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Moved unit tests into master IntervalUtilsUnitTest

This commit is contained in:
Mark DePristo 2011-11-02 10:52:00 -04:00
parent c2b97030a4
commit 392e0aeace
1 changed files with 93 additions and 14 deletions
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107
public/java/test/org/broadinstitute/sting/utils/interval/IntervalUtilsUnitTest.java
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@ -134,16 +134,17 @@ public class IntervalUtilsUnitTest extends BaseTest {
// -------------------------------------------------------------------------------------
//
// tests to ensure the quality of the interval cuts of the interval cutting functions
// splitLocusIntervals tests
//
// -------------------------------------------------------------------------------------
private class IntervalRepartitionTest extends TestDataProvider {
/** large scale tests for many intervals */
private class SplitLocusIntervalsTest extends TestDataProvider {
final List<GenomeLoc> originalIntervals;
final public int parts;
private IntervalRepartitionTest(final String name, List<GenomeLoc> originalIntervals, final int parts) {
super(IntervalRepartitionTest.class, name);
private SplitLocusIntervalsTest(final String name, List<GenomeLoc> originalIntervals, final int parts) {
super(SplitLocusIntervalsTest.class, name);
this.parts = parts;
this.originalIntervals = originalIntervals;
}
@ -155,27 +156,105 @@ public class IntervalUtilsUnitTest extends BaseTest {
@DataProvider(name = "IntervalRepartitionTest")
public Object[][] createIntervalRepartitionTest() {
for ( int parts : Arrays.asList(1, 10, 100, 1000, 10000) ) {
new IntervalRepartitionTest("hg19RefLocs", hg19ReferenceLocs, parts);
new IntervalRepartitionTest("hg19ExomeLocs", hg19exomeIntervals, parts);
for ( int parts : Arrays.asList(1, 2, 3, 10, 13, 100, 151, 1000, 10000) ) {
//for ( int parts : Arrays.asList(10) ) {
new SplitLocusIntervalsTest("hg19RefLocs", hg19ReferenceLocs, parts);
new SplitLocusIntervalsTest("hg19ExomeLocs", hg19exomeIntervals, parts);
}
return IntervalSlicingTest.getTests(IntervalRepartitionTest.class);
return SplitLocusIntervalsTest.getTests(SplitLocusIntervalsTest.class);
}
@Test(enabled = true, dataProvider = "IntervalRepartitionTest")
public void testIntervalRepartition(IntervalRepartitionTest test) {
public void testIntervalRepartition(SplitLocusIntervalsTest test) {
List<List<GenomeLoc>> splitByLocus = IntervalUtils.splitLocusIntervals(test.originalIntervals, test.parts);
Assert.assertEquals(test.parts, splitByLocus.size(), "SplitLocusIntervals failed to generate correct number of intervals");
Assert.assertEquals(splitByLocus.size(), test.parts, "SplitLocusIntervals failed to generate correct number of intervals");
List<GenomeLoc> flat = IntervalUtils.flattenSplitIntervals(splitByLocus);
// test overall size
final long originalSize = IntervalUtils.intervalSize(test.originalIntervals);
final long flatSize = IntervalUtils.intervalSize(flat);
Assert.assertEquals(flatSize, originalSize, "SplitLocusIntervals locs cover an incorrect number of bases");
// test size of each split
final long ideal = (long)Math.floor(originalSize / (1.0 * test.parts));
final long maxSize = ideal + (originalSize % test.parts) * test.parts; // no more than N * rounding error in size
for ( final List<GenomeLoc> split : splitByLocus ) {
final long splitSize = IntervalUtils.intervalSize(split);
Assert.assertTrue(splitSize >= ideal && splitSize <= maxSize,
String.format("SplitLocusIntervals interval (start=%s) has size %d outside of bounds ideal=%d, max=%d",
split.get(0), splitSize, ideal, maxSize));
}
