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Delete the test BAI file as well as the BAM

This commit is contained in:
Joel Thibault 2012-12-31 17:22:57 -05:00
parent 5afeb465aa
commit 7748b3816f
1 changed files with 3 additions and 0 deletions
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3
public/java/test/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegionsTest.java
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@ -104,6 +104,7 @@ public class TraverseActiveRegionsTest extends BaseTest {
private List<GenomeLoc> intervals; private List<GenomeLoc> intervals;
private static final String testBAM = "TraverseActiveRegionsTest.bam"; private static final String testBAM = "TraverseActiveRegionsTest.bam";
private static final String testBAI = "TraverseActiveRegionsTest.bai";
@BeforeClass @BeforeClass
private void init() throws FileNotFoundException { private void init() throws FileNotFoundException {
@ -149,6 +150,8 @@ public class TraverseActiveRegionsTest extends BaseTest {
private void createBAM(List<GATKSAMRecord> reads) { private void createBAM(List<GATKSAMRecord> reads) {
File outFile = new File(testBAM); File outFile = new File(testBAM);
outFile.deleteOnExit(); outFile.deleteOnExit();
File indexFile = new File(testBAI);
indexFile.deleteOnExit();
SAMFileWriter out = new SAMFileWriterFactory().makeBAMWriter(reads.get(0).getHeader(), true, outFile); SAMFileWriter out = new SAMFileWriterFactory().makeBAMWriter(reads.get(0).getHeader(), true, outFile);
for (GATKSAMRecord read : ReadUtils.sortReadsByCoordinate(reads)) { for (GATKSAMRecord read : ReadUtils.sortReadsByCoordinate(reads)) {