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Fixed ReduceReads bug where variant regions were missing. 

This affected variant regions with more than 100 reads and less than 250 reads. Only bams reduced with GATK v2 and 2.1 were affected.
This commit is contained in:
Mauricio Carneiro 2012-09-19 16:09:08 -04:00
parent eb63221875
commit 7cf9911924
2 changed files with 9 additions and 10 deletions
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7
protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SlidingWindow.java
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@ -5,7 +5,7 @@ import net.sf.samtools.Cigar;
import net.sf.samtools.CigarElement; import net.sf.samtools.CigarElement;
import net.sf.samtools.CigarOperator; import net.sf.samtools.CigarOperator;
import net.sf.samtools.SAMFileHeader; import net.sf.samtools.SAMFileHeader;
import org.broadinstitute.sting.gatk.downsampling.FractionalDownsampler; import org.broadinstitute.sting.gatk.downsampling.ReservoirDownsampler;
import org.broadinstitute.sting.utils.collections.Pair; import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.sam.GATKSAMReadGroupRecord; import org.broadinstitute.sting.utils.sam.GATKSAMReadGroupRecord;
@ -540,11 +540,10 @@ public class SlidingWindow {
if (nReads == 0) if (nReads == 0)
return allReads; return allReads;
double fraction = 100 / allReads.size(); if (downsampleCoverage >= nReads)
if (fraction >= 1)
return allReads; return allReads;
FractionalDownsampler <GATKSAMRecord> downsampler = new FractionalDownsampler<GATKSAMRecord>(fraction); ReservoirDownsampler <GATKSAMRecord> downsampler = new ReservoirDownsampler<GATKSAMRecord>(downsampleCoverage);
downsampler.submit(allReads); downsampler.submit(allReads);
return downsampler.consumeDownsampledItems(); return downsampler.consumeDownsampledItems();
} }

12
protected/java/test/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReadsIntegrationTest.java
View File

@ -23,28 +23,28 @@ public class ReduceReadsIntegrationTest extends WalkerTest {
@Test(enabled = true) @Test(enabled = true)
public void testDefaultCompression() { public void testDefaultCompression() {
RRTest("testDefaultCompression ", L, "72eb6db9d7a09a0cc25eaac1aafa97b7"); RRTest("testDefaultCompression ", L, "323dd4deabd7767efa0f2c6e7fa4189f");
} }
@Test(enabled = true) @Test(enabled = true)
public void testMultipleIntervals() { public void testMultipleIntervals() {
String intervals = "-L 20:10,100,000-10,100,500 -L 20:10,200,000-10,200,500 -L 20:10,300,000-10,300,500 -L 20:10,400,000-10,500,000 -L 20:10,500,050-10,500,060 -L 20:10,600,000-10,600,015 -L 20:10,700,000-10,700,110"; String intervals = "-L 20:10,100,000-10,100,500 -L 20:10,200,000-10,200,500 -L 20:10,300,000-10,300,500 -L 20:10,400,000-10,500,000 -L 20:10,500,050-10,500,060 -L 20:10,600,000-10,600,015 -L 20:10,700,000-10,700,110";
RRTest("testMultipleIntervals ", intervals, "104b1a1d9fa5394c6fea95cd32967b78"); RRTest("testMultipleIntervals ", intervals, "c437fb160547ff271f8eba30e5f3ff76");
} }
@Test(enabled = true) @Test(enabled = true)
public void testHighCompression() { public void testHighCompression() {
RRTest("testHighCompression ", " -cs 10 -minvar 0.3 -mindel 0.3 " + L, "c55140cec60fa8c35161680289d74d47"); RRTest("testHighCompression ", " -cs 10 -minvar 0.3 -mindel 0.3 " + L, "3a607bc3ebaf84e9dc44e005c5f8a047");
} }
@Test(enabled = true) @Test(enabled = true)
public void testLowCompression() { public void testLowCompression() {
RRTest("testLowCompression ", " -cs 30 -minvar 0.01 -mindel 0.01 -minmap 5 -minqual 5 " + L, "0f2e57b7f6de03cc4da1ffcc8cf8f1a7"); RRTest("testLowCompression ", " -cs 30 -minvar 0.01 -mindel 0.01 -minmap 5 -minqual 5 " + L, "7c9b4a70c2c90b0a995800aa42852e63");
} }
@Test(enabled = true) @Test(enabled = true)
public void testIndelCompression() { public void testIndelCompression() {
RRTest("testIndelCompression ", " -cs 50 -L 20:10,100,500-10,100,600 ", "dda0c95f56f90e5f633c2437c2b21031"); RRTest("testIndelCompression ", " -cs 50 -L 20:10,100,500-10,100,600 ", "f7b9fa44c10bc4b2247813d2b8dc1973");
} }
@Test(enabled = true) @Test(enabled = true)
@ -74,7 +74,7 @@ public class ReduceReadsIntegrationTest extends WalkerTest {
@Test(enabled = true) @Test(enabled = true)
public void testDivideByZero() { public void testDivideByZero() {
String base = String.format("-T ReduceReads %s -npt -R %s -I %s", DIVIDEBYZERO_L, REF, DIVIDEBYZERO_BAM) + " -o %s "; String base = String.format("-T ReduceReads %s -npt -R %s -I %s", DIVIDEBYZERO_L, REF, DIVIDEBYZERO_BAM) + " -o %s ";
executeTest("testDivideByZero", new WalkerTestSpec(base, Arrays.asList("137505c3efd1e9f8d9209dbdf8419ff9"))); executeTest("testDivideByZero", new WalkerTestSpec(base, Arrays.asList("93ffdc209d4cc0fc4f0169ca9be55cc2")));
} }
} }