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eagerDecode is now false. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3733 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2010-07-07 22:51:48 +00:00
parent 4bc3ad2194
commit 9fc05ac2ae
2 changed files with 4 additions and 4 deletions
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2
java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMDataSource.java
View File

@ -533,7 +533,7 @@ public class SAMDataSource implements SimpleDataSource {
*/
public SAMReaders(Reads sourceInfo) {
for(File readsFile: sourceInfo.getReadsFiles()) {
SAMFileReader reader = new SAMFileReader(readsFile,true);
SAMFileReader reader = new SAMFileReader(readsFile);
reader.enableFileSource(true);
reader.enableIndexCaching(true);
reader.setValidationStringency(sourceInfo.getValidationStringency());

6
java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java
View File

@ -9,7 +9,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
@Test
public void testRealignerLod5() {
String[] md5s = {"726c629a382e4da0dffd4de2e439aa91", "18fca887d1eb7dc300e717ae03b9da62"};
String[] md5s = {"ce789182974609da27f3eadbbbcd98c4", "18fca887d1eb7dc300e717ae03b9da62"};
WalkerTestSpec spec = new WalkerTestSpec(
"-T IndelRealigner -noPG -LOD 5 -maxConsensuses 100 -greedy 100 -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "NA12878.chrom1.SLX.SRP000032.2009_06.bam -L 1:10023000-10030000 -compress 1 -targetIntervals " + validationDataLocation + "cleaner.test.intervals -O %s -stats %s --sortInCoordinateOrderEvenThoughItIsHighlyUnsafe",
2,
@ -19,7 +19,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
@Test
public void testRealignerLod50() {
String[] md5s = {"726c629a382e4da0dffd4de2e439aa91", "9537e4f195ce5840136f60fb61201369"};
String[] md5s = {"ce789182974609da27f3eadbbbcd98c4", "9537e4f195ce5840136f60fb61201369"};
WalkerTestSpec spec = new WalkerTestSpec(
"-T IndelRealigner -noPG -LOD 50 -maxConsensuses 100 -greedy 100 -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "NA12878.chrom1.SLX.SRP000032.2009_06.bam -L 1:10023000-10030000 -compress 1 -targetIntervals " + validationDataLocation + "cleaner.test.intervals -O %s -stats %s --sortInCoordinateOrderEvenThoughItIsHighlyUnsafe",
2,
@ -29,7 +29,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
@Test
public void testRealignerKnownsOnly() {
String[] md5s = {"d609430ffbc0fd8b68f383b9eec17e8b", "1091436c40d5ba557d85662999cc0c1d"};
String[] md5s = {"f50b9bddd78ed6fb820d2cbdfbff8300", "1091436c40d5ba557d85662999cc0c1d"};
WalkerTestSpec spec = new WalkerTestSpec(
"-T IndelRealigner -noPG -LOD 1.0 -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "NA12878.chrom1.SLX.SRP000032.2009_06.bam -L 1:10023000-10076000 -compress 1 -targetIntervals " + validationDataLocation + "NA12878.indels.intervals -B knownIndels,VCF," + validationDataLocation + "NA12878.indels.vcf -O %s -stats %s --sortInCoordinateOrderEvenThoughItIsHighlyUnsafe -knownsOnly",
2,