitTest { 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.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"); - missingSamplePileup = pileup.getPileupForSampleName("not here"); + missingSamplePileup = pileup.getPileupForSample("not here"); Assert.assertNull(missingSamplePileup,"Pileup for sample 'not here' should be null but isn't"); } }