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Merge pull request #299 from broadinstitute/eb_mate_fixer_confused_by_nonprimary_alignment 

Another fix for the Indel Realigner that arises because of secondary alignments.
This commit is contained in:
Yossi Farjoun 2013-06-24 06:58:27 -07:00
parent dee51c4189 d976aae2b1
commit d8ca4d3e6d
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"));
}
}