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Merged bug fix from Stable into Unstable

This commit is contained in:
Mark DePristo 2011-10-13 18:02:06 -04:00
parent 5a881360df 2ebdff074c
commit 404ef741f1
2 changed files with 3 additions and 3 deletions
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2
public/java/test/org/broadinstitute/sting/MD5DB.java
View File

@ -239,7 +239,7 @@ 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();