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Fixed divide by zero bug when downsampler goes over regions where reads are all filtered out. Added Guillermo's bug report as an integration test

This commit is contained in:
Mauricio Carneiro 2012-08-09 13:02:11 -04:00
parent 78c1556186
commit c6132ebe26
3 changed files with 19 additions and 1 deletions
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5
protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SlidingWindow.java
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@ -536,6 +536,10 @@ public class SlidingWindow {
* @return a list of reads selected by the downsampler to cover the window to at least the desired coverage * @return a list of reads selected by the downsampler to cover the window to at least the desired coverage
*/ */
protected List<GATKSAMRecord> downsampleVariantRegion(final List<GATKSAMRecord> allReads) { protected List<GATKSAMRecord> downsampleVariantRegion(final List<GATKSAMRecord> allReads) {
int nReads = allReads.size();
if (nReads == 0)
return allReads;
double fraction = 100 / allReads.size(); double fraction = 100 / allReads.size();
if (fraction >= 1) if (fraction >= 1)
return allReads; return allReads;
@ -545,6 +549,7 @@ public class SlidingWindow {
return downsampler.consumeDownsampledItems(); return downsampler.consumeDownsampledItems();
} }
/** /**
* Properly closes a Sliding Window, finalizing all consensus and variant * Properly closes a Sliding Window, finalizing all consensus and variant
* regions that still exist regardless of being able to fulfill the * regions that still exist regardless of being able to fulfill the

2
protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SyntheticRead.java
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@ -102,7 +102,7 @@ public class SyntheticRead {
* @param base the base to add * @param base the base to add
* @param count number of reads with this base * @param count number of reads with this base
*/ */
@Requires("count < Byte.MAX_VALUE") @Requires("count <= Byte.MAX_VALUE")
public void add(BaseIndex base, byte count, byte qual, byte insQual, byte delQual, double mappingQuality) { public void add(BaseIndex base, byte count, byte qual, byte insQual, byte delQual, double mappingQuality) {
counts.add(count); counts.add(count);
bases.add(base); bases.add(base);

13
protected/java/test/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReadsIntegrationTest.java
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@ -11,6 +11,8 @@ public class ReduceReadsIntegrationTest extends WalkerTest {
final String DELETION_BAM = validationDataLocation + "filtered_deletion_for_reduce_reads.bam"; final String DELETION_BAM = validationDataLocation + "filtered_deletion_for_reduce_reads.bam";
final String STASH_BAM = validationDataLocation + "ReduceReadsStashBug.bam"; final String STASH_BAM = validationDataLocation + "ReduceReadsStashBug.bam";
final String STASH_L = " -L 14:73718184-73718284 -L 14:73718294-73718330 -L 14:73718360-73718556"; final String STASH_L = " -L 14:73718184-73718284 -L 14:73718294-73718330 -L 14:73718360-73718556";
final String DIVIDEBYZERO_BAM = validationDataLocation + "ReduceReadsDivideByZeroBug.bam";
final String DIVIDEBYZERO_L = " -L " + validationDataLocation + "ReduceReadsDivideByZeroBug.intervals";
final String L = " -L 20:10,100,000-10,120,000 "; final String L = " -L 20:10,100,000-10,120,000 ";
private void RRTest(String testName, String args, String md5) { private void RRTest(String testName, String args, String md5) {
@ -64,5 +66,16 @@ public class ReduceReadsIntegrationTest extends WalkerTest {
String base = String.format("-T ReduceReads %s -npt -R %s -I %s", STASH_L, REF, STASH_BAM) + " -o %s "; String base = String.format("-T ReduceReads %s -npt -R %s -I %s", STASH_L, REF, STASH_BAM) + " -o %s ";
executeTest("testAddingReadAfterTailingTheStash", new WalkerTestSpec(base, Arrays.asList("886b43e1f26ff18425814dc7563931c6"))); executeTest("testAddingReadAfterTailingTheStash", new WalkerTestSpec(base, Arrays.asList("886b43e1f26ff18425814dc7563931c6")));
} }
/**
* Divide by zero bug reported by GdA and users in the forum. Happens when the downsampler goes over a region where all reads get
* filtered out.
*/
@Test(enabled = true)
public void testDivideByZero() {
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")));
}
} }