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Merge branch 'master' of github.com:broadinstitute/gsa-unstable

This commit is contained in:
Ryan Poplin 2013-01-31 11:51:08 -05:00
parent ac033ce41a 9c0207f8ef
commit 496727ac5e
2 changed files with 23 additions and 1 deletions
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7
public/java/src/org/broadinstitute/sting/utils/baq/BAQ.java
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@ -673,7 +673,9 @@ public class BAQ {
} else if ( excludeReadFromBAQ(read) ) { } else if ( excludeReadFromBAQ(read) ) {
; // just fall through ; // just fall through
} else { } else {
if ( calculationType == CalculationMode.RECALCULATE || ! hasBAQTag(read) ) { final boolean readHasBAQTag = hasBAQTag(read);
if ( calculationType == CalculationMode.RECALCULATE || ! readHasBAQTag ) {
if ( DEBUG ) System.out.printf(" Calculating BAQ on the fly%n"); if ( DEBUG ) System.out.printf(" Calculating BAQ on the fly%n");
BAQCalculationResult hmmResult = calcBAQFromHMM(read, refReader); BAQCalculationResult hmmResult = calcBAQFromHMM(read, refReader);
if ( hmmResult != null ) { if ( hmmResult != null ) {
@ -683,6 +685,9 @@ public class BAQ {
case DONT_MODIFY: BAQQuals = hmmResult.bq; break; case DONT_MODIFY: BAQQuals = hmmResult.bq; break;
default: throw new ReviewedStingException("BUG: unexpected qmode " + qmode); default: throw new ReviewedStingException("BUG: unexpected qmode " + qmode);
} }
} else if ( readHasBAQTag ) {
// remove the BAQ tag if it's there because we cannot trust it
read.setAttribute(BAQ_TAG, null);
} }
} else if ( qmode == QualityMode.OVERWRITE_QUALS ) { // only makes sense if we are overwriting quals } else if ( qmode == QualityMode.OVERWRITE_QUALS ) { // only makes sense if we are overwriting quals
if ( DEBUG ) System.out.printf(" Taking BAQ from tag%n"); if ( DEBUG ) System.out.printf(" Taking BAQ from tag%n");

17
public/java/test/org/broadinstitute/sting/utils/baq/BAQUnitTest.java
View File

@ -203,6 +203,23 @@ public class BAQUnitTest extends BaseTest {
Assert.assertTrue(baq.calcEpsilon( ref, alt, (byte)i) >= 0.0, "Failed to get baq epsilon range"); Assert.assertTrue(baq.calcEpsilon( ref, alt, (byte)i) >= 0.0, "Failed to get baq epsilon range");
} }
@Test(enabled = true)
public void testBAQOverwritesExistingTagWithNull() {
// create a read with a single base off the end of the contig, which cannot be BAQed
final SAMRecord read = ArtificialSAMUtils.createArtificialRead(header, "foo", 0, fasta.getSequenceDictionary().getSequence("chr1").getSequenceLength() + 1, 1);
read.setReadBases(new byte[] {(byte) 'A'});
read.setBaseQualities(new byte[] {(byte) 20});
read.setCigarString("1M");
read.setAttribute("BQ", "A");
// try to BAQ and tell it to RECALCULATE AND ADD_TAG
BAQ baq = new BAQ(1e-3, 0.1, 7, (byte)4, false);
baq.baqRead(read, fasta, BAQ.CalculationMode.RECALCULATE, BAQ.QualityMode.ADD_TAG);
// did we remove the existing tag?
Assert.assertTrue(read.getAttribute("BQ") == null);
}
public void testBAQ(BAQTest test, boolean lookupWithFasta) { public void testBAQ(BAQTest test, boolean lookupWithFasta) {
BAQ baqHMM = new BAQ(1e-3, 0.1, 7, (byte)4, false); // matches current samtools parameters BAQ baqHMM = new BAQ(1e-3, 0.1, 7, (byte)4, false); // matches current samtools parameters