// test that every base in original is covered once by a base in split by locus intervals
String diff = IntervalUtils.equateIntervals(test.originalIntervals, flat);
Assert.assertNull(diff, diff);
}
/** small scale tests where the expected cuts are enumerated upfront for testing */
private class SplitLocusIntervalsSmallTest extends TestDataProvider {
final List<GenomeLoc> original;
final public int parts;
final public int expectedParts;
final List<GenomeLoc> expected;
private SplitLocusIntervalsSmallTest(final String name, List<GenomeLoc> originalIntervals, final int parts, List<GenomeLoc> expected) {
this(name, originalIntervals, parts, expected, parts);
}
private SplitLocusIntervalsSmallTest(final String name, List<GenomeLoc> originalIntervals, final int parts, List<GenomeLoc> expected, int expectedParts) {
super(SplitLocusIntervalsSmallTest.class, name);
this.parts = parts;
this.expectedParts = expectedParts;
this.original = originalIntervals;
this.expected = expected;
}
public String toString() {
return String.format("%s parts=%d", super.toString(), parts);
}
}
@DataProvider(name = "SplitLocusIntervalsSmallTest")
public Object[][] createSplitLocusIntervalsSmallTest() {
GenomeLoc bp01_10 = hg19GenomeLocParser.createGenomeLoc("1", 1, 10);
GenomeLoc bp1_5 = hg19GenomeLocParser.createGenomeLoc("1", 1, 5);
GenomeLoc bp6_10 = hg19GenomeLocParser.createGenomeLoc("1", 6, 10);
new SplitLocusIntervalsSmallTest("cut into two", Arrays.asList(bp01_10), 2, Arrays.asList(bp1_5, bp6_10));
GenomeLoc bp20_30 = hg19GenomeLocParser.createGenomeLoc("1", 20, 30);
new SplitLocusIntervalsSmallTest("two in two", Arrays.asList(bp01_10, bp20_30), 2, Arrays.asList(bp01_10, bp20_30));
GenomeLoc bp1_7 = hg19GenomeLocParser.createGenomeLoc("1", 1, 7);
GenomeLoc bp8_10 = hg19GenomeLocParser.createGenomeLoc("1", 8, 10);
GenomeLoc bp20_23 = hg19GenomeLocParser.createGenomeLoc("1", 20, 23);
GenomeLoc bp24_30 = hg19GenomeLocParser.createGenomeLoc("1", 24, 30);
new SplitLocusIntervalsSmallTest("two in three", Arrays.asList(bp01_10, bp20_30), 3,
Arrays.asList(bp1_7, bp8_10, bp20_23, bp24_30));
GenomeLoc bp1_2 = hg19GenomeLocParser.createGenomeLoc("1", 1, 2);
GenomeLoc bp1_1 = hg19GenomeLocParser.createGenomeLoc("1", 1, 1);
GenomeLoc bp2_2 = hg19GenomeLocParser.createGenomeLoc("1", 2, 2);
new SplitLocusIntervalsSmallTest("too many pieces", Arrays.asList(bp1_2), 5, Arrays.asList(bp1_1, bp2_2), 2);
new SplitLocusIntervalsSmallTest("emptyList", Collections.<GenomeLoc>emptyList(), 5, Collections.<GenomeLoc>emptyList(), 0);
return SplitLocusIntervalsSmallTest.getTests(SplitLocusIntervalsSmallTest.class);
}
@Test(enabled = true, dataProvider = "SplitLocusIntervalsSmallTest")
public void splitLocusIntervalsSmallTest(SplitLocusIntervalsSmallTest test) {
List<List<GenomeLoc>> splitByLocus = IntervalUtils.splitLocusIntervals(test.original, test.parts);
Assert.assertEquals(splitByLocus.size(), test.expectedParts, "SplitLocusIntervals failed to generate correct number of intervals");
List<GenomeLoc> flat = IntervalUtils.flattenSplitIntervals(splitByLocus);
// test sizes
final long originalSize = IntervalUtils.intervalSize(test.originalIntervals);
final long originalSize = IntervalUtils.intervalSize(test.original);
final long splitSize = IntervalUtils.intervalSize(flat);
Assert.assertEquals(originalSize, splitSize, "SplitLocusIntervals locs cover an incorrect number of bases");
Assert.assertEquals(splitSize, originalSize, "SplitLocusIntervals locs cover an incorrect number of bases");
// test that every base in original is covered once by a base in split by locus intervals
// todo implement test (complex)
Assert.assertEquals(flat, test.expected, "SplitLocusIntervals locs not expected intervals");
}
//