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Reduce the number of test combinations in ReadBasedREferenceOrderedView

This commit is contained in:
Mark DePristo 2012-08-30 15:56:58 -04:00
parent 7a462399ce
commit 1212dfd2ef
1 changed files with 7 additions and 6 deletions
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13
public/java/test/org/broadinstitute/sting/gatk/datasources/providers/ReadBasedReferenceOrderedViewUnitTest.java
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@ -121,7 +121,7 @@ public class ReadBasedReferenceOrderedViewUnitTest extends BaseTest {
// test in the present of a large spanning element // test in the present of a large spanning element
{ {
List<Feature> oneLargeSpan = new ArrayList<Feature>(handPickedFeatures); List<Feature> oneLargeSpan = new ArrayList<Feature>(handPickedFeatures);
oneLargeSpan.add(new BasicFeature(contig, 1, 100)); oneLargeSpan.add(new BasicFeature(contig, 1, 30));
createTestsForFeatures(oneLargeSpan); createTestsForFeatures(oneLargeSpan);
} }
@ -135,7 +135,7 @@ public class ReadBasedReferenceOrderedViewUnitTest extends BaseTest {
// test in the presence of a partially spanning element at the end // test in the presence of a partially spanning element at the end
{ {
List<Feature> partialSpanEnd = new ArrayList<Feature>(handPickedFeatures); List<Feature> partialSpanEnd = new ArrayList<Feature>(handPickedFeatures);
partialSpanEnd.add(new BasicFeature(contig, 10, 100)); partialSpanEnd.add(new BasicFeature(contig, 10, 30));
createTestsForFeatures(partialSpanEnd); createTestsForFeatures(partialSpanEnd);
} }
@ -165,7 +165,7 @@ public class ReadBasedReferenceOrderedViewUnitTest extends BaseTest {
int featuresStart = 1; for ( final Feature f : features ) featuresStart = Math.min(featuresStart, f.getStart()); int featuresStart = 1; for ( final Feature f : features ) featuresStart = Math.min(featuresStart, f.getStart());
int featuresStop = 1; for ( final Feature f : features ) featuresStop = Math.max(featuresStop, f.getEnd()); int featuresStop = 1; for ( final Feature f : features ) featuresStop = Math.max(featuresStop, f.getEnd());
for ( final int size : Arrays.asList(1, 5, 10, 100, 1000) ) { for ( final int size : Arrays.asList(1, 5, 10, 100) ) {
final List<GenomeLoc> allIntervals = new ArrayList<GenomeLoc>(); final List<GenomeLoc> allIntervals = new ArrayList<GenomeLoc>();
// regularly spaced // regularly spaced
for ( int start = featuresStart; start < featuresStop; start++) { for ( int start = featuresStart; start < featuresStop; start++) {
@ -256,11 +256,12 @@ public class ReadBasedReferenceOrderedViewUnitTest extends BaseTest {
} }
// all 3 way pairwise tests // all 3 way pairwise tests
for ( List<ReadMetaDataTrackerRODStreamTest> singleTest : Utils.makePermutations(multiSiteTests, 3, false)) { //for ( List<ReadMetaDataTrackerRODStreamTest> singleTest : Utils.makePermutations(multiSiteTests, 3, false)) {
tests.add(new Object[]{singleTest, testStateless}); // tests.add(new Object[]{singleTest, testStateless});
} //}
} }
logger.warn("Creating " + tests.size() + " tests for ReadMetaDataTrackerTests");
return tests.toArray(new Object[][]{}); return tests.toArray(new Object[][]{});
} }