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Test cleanup of Sample object

This commit is contained in:
Mark DePristo 2011-09-29 15:13:05 -04:00
parent 625ffb6a07
commit 9458f01409
2 changed files with 10 additions and 10 deletions
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2
public/java/test/org/broadinstitute/sting/gatk/datasources/reads/DownsamplerBenchmark.java
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@ -89,7 +89,7 @@ public class DownsamplerBenchmark extends ReadProcessingBenchmark {
// Filter unmapped reads. TODO: is this always strictly necessary? Who in the GATK normally filters these out? // Filter unmapped reads. TODO: is this always strictly necessary? Who in the GATK normally filters these out?
Iterator<SAMRecord> readIterator = new FilteringIterator(reader.iterator(),new UnmappedReadFilter()); Iterator<SAMRecord> readIterator = new FilteringIterator(reader.iterator(),new UnmappedReadFilter());
LocusIteratorByState locusIteratorByState = new LocusIteratorByState(readIterator,readProperties,genomeLocParser,sampleDataSource); LocusIteratorByState locusIteratorByState = new LocusIteratorByState(readIterator,readProperties,genomeLocParser,sampleDataSource.getSampleNames());
while(locusIteratorByState.hasNext()) { while(locusIteratorByState.hasNext()) {
locusIteratorByState.next().getLocation(); locusIteratorByState.next().getLocation();
} }

18
public/java/test/org/broadinstitute/sting/utils/pileup/ReadBackedPileupUnitTest.java
View File

@ -141,9 +141,9 @@ public class ReadBackedPileupUnitTest {
ReadBackedPileupImpl sample2Pileup = new ReadBackedPileupImpl(null, ReadBackedPileupImpl sample2Pileup = new ReadBackedPileupImpl(null,
Arrays.asList(read2,read4), Arrays.asList(read2,read4),
Arrays.asList(1,1)); Arrays.asList(1,1));
Map<Sample,ReadBackedPileupImpl> sampleToPileupMap = new HashMap<Sample,ReadBackedPileupImpl>(); Map<String,ReadBackedPileupImpl> sampleToPileupMap = new HashMap<String,ReadBackedPileupImpl>();
sampleToPileupMap.put(new Sample(readGroupOne.getSample(), null),sample1Pileup); sampleToPileupMap.put(readGroupOne.getSample(),sample1Pileup);
sampleToPileupMap.put(new Sample(readGroupTwo.getSample(), null),sample2Pileup); sampleToPileupMap.put(readGroupTwo.getSample(),sample2Pileup);
ReadBackedPileup compositePileup = new ReadBackedPileupImpl(null,sampleToPileupMap); ReadBackedPileup compositePileup = new ReadBackedPileupImpl(null,sampleToPileupMap);
@ -164,13 +164,13 @@ public class ReadBackedPileupUnitTest {
@Test @Test
public void testGetPileupForSample() { public void testGetPileupForSample() {
Sample sample1 = new Sample("sample1", null); String sample1 = "sample1";
Sample sample2 = new Sample("sample2", null); String sample2 = "sample2";
SAMReadGroupRecord readGroupOne = new SAMReadGroupRecord("rg1"); SAMReadGroupRecord readGroupOne = new SAMReadGroupRecord("rg1");
readGroupOne.setSample(sample1.getID()); readGroupOne.setSample(sample1);
SAMReadGroupRecord readGroupTwo = new SAMReadGroupRecord("rg2"); SAMReadGroupRecord readGroupTwo = new SAMReadGroupRecord("rg2");
readGroupTwo.setSample(sample2.getID()); readGroupTwo.setSample(sample2);
SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(1,1,1000); SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(1,1,1000);
header.addReadGroup(readGroupOne); header.addReadGroup(readGroupOne);
@ -181,13 +181,13 @@ public class ReadBackedPileupUnitTest {
SAMRecord read2 = ArtificialSAMUtils.createArtificialRead(header,"read2",0,1,10); SAMRecord read2 = ArtificialSAMUtils.createArtificialRead(header,"read2",0,1,10);
read2.setAttribute("RG",readGroupTwo.getId()); read2.setAttribute("RG",readGroupTwo.getId());
Map<Sample,ReadBackedPileupImpl> sampleToPileupMap = new HashMap<Sample,ReadBackedPileupImpl>(); Map<String,ReadBackedPileupImpl> sampleToPileupMap = new HashMap<String,ReadBackedPileupImpl>();
sampleToPileupMap.put(sample1,new ReadBackedPileupImpl(null,Collections.singletonList(read1),0)); sampleToPileupMap.put(sample1,new ReadBackedPileupImpl(null,Collections.singletonList(read1),0));
sampleToPileupMap.put(sample2,new ReadBackedPileupImpl(null,Collections.singletonList(read2),0)); sampleToPileupMap.put(sample2,new ReadBackedPileupImpl(null,Collections.singletonList(read2),0));
ReadBackedPileup pileup = new ReadBackedPileupImpl(null,sampleToPileupMap); ReadBackedPileup pileup = new ReadBackedPileupImpl(null,sampleToPileupMap);
ReadBackedPileup sample2Pileup = pileup.getPileupForSampleName(sample2.getID()); ReadBackedPileup sample2Pileup = pileup.getPileupForSampleName(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");