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one broken build short of the hat trick. Fixing the unix test which expects the sequence dictionary of the Tribble track to equal the reference; we actually return the sequence dictionary of the track iself, with each contig set to the length of the sequence dictionary contig entry. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4322 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
aaron 2010-09-21 18:47:20 +00:00
parent b968af5db5
commit 3938d53738
1 changed files with 1 additions and 4 deletions
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5
java/test/org/broadinstitute/sting/gatk/refdata/tracks/builders/RMDTrackBuilderUnitTest.java
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@ -151,11 +151,8 @@ public class RMDTrackBuilderUnitTest extends BaseTest {
try { try {
Index idx = builder.loadIndex(vcfFile, new VCFCodec()); Index idx = builder.loadIndex(vcfFile, new VCFCodec());
RMDTrackBuilder.setIndexSequenceDictionary(idx,seq.getSequenceDictionary(),vcfFile,false); RMDTrackBuilder.setIndexSequenceDictionary(idx,seq.getSequenceDictionary(),vcfFile,false);
// catch any exception; this call should pass correctly
SAMSequenceDictionary dict = RMDTrackBuilder.getSequenceDictionaryFromProperties(idx); SAMSequenceDictionary dict = RMDTrackBuilder.getSequenceDictionaryFromProperties(idx);
for (SAMSequenceRecord ent : seq.getSequenceDictionary().getSequences()) {
Assert.assertNotNull("Sequence missing from set dictionary: " + ent.getSequenceName(),dict.getSequence(ent.getSequenceName()));
Assert.assertEquals(ent.getSequenceLength(),dict.getSequence(ent.getSequenceName()).getSequenceLength());
}
} catch (IOException e) { } catch (IOException e) {
e.printStackTrace(); e.printStackTrace();
Assert.fail("IO exception unexpected" + e.getMessage()); Assert.fail("IO exception unexpected" + e.getMessage());