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Added integration test to catch the read off contig in ReduceReads. 

So upstream changes won't break it again.
This commit is contained in:
Mauricio Carneiro 2012-12-12 13:41:01 -05:00
parent a52e3c7e15
commit 33290bfe0c
1 changed files with 11 additions and 0 deletions
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11
protected/java/test/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReadsIntegrationTest.java
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@ -17,6 +17,7 @@ public class ReduceReadsIntegrationTest extends WalkerTest {
final String COREDUCTION_BAM_A = validationDataLocation + "coreduction.test.A.bam"; final String COREDUCTION_BAM_A = validationDataLocation + "coreduction.test.A.bam";
final String COREDUCTION_BAM_B = validationDataLocation + "coreduction.test.B.bam"; final String COREDUCTION_BAM_B = validationDataLocation + "coreduction.test.B.bam";
final String COREDUCTION_L = " -L 1:1,853,860-1,854,354 -L 1:1,884,131-1,892,057"; final String COREDUCTION_L = " -L 1:1,853,860-1,854,354 -L 1:1,884,131-1,892,057";
final String OFFCONTIG_BAM = privateTestDir + "readOffb37contigMT.bam";
private void RRTest(String testName, String args, String md5) { private void RRTest(String testName, String args, String md5) {
String base = String.format("-T ReduceReads -npt -R %s -I %s ", REF, BAM) + " -o %s "; String base = String.format("-T ReduceReads -npt -R %s -I %s ", REF, BAM) + " -o %s ";
@ -86,5 +87,15 @@ public class ReduceReadsIntegrationTest extends WalkerTest {
executeTest("testCoReduction", new WalkerTestSpec(base, Arrays.asList("5c30fde961a1357bf72c15144c01981b"))); executeTest("testCoReduction", new WalkerTestSpec(base, Arrays.asList("5c30fde961a1357bf72c15144c01981b")));
} }
/**
* Bug happens when reads are soft-clipped off the contig (usually in the MT). This test guarantees no changes to the upstream code will
* break the current hard-clipping routine that protects reduce reads from such reads.
*/
@Test(enabled = true)
public void testReadOffContig() {
String base = String.format("-T ReduceReads -npt -R %s -I %s ", REF, OFFCONTIG_BAM) + " -o %s ";
executeTest("testReadOffContig", new WalkerTestSpec(base, Arrays.asList("53e16367d333da0b7d40a7683a35c95f")));
}
} }