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Test to ensure that ReadBasedReferenceOrderedView produces stateless objects 

-- Stateless objects are required for nano-scheduling.  This means you can take the RefMetaDataTracker provided by ReadBasedReferenceOrderedView, store it way, get another from the same view, and the original one behaves the same.
This commit is contained in:
Mark DePristo 2012-08-30 10:10:00 -04:00
parent ce3d1f89ea
commit 21dd70ed36
1 changed files with 44 additions and 28 deletions
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72
public/java/test/org/broadinstitute/sting/gatk/datasources/providers/ReadBasedReferenceOrderedViewUnitTest.java
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@ -249,21 +249,23 @@ public class ReadBasedReferenceOrderedViewUnitTest extends BaseTest {
multiSiteTests.add((ReadMetaDataTrackerRODStreamTest)singleTest[0]);
}
// all pairwise tests
for ( List<ReadMetaDataTrackerRODStreamTest> singleTest : Utils.makePermutations(multiSiteTests, 2, false)) {
tests.add(new Object[]{singleTest});
}
for ( final boolean testStateless : Arrays.asList(true, false) ) {
// all pairwise tests
for ( List<ReadMetaDataTrackerRODStreamTest> singleTest : Utils.makePermutations(multiSiteTests, 2, false)) {
tests.add(new Object[]{singleTest, testStateless});
}
// all 3 way pairwise tests
for ( List<ReadMetaDataTrackerRODStreamTest> singleTest : Utils.makePermutations(multiSiteTests, 3, false)) {
tests.add(new Object[]{singleTest});
// all 3 way pairwise tests
for ( List<ReadMetaDataTrackerRODStreamTest> singleTest : Utils.makePermutations(multiSiteTests, 3, false)) {
tests.add(new Object[]{singleTest, testStateless});
}
}
return tests.toArray(new Object[][]{});
}
@Test(enabled = true, dataProvider = "ReadMetaDataTrackerTests", dependsOnMethods = "runReadMetaDataTrackerRODStreamTest_multipleQueries")
public void runReadMetaDataTrackerTest(final List<ReadMetaDataTrackerRODStreamTest> RODs) {
public void runReadMetaDataTrackerTest(final List<ReadMetaDataTrackerRODStreamTest> RODs, final boolean testStateless) {
final List<String> names = new ArrayList<String>();
final List<PeekableIterator<RODRecordList>> iterators = new ArrayList<PeekableIterator<RODRecordList>>();
final List<GenomeLoc> intervals = new ArrayList<GenomeLoc>();
@ -282,31 +284,45 @@ public class ReadBasedReferenceOrderedViewUnitTest extends BaseTest {
final GenomeLoc span = span(intervals);
final ReadBasedReferenceOrderedView view = new ReadBasedReferenceOrderedView(genomeLocParser, span, names, iterators);
for ( final GenomeLoc interval : intervals ) {
final RefMetaDataTracker tracker = view.getReferenceOrderedDataForInterval(interval);
if ( testStateless ) {
// test each tracker is well formed, as each is created
for ( final GenomeLoc interval : intervals ) {
final RefMetaDataTracker tracker = view.getReferenceOrderedDataForInterval(interval);
testMetaDataTrackerBindings(tracker, interval, RODs, rodBindings);
}
} else {
// tests all trackers are correct after reading them into an array
// this checks that the trackers are be safely stored away and analyzed later (critical for nano-scheduling)
final List<RefMetaDataTracker> trackers = new ArrayList<RefMetaDataTracker>();
for ( final GenomeLoc interval : intervals ) {
final RefMetaDataTracker tracker = view.getReferenceOrderedDataForInterval(interval);
trackers.add(tracker);
}
for ( int i = 0; i < RODs.size(); i++ ) {
final ReadMetaDataTrackerRODStreamTest test = RODs.get(i);
final List<Feature> queryFeaturesList = tracker.getValues(rodBindings.get(i));
final Set<Feature> queryFeatures = new HashSet<Feature>(queryFeaturesList);
final Set<Feature> overlaps = test.getExpectedOverlaps(interval);
Assert.assertEquals(queryFeatures.size(), overlaps.size(), "IntervalOverlappingRODsFromStream didn't return the expected set of overlapping features." +
" Expected size = " + overlaps.size() + " but saw " + queryFeatures.size());
BaseTest.assertEqualsSet(queryFeatures, overlaps, "IntervalOverlappingRODsFromStream didn't return the expected set of overlapping features." +
" Expected = " + Utils.join(",", overlaps) + " but saw " + Utils.join(",", queryFeatures));
for ( int i = 0; i < trackers.size(); i++) {
testMetaDataTrackerBindings(trackers.get(i), intervals.get(i), RODs, rodBindings);
}
}
}
/**
* Created with IntelliJ IDEA.
* User: depristo
* Date: 8/29/12
* Time: 1:19 PM
* To change this template use File | Settings | File Templates.
*/
private void testMetaDataTrackerBindings(final RefMetaDataTracker tracker,
final GenomeLoc interval,
final List<ReadMetaDataTrackerRODStreamTest> RODs,
final List<RodBinding<Feature>> rodBindings) {
for ( int i = 0; i < RODs.size(); i++ ) {
final ReadMetaDataTrackerRODStreamTest test = RODs.get(i);
final List<Feature> queryFeaturesList = tracker.getValues(rodBindings.get(i));
final Set<Feature> queryFeatures = new HashSet<Feature>(queryFeaturesList);
final Set<Feature> overlaps = test.getExpectedOverlaps(interval);
Assert.assertEquals(queryFeatures.size(), overlaps.size(), "IntervalOverlappingRODsFromStream didn't return the expected set of overlapping features." +
" Expected size = " + overlaps.size() + " but saw " + queryFeatures.size());
BaseTest.assertEqualsSet(queryFeatures, overlaps, "IntervalOverlappingRODsFromStream didn't return the expected set of overlapping features." +
" Expected = " + Utils.join(",", overlaps) + " but saw " + Utils.join(",", queryFeatures));
}
}
static class TribbleIteratorFromCollection implements Iterator<RODRecordList> {
// current location
private final String name;