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Close SamReader

This commit is contained in:
Ron Levine 2017-06-08 10:37:32 -04:00
parent e8b42c4dfd
commit 18c9fe41c7
1 changed files with 4 additions and 2 deletions
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6
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
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@ -113,11 +113,12 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
/** /**
* Check that the bamout program records (@PG) contain all of the program records forwarded from the input BAMs * Check that the bamout program records (@PG) contain all of the program records forwarded from the input BAMs
*/ */
private void validateForwardedProgramRecords(final List<File> bamInFiles, final String bamOutMd5) throws FileNotFoundException { private void validateForwardedProgramRecords(final List<File> bamInFiles, final String bamOutMd5) throws IOException {
final List<SAMProgramRecord> bamInProgramRecords = new ArrayList<>(); final List<SAMProgramRecord> bamInProgramRecords = new ArrayList<>();
for (final File file : bamInFiles) { for (final File file : bamInFiles) {
final SamReader bamInReader = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT).open(file); final SamReader bamInReader = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT).open(file);
bamInProgramRecords.addAll(bamInReader.getFileHeader().getProgramRecords()); bamInProgramRecords.addAll(bamInReader.getFileHeader().getProgramRecords());
bamInReader.close();
} }
final String bamOutFilePath = new MD5DB().getMD5FilePath(bamOutMd5, null); final String bamOutFilePath = new MD5DB().getMD5FilePath(bamOutMd5, null);
if (bamOutFilePath == null) { if (bamOutFilePath == null) {
@ -126,6 +127,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
final SamReader bamOutReader = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT). final SamReader bamOutReader = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT).
open(new File(bamOutFilePath)); open(new File(bamOutFilePath));
final List<SAMProgramRecord> bamOutProgramRecords = bamOutReader.getFileHeader().getProgramRecords(); final List<SAMProgramRecord> bamOutProgramRecords = bamOutReader.getFileHeader().getProgramRecords();
bamOutReader.close();
Assert.assertTrue(bamOutProgramRecords.containsAll(bamInProgramRecords)); Assert.assertTrue(bamOutProgramRecords.containsAll(bamInProgramRecords));
} }
@ -326,7 +328,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
private static final String LEFT_ALIGNMENT_BAMOUT_TEST_OUTPUT = privateTestDir + "/bamout-indel-left-align-bugfix-expected-output.bam"; private static final String LEFT_ALIGNMENT_BAMOUT_TEST_OUTPUT = privateTestDir + "/bamout-indel-left-align-bugfix-expected-output.bam";
@Test @Test
public void testLeftAlignmentBamOutBugFix() throws FileNotFoundException { public void testLeftAlignmentBamOutBugFix() throws IOException {
final String outputVCF = createTempFile("temp", ".vcf").getAbsolutePath(); final String outputVCF = createTempFile("temp", ".vcf").getAbsolutePath();
final String md5BAMOut = "27e729df3b166c81792a62a5b57ef7b3"; final String md5BAMOut = "27e729df3b166c81792a62a5b57ef7b3";
final String base = String.format("-T HaplotypeCaller -R %s -I %s", REF, LEFT_ALIGNMENT_BAMOUT_TEST_INPUT) final String base = String.format("-T HaplotypeCaller -R %s -I %s", REF, LEFT_ALIGNMENT_BAMOUT_TEST_INPUT)