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When using the BWA bindings, you have to explicitly call close() to get the 

bindings to release memory.
It may or may not be possible to implicitly close triggered by the GC; I'll add a JIRA.
This commit is contained in:
Matt Hanna 2011-07-21 12:13:29 -04:00
parent 15610ce0c3
commit 7054c5342f
2 changed files with 5 additions and 2 deletions
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3
public/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java
View File

@ -228,6 +228,9 @@ public class ValidationAmplicons extends RodWalker<Integer,Integer> {
} }
public void onTraversalDone(Integer fin ) { public void onTraversalDone(Integer fin ) {
if(aligner != null)
aligner.close();
validateSequence(); validateSequence();
if ( doNotUseBWA ) { if ( doNotUseBWA ) {
lowerRepeats(); lowerRepeats();

4
public/java/test/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmpliconsIntegrationTest.java
View File

@ -14,7 +14,7 @@ import java.util.Arrays;
*/ */
public class ValidationAmpliconsIntegrationTest extends WalkerTest { public class ValidationAmpliconsIntegrationTest extends WalkerTest {
@Test(enabled=false) @Test(enabled=true)
public void testWikiExample() { public void testWikiExample() {
String siteVCF = validationDataLocation + "sites_to_validate.vcf"; String siteVCF = validationDataLocation + "sites_to_validate.vcf";
String maskVCF = validationDataLocation + "amplicon_mask_sites.vcf"; String maskVCF = validationDataLocation + "amplicon_mask_sites.vcf";
@ -40,7 +40,7 @@ public class ValidationAmpliconsIntegrationTest extends WalkerTest {
executeTest("Test probes", spec); executeTest("Test probes", spec);
} }
@Test(enabled=false) @Test(enabled=true)
public void testWikiExampleMonoFilter() { public void testWikiExampleMonoFilter() {
String siteVCF = validationDataLocation + "sites_to_validate.vcf"; String siteVCF = validationDataLocation + "sites_to_validate.vcf";
String maskVCF = validationDataLocation + "amplicon_mask_sites.vcf"; String maskVCF = validationDataLocation + "amplicon_mask_sites.vcf";