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Merged bug fix from Stable into Unstable

This commit is contained in:
Mauricio Carneiro 2012-09-19 16:09:45 -04:00
parent 26e35e5ee2 7cf9911924
commit ee31a54a03
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
View File

@ -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.consumeFinalizedItems(); return downsampler.consumeFinalizedItems();
} }

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")));
} }
} }