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Another fix for the Indel Realigner that arises because of secondary alignments. 

This time we don't accidentally drop reads (phew), but this bug does cause us not to
update the alignment start of the mate.  Fixed and added unit test to cover it.
This commit is contained in:
Eric Banks 2013-06-21 16:59:22 -04:00
parent dee51c4189
commit d976aae2b1
2 changed files with 32 additions and 4 deletions
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8
protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/ConstrainedMateFixingManager.java
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@ -130,7 +130,7 @@ public class ConstrainedMateFixingManager {
private static final boolean DEBUG = false;
/** How often do we check whether we want to emit reads? */
private final static int EMIT_FREQUENCY = 1000;
protected final static int EMIT_FREQUENCY = 1000;
/**
* How much could a single read move in position from its original position?
@ -324,7 +324,8 @@ public class ConstrainedMateFixingManager {
|| 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());
if ( !read.getNotPrimaryAlignmentFlag() )
forMateMatching.remove(read.getReadName());
if ( DEBUG )
logger.warn(String.format("EMIT! At %d: read %s at %d with isize %d, mate start %d, op = %s",
@ -346,7 +347,8 @@ public class ConstrainedMateFixingManager {
private void writeRead(SAMRecord read) {
try {
writer.addAlignment(read);
if ( writer != null )
writer.addAlignment(read);
} catch (IllegalArgumentException e) {
throw new UserException("If the maximum allowable reads in memory is too small, it may cause reads to be written out of order when trying to write the BAM; please see the --maxReadsInMemory argument for details. " + e.getMessage(), e);
}

28
protected/java/test/org/broadinstitute/sting/gatk/walkers/indels/ConstrainedMateFixingManagerUnitTest.java
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@ -66,9 +66,10 @@ public class ConstrainedMateFixingManagerUnitTest extends BaseTest {
@BeforeClass
public void beforeClass() {
header = ArtificialSAMUtils.createArtificialSamHeader(3, 1, 100);
header = ArtificialSAMUtils.createArtificialSamHeader(3, 1, 10000);
genomeLocParser = new GenomeLocParser(header.getSequenceDictionary());
}
@Test
public void testSecondaryAlignmentsDoNotInterfere() {
final List<GATKSAMRecord> properReads = ArtificialSAMUtils.createPair(header, "foo", 1, 10, 30, true, false);
@ -105,4 +106,29 @@ public class ConstrainedMateFixingManagerUnitTest extends BaseTest {
}
}
@Test
public void testSecondaryAlignmentsDoNotCauseAccidentalRemovalOfMate() {
final List<GATKSAMRecord> properReads = ArtificialSAMUtils.createPair(header, "foo", 1, 530, 1594, true, false);
final GATKSAMRecord read1 = properReads.get(0);
read1.setFlags(99); // first in proper pair, mate negative strand
final GATKSAMRecord read2Primary = properReads.get(1);
read2Primary.setFlags(147); // second in pair, mate unmapped, not primary alignment
read2Primary.setAlignmentStart(1596); // move the read
final GATKSAMRecord read2NonPrimary = new GATKSAMRecord(read2Primary);
read2NonPrimary.setReadName("foo");
read2NonPrimary.setFlags(393); // second in proper pair, on reverse strand
read2NonPrimary.setAlignmentStart(451);
read2NonPrimary.setMateAlignmentStart(451);
final ConstrainedMateFixingManager manager = new ConstrainedMateFixingManager(null, genomeLocParser, 10000, 200, 10000);
manager.addRead(read2NonPrimary, false, false);
manager.addRead(read1, false, false);
for ( int i = 0; i < ConstrainedMateFixingManager.EMIT_FREQUENCY; i++ )
manager.addRead(ArtificialSAMUtils.createArtificialRead(header, "foo" + i, 0, 1500, 10), false, false);
Assert.assertTrue(manager.forMateMatching.containsKey("foo"));
}
}