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Putative fix for BAQ array out of bounds 

-- Old code required qual to be <64, which isn't strictly necessary.  Now uses the Picard SAMUtils.MAX_PHRED_SCORE constant
-- Unittest to enforce this behavior
This commit is contained in:
Mark DePristo 2011-09-21 11:25:08 -04:00
parent ecc7f34774
commit 6592972f82
2 changed files with 12 additions and 1 deletions
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2
public/java/src/org/broadinstitute/sting/utils/baq/BAQ.java
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@ -152,7 +152,7 @@ public class BAQ {
}
}
private double calcEpsilon( byte ref, byte read, byte qualB ) {
protected double calcEpsilon( byte ref, byte read, byte qualB ) {
return EPSILONS[ref][read][qualB];
}

11
public/java/test/org/broadinstitute/sting/utils/baq/BAQUnitTest.java
View File

@ -172,6 +172,17 @@ public class BAQUnitTest extends BaseTest {
}
}
@Test(enabled = true)
public void testBAQQualRange() {
BAQ baq = new BAQ(1e-3, 0.1, 7, (byte)4, false); // matches current samtools parameters
final byte ref = (byte)'A';
final byte alt = (byte)'A';
for ( int i = 0; i <= SAMUtils.MAX_PHRED_SCORE; i++ )
Assert.assertTrue(baq.calcEpsilon( ref, alt, (byte)i) >= 0.0, "Failed to get baq epsilon range");
}
public void testBAQ(BAQTest test, boolean lookupWithFasta) {
BAQ baqHMM = new BAQ(1e-3, 0.1, 7, (byte)4, false); // matches current samtools parameters