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Merge pull request #120 from broadinstitute/aw_reduce_reads_clear_name_cache 

Clear ReduceReads name cache after each set of reads produced by ReduceR...
This commit is contained in:
Eric Banks 2013-03-20 19:47:42 -07:00
parent 7e29beadff bccc9d79e5
commit 1fae750ebe
2 changed files with 25 additions and 7 deletions
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7
protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReads.java
View File

@ -408,6 +408,13 @@ public class ReduceReads extends ReadWalker<ObjectArrayList<GATKSAMRecord>, Redu
for (GATKSAMRecord compressedRead : stash.compress(readReady))
outputRead(compressedRead);
// We only care about maintaining the link between read pairs if they are in the same variant
// region. Since an entire variant region's worth of reads is returned in a single call to
// stash.compress(), the readNameHash can be cleared after the for() loop above.
// The advantage of clearing the hash is that otherwise it holds all reads that have been encountered,
// which can use a lot of memory and cause RR to slow to a crawl and/or run out of memory.
readNameHash.clear();
}
} else
stash.add(read);

25
protected/java/test/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReadsIntegrationTest.java
View File

@ -64,6 +64,7 @@ public class ReduceReadsIntegrationTest extends WalkerTest {
final String COREDUCTION_BAM_B = validationDataLocation + "coreduction.test.B.bam";
final String COREDUCTION_L = " -L 1:1,853,860-1,854,354 -L 1:1,884,131-1,892,057";
final String OFFCONTIG_BAM = privateTestDir + "readOffb37contigMT.bam";
final String BOTH_ENDS_OF_PAIR_IN_VARIANT_REGION_BAM = privateTestDir + "bothEndsOfPairInVariantRegion.bam";
final String INSERTIONS_AT_EDGE_OF_CONSENSUS_BAM = privateTestDir + "rr-too-many-insertions.bam";
private void RRTest(String testName, String args, String md5) {
@ -74,29 +75,29 @@ public class ReduceReadsIntegrationTest extends WalkerTest {
@Test(enabled = true)
public void testDefaultCompression() {
RRTest("testDefaultCompression ", L, "17908e8515217c4693d303ed68108ccc");
RRTest("testDefaultCompression ", L, "16d97a47b8dbfae4ea64fbdf522b693c");
}
@Test(enabled = true)
public void testInsertionsAtEdgeOfConsensus() {
String base = String.format("-T ReduceReads -npt -R %s -I %s ", REF, INSERTIONS_AT_EDGE_OF_CONSENSUS_BAM) + " -o %s ";
executeTest("testInsertionsAtEdgeOfConsensus", new WalkerTestSpec(base, Arrays.asList("3103667fc68c3136a8cfa8e22429f94e")));
executeTest("testInsertionsAtEdgeOfConsensus", new WalkerTestSpec(base, Arrays.asList("f7a9a27c5eaf791b67a768fff960a9e1")));
}
@Test(enabled = true)
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";
RRTest("testMultipleIntervals ", intervals, "497c5e36c2beaad2fcdbd02a0b9c121b");
RRTest("testMultipleIntervals ", intervals, "8886ba383e21883241b386882e8e5063");
}
@Test(enabled = true)
public void testHighCompression() {
RRTest("testHighCompression ", " -cs 10 -minvar 0.3 -mindel 0.3 " + L, "0ff4142e4d7b6a9a9c76012246ad9e2d");
RRTest("testHighCompression ", " -cs 10 -minvar 0.3 -mindel 0.3 " + L, "54253f25d363852a1182aff33e500b92");
}
@Test(enabled = true)
public void testLowCompression() {
RRTest("testLowCompression ", " -cs 30 -minvar 0.01 -mindel 0.01 -minmap 5 -minqual 5 " + L, "7890a37444a0e05b902f63a83238ce37");
RRTest("testLowCompression ", " -cs 30 -minvar 0.01 -mindel 0.01 -minmap 5 -minqual 5 " + L, "1d7d2d28900db57dad65a8beef64b8cb");
}
@Test(enabled = true)
@ -137,7 +138,7 @@ public class ReduceReadsIntegrationTest extends WalkerTest {
@Test(enabled = true)
public void testCoReduction() {
String base = String.format("-T ReduceReads %s -npt -R %s -I %s -I %s", COREDUCTION_L, REF, COREDUCTION_BAM_A, COREDUCTION_BAM_B) + " -o %s ";
executeTest("testCoReduction", new WalkerTestSpec(base, Arrays.asList("13c44a9afa92ae728bf55b7075cc5de3")));
executeTest("testCoReduction", new WalkerTestSpec(base, Arrays.asList("81312c31b9910a42bff6acb5167592ab")));
}
/**
@ -147,8 +148,18 @@ public class ReduceReadsIntegrationTest extends WalkerTest {
@Test(enabled = true)
public void testReadOffContig() {
String base = String.format("-T ReduceReads -npt -R %s -I %s ", REF, OFFCONTIG_BAM) + " -o %s ";
executeTest("testReadOffContig", new WalkerTestSpec(base, Arrays.asList("c57cd191dc391983131be43f6cc2e381")));
executeTest("testReadOffContig", new WalkerTestSpec(base, Arrays.asList("b4dc66445ddf5f467f67860bed023ef8")));
}
/**
* Confirm that if both ends of pair are in same variant region, compressed names of both ends of pair are the same.
*/
@Test(enabled = true)
public void testPairedReadsInVariantRegion() {
String base = String.format("-T ReduceReads -npt -R %s -I %s ", hg19Reference, BOTH_ENDS_OF_PAIR_IN_VARIANT_REGION_BAM) +
" -o %s --downsample_coverage 250 -dcov 50 ";
executeTest("testPairedReadsInVariantRegion", new WalkerTestSpec(base, Arrays.asList("9bed260b6245f5ff47db8541405504aa")));
}
}