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'-L unmapped': adding integration tests for explicitly including (-L unmapped) 

unmapped reads and explicitly excluding (-XL unmapped) unmapped reads, augmenting
the suite of unit tests already put in place.

'-L unmapped' seems safe to use; go for it, but please validate results against
samtools flagstat when the process finishes.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4849 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2010-12-15 23:11:46 +00:00
parent aea481ae01
commit acfe83920b
1 changed files with 32 additions and 0 deletions
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32
java/test/org/broadinstitute/sting/utils/interval/IntervalIntegrationTest.java
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@ -60,4 +60,36 @@ public class IntervalIntegrationTest extends WalkerTest {
Arrays.asList(md5));
executeTest("testAllIntervalsExplicit",spec);
}
@Test
public void testUnmappedReadInclusion() {
String md5 = "fcd11cfa8474472c617d400623a30fcd";
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T PrintReads" +
" -I " + validationDataLocation + "MV1994.bam" +
" -R " + validationDataLocation + "Escherichia_coli_K12_MG1655.fasta" +
" -L unmapped" +
" -o %s" +
" -U",
1, // just one output file
Arrays.asList(md5));
executeTest("testUnmappedReadInclusion",spec);
}
@Test
public void testUnmappedReadExclusion() {
String md5 = "3153593c9f9ff80a8551fff5655e65ec";
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T PrintReads" +
" -I " + validationDataLocation + "MV1994.bam" +
" -R " + validationDataLocation + "Escherichia_coli_K12_MG1655.fasta" +
" -XL unmapped" +
" -o %s" +
" -U",
1, // just one output file
Arrays.asList(md5));
executeTest("testUnmappedReadExclusion",spec);
}
}