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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.
This commit is contained in:
Mark DePristo 2011-10-13 18:01:51 -04:00
parent 7cab6f6bb0
commit 2ebdff074c
2 changed files with 3 additions and 3 deletions
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2
public/java/test/org/broadinstitute/sting/MD5DB.java
View File

@ -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);

4
public/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java
View File

@ -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<String, String> e = new HashMap<String, String>();
e.put( validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", "7d5edb75b176e4151de225f699719ee4" );
e.put( validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", "2ad4c17ac3ed380071137e4e53a398a5" );
for ( Map.Entry<String, String> entry : e.entrySet() ) {
String bam = entry.getKey();