From 2ebdff074c6240438daf79ba21b3b2e8c5467afa Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Thu, 13 Oct 2011 18:01:51 -0400 Subject: [PATCH] Update MD5s for SOLiD recalibration -- MD5 db had spelling error; fixed -- Bug in AlignmentUtils resulted in some bases not being color space corrected. The integration test caught the change, and it's clear that the new version is correct, as the prev. version was not considering the last the N qualities for reads with a ND operation. --- public/java/test/org/broadinstitute/sting/MD5DB.java | 2 +- .../recalibration/RecalibrationWalkersIntegrationTest.java | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/public/java/test/org/broadinstitute/sting/MD5DB.java b/public/java/test/org/broadinstitute/sting/MD5DB.java index 0194e114a..2fd8f8b6d 100644 --- a/public/java/test/org/broadinstitute/sting/MD5DB.java +++ b/public/java/test/org/broadinstitute/sting/MD5DB.java @@ -224,7 +224,7 @@ public class MD5DB { if ( ! expectedMD5.equals(filemd5sum) ) { // we are going to fail for real in assertEquals (so we are counted by the testing framework). // prepare ourselves for the comparison - System.out.printf("##### Test %s is going fail #####%n", name); + System.out.printf("##### Test %s is going to fail #####%n", name); String pathToExpectedMD5File = getMD5FilePath(expectedMD5, "[No DB file found]"); String pathToFileMD5File = getMD5FilePath(filemd5sum, "[No DB file found]"); System.out.printf("##### Path to expected file (MD5=%s): %s%n", expectedMD5, pathToExpectedMD5File); diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java index b2833b935..cbcd5835f 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java @@ -89,7 +89,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest { @DataProvider(name = "trtestdata") public Object[][] createTRTestData() { new TRTest( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "2864f231fab7030377f3c8826796e48f" ); - new TRTest( validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", "c164dd635721ba6df3f06dac1877c32d"); + new TRTest( validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", "d04cf1f6df486e45226ebfbf93a188a5"); new TRTest( validationDataLocation + "NA12873.454.SRP000031.2009_06.chr1.10_20mb.bam", "74314e5562c1a65547bb0edaacffe602" ); new TRTest( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam", "2a37c6001826bfabf87063b1dfcf594f" ); return TRTest.getTests(TRTest.class); @@ -200,7 +200,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest { @Test public void testTableRecalibratorSolidIndelsRemoveRefBias() { HashMap e = new HashMap(); - e.put( validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", "7d5edb75b176e4151de225f699719ee4" ); + e.put( validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", "2ad4c17ac3ed380071137e4e53a398a5" ); for ( Map.Entry entry : e.entrySet() ) { String bam = entry.getKey();