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Only store a read in the mate hash if it could possibly be moved. This reduces memory consumption especially when dealing with a case of tons of unmapped reads at the end of the bam; however, it's only mildly helpful for chr1 of the Papuans (there's a truly massive pileup 120Mb into it; more thought needed at a later point). Integration tests changed only because some of the reads in the original bam were busted to begin with (it's an old pilot 1000G bam). 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5580 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2011-04-05 22:20:09 +00:00
parent 79b5fa6cc5
commit 4b451314b2
2 changed files with 61 additions and 56 deletions
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15
java/src/org/broadinstitute/sting/gatk/walkers/indels/ConstrainedMateFixingManager.java
View File

@ -228,7 +228,7 @@ public class ConstrainedMateFixingManager {
}
forMateMatching.remove(newRead.getReadName());
} else {
} else if ( pairedReadIsMovable(newRead) ) {
forMateMatching.put(newRead.getReadName(), newRead);
}
}
@ -240,10 +240,8 @@ public class ConstrainedMateFixingManager {
SAMRecord read = waitingReads.peek();
if ( noReadCanMoveBefore(read.getAlignmentStart(), newRead) &&
(iSizeTooBigToMove(read) // we won't try to move such a read
|| ! read.getReadPairedFlag() // we're not a paired read
|| read.getReadUnmappedFlag() && read.getMateUnmappedFlag() // both reads are unmapped
|| noReadCanMoveBefore(read.getMateAlignmentStart(), newRead ) ) ) { // we're already past where the mate started
(!pairedReadIsMovable(read) // we won't try to move such a read
|| noReadCanMoveBefore(read.getMateAlignmentStart(), newRead ) ) ) { // we're already past where the mate started
// remove reads from the map that we have emitted -- useful for case where the mate never showed up
forMateMatching.remove(read.getReadName());
@ -279,6 +277,13 @@ public class ConstrainedMateFixingManager {
|| Math.abs(read.getInferredInsertSize()) > maxInsertSizeForMovingReadPairs; // we won't try to move such a read
}
private boolean pairedReadIsMovable(SAMRecord read) {
return read.getReadPairedFlag() // we're a paired read
&& (!read.getReadUnmappedFlag() || !read.getMateUnmappedFlag()) // at least one read is mapped
&& !iSizeTooBigToMove(read); // insert size isn't too big
}
public void close() {
// write out all of the remaining reads
while ( ! waitingReads.isEmpty() ) { // there's something in the queue

