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A fix for an integration test that was broken by on-the-fly indexing. Also, better reporting of Tribble exceptions in GATK integration tests. Trying to get the tests back up and running... 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4483 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
aaron 2010-10-12 18:39:56 +00:00
parent 69652e08c6
commit ff0df1a2da
3 changed files with 5 additions and 11 deletions
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4
java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/RMDTrackBuilder.java
View File

@ -166,7 +166,7 @@ public class RMDTrackBuilder extends PluginManager<FeatureCodec> {
try {
return new Pair<BasicFeatureSource, SAMSequenceDictionary>(BasicFeatureSource.getFeatureSource(inputFile.getAbsolutePath(), createCodec(targetClass, name)),null);
} catch (TribbleException e) {
throw new UserException(e.getTribbleExceptionMessage(), e);
throw new UserException(e.getMessage(), e);
}
}
@ -208,7 +208,7 @@ public class RMDTrackBuilder extends PluginManager<FeatureCodec> {
createCodec(targetClass, name)),
dictFromIndex);
} catch (TribbleException e) {
throw new UserException(e.getTribbleExceptionMessage());
throw new UserException(e.getMessage());
} catch (IOException e) {
throw new UserException("Unable to create the index file for " + inputFile, e);
}

8
java/src/org/broadinstitute/sting/oneoffprojects/walkers/TestVariantContextWalker.java
View File

@ -59,16 +59,10 @@ public class TestVariantContextWalker extends RodWalker<Integer, Integer> {
boolean printContexts = false;
@Argument(fullName="outputVCF", doc="If provided, we'll convert the first input context into a VCF", required=false)
String outputVCF = null;
VCFWriter writer = null;
private VCFWriter writer = null;
private boolean wroteHeader = false;
public void initialize() {
if ( outputVCF != null )
writer = new StandardVCFWriter(new File(outputVCF));
}
public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
if ( ref == null )
return 0;

4
java/test/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextIntegrationTest.java
View File

@ -46,7 +46,7 @@ public class VariantContextIntegrationTest extends WalkerTest {
public void testToVCF() {
// this really just tests that we are seeing the same number of objects over all of chr1
WalkerTestSpec spec = new WalkerTestSpec( cmdRoot + " -B:vcf,VCF " + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.500.vcf -L 1:1-1000000 -o %s --outputVCF %s",
WalkerTestSpec spec = new WalkerTestSpec( cmdRoot + " -NO_HEADER -B:vcf,VCF " + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.500.vcf -L 1:1-1000000 -o %s --outputVCF %s",
2, // just one output file
Arrays.asList("e3c35d0c4b5d4935c84a270f9df0951f", "f4db5f7346792b1155693722bc190f63"));
executeTest("testToVCF", spec);
@ -57,7 +57,7 @@ public class VariantContextIntegrationTest extends WalkerTest {
// this really just tests that we are seeing the same number of objects over all of chr1
WalkerTestSpec spec = new WalkerTestSpec( root + " -L 1" + " -o %s",
1, // just one output file
Arrays.asList("3fcdd982df080e6abc0afaba6abdf386"));
Arrays.asList("d2a3f2fe329a0a64145cfd19fde45b99"));
executeTest("testLargeScaleConversion", spec);
}
}