From 6592972f82bab1bc0903460241b7b1656902e4cd Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Wed, 21 Sep 2011 11:25:08 -0400 Subject: [PATCH] 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 --- .../src/org/broadinstitute/sting/utils/baq/BAQ.java | 2 +- .../broadinstitute/sting/utils/baq/BAQUnitTest.java | 11 +++++++++++ 2 files changed, 12 insertions(+), 1 deletion(-) diff --git a/public/java/src/org/broadinstitute/sting/utils/baq/BAQ.java b/public/java/src/org/broadinstitute/sting/utils/baq/BAQ.java index 1723557c4..4f096f86e 100644 --- a/public/java/src/org/broadinstitute/sting/utils/baq/BAQ.java +++ b/public/java/src/org/broadinstitute/sting/utils/baq/BAQ.java @@ -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]; } diff --git a/public/java/test/org/broadinstitute/sting/utils/baq/BAQUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/baq/BAQUnitTest.java index 2e4dac6da..67943ccb4 100644 --- a/public/java/test/org/broadinstitute/sting/utils/baq/BAQUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/utils/baq/BAQUnitTest.java @@ -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