102
java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java
View File

@ -15,7 +15,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
private static final String knownIndels = validationDataLocation + "indelRealignerTest.pilot1.ceu.vcf";
private static final String baseCommandPrefix = "-T IndelRealigner -noPG -R " + b36KGReference + " -I " + mainTestBam + " -targetIntervals " + mainTestIntervals + " -compress 0 -L 20:49,500-55,500 ";
private static final String baseCommand = baseCommandPrefix + "-o %s ";
private static final String base_md5 = "282070822dc5495eb20dad157d827133";
private static final String base_md5 = "28c045a821e541820a049595759fe962";
@Test
public void testDefaults() {
@ -40,6 +40,54 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
}
@Test(dependsOnMethods = { "testDefaults" })
public void testKnownsOnly() {
WalkerTestSpec spec1 = new WalkerTestSpec(
baseCommand + "-knownsOnly -B:indels,vcf " + knownIndels,
1,
Arrays.asList("ea91283e0af5432c1d63b052ed3dcfe4"));
executeTest("realigner known indels only from VCF", spec1);
WalkerTestSpec spec2 = new WalkerTestSpec(
baseCommand + "-knownsOnly -D " + GATKDataLocation + "dbsnp_129_b36.rod",
1,
Arrays.asList("3eed07873a474d8d8d4935399c99f793"));
executeTest("realigner known indels only from dbsnp", spec2);
}
@Test(dependsOnMethods = { "testKnownsOnly" })
public void testLods() {
HashMap<String, String> e = new HashMap<String, String>();
e.put( "-LOD 60", base_md5 );
e.put( "-LOD 1", "9a59cd8508f72f8935410b6fb2e6e7d3" );
for ( Map.Entry<String, String> entry : e.entrySet() ) {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
baseCommand + entry.getKey(),
1,
Arrays.asList(entry.getValue()));
executeTest(String.format("realigner [%s]", entry.getKey()), spec);
}
}
@Test(dependsOnMethods = { "testLods" })
public void testLongRun() {
WalkerTestSpec spec = new WalkerTestSpec(
"-T IndelRealigner -noPG -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.chrom1.SLX.SRP000032.2009_06.bam -L 1:10,000,000-11,000,000 -targetIntervals " + validationDataLocation + "indelRealignerTest.NA12878.chrom1.intervals -compress 0 -o %s",
1,
Arrays.asList("be859f9a98d738becee0526887cae42e"));
executeTest("realigner long run", spec);
}
@Test(dependsOnMethods = { "testLongRun" })
public void testNoTags() {
WalkerTestSpec spec = new WalkerTestSpec(
baseCommand + "--noOriginalAlignmentTags",
1,
Arrays.asList("4bbd9a0d998bc0483cd9bbbdac8cb9c2"));
executeTest("realigner no output tags", spec);
}
@Test(dependsOnMethods = { "testNoTags" })
public void testStats() {
WalkerTestSpec spec1 = new WalkerTestSpec(
@ -52,61 +100,13 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
baseCommandPrefix + "-LOD 60 -stats %s -o /dev/null",
1,
Arrays.asList("ffab7d9ca19daa8a21e0b8f0072d39e9"));
executeTest("realigner stats", spec2);
}
@Test(dependsOnMethods = { "testKnownsOnly" })
public void testLods() {
HashMap<String, String> e = new HashMap<String, String>();
e.put( "-LOD 60", base_md5 );
e.put( "-LOD 1", "c98d699d94f01bd0089f12646c764dfc" );
for ( Map.Entry<String, String> entry : e.entrySet() ) {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
baseCommand + entry.getKey(),
1,
Arrays.asList(entry.getValue()));
executeTest(String.format("realigner [%s]", entry.getKey()), spec);
}
}
@Test(dependsOnMethods = { "testDefaults" })
public void testKnownsOnly() {
WalkerTestSpec spec1 = new WalkerTestSpec(
baseCommand + "-knownsOnly -B:indels,vcf " + knownIndels,
1,
Arrays.asList("36644c80f5e7b7c8679c0485ef681cd8"));
executeTest("realigner known indels only from VCF", spec1);
WalkerTestSpec spec2 = new WalkerTestSpec(
baseCommand + "-knownsOnly -D " + GATKDataLocation + "dbsnp_129_b36.rod",
1,
Arrays.asList("eab2cce434435da7dabb0926101c5586"));
executeTest("realigner known indels only from dbsnp", spec2);
}
@Test(dependsOnMethods = { "testLongRun" })
public void testNoTags() {
WalkerTestSpec spec = new WalkerTestSpec(
baseCommand + "--noOriginalAlignmentTags",
1,
Arrays.asList("00ecb9df5afe3e9d61a75a2d019cb425"));
executeTest("realigner no output tags", spec);
}
@Test(dependsOnMethods = { "testLods" })
public void testLongRun() {
WalkerTestSpec spec = new WalkerTestSpec(
"-T IndelRealigner -noPG -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.chrom1.SLX.SRP000032.2009_06.bam -L 1:10,000,000-11,000,000 -targetIntervals " + validationDataLocation + "indelRealignerTest.NA12878.chrom1.intervals -compress 0 -o %s",
1,
Arrays.asList("be859f9a98d738becee0526887cae42e"));
executeTest("realigner long run", spec);
executeTest("realigner stats", spec2);
}
@Test(dependsOnMethods = { "testStats" })
public void testMaxReadsInMemory() {
HashMap<String, String> e = new HashMap<String, String>();
e.put( "--maxReadsInMemory 10000", "424271ca000442e8b338c67d95dadb82" );
e.put( "--maxReadsInMemory 10000", "f8e4279cba9fb3a2181d1ce28f7a62af" );
e.put( "--maxReadsInMemory 40000", base_md5 );
for ( Map.Entry<String, String> entry : e.entrySet() ) {