Initial read mapping tests
- Failing tests are commented out
This commit is contained in:
Joel Thibault
parent
3ad9128800
commit
c68bc95db6
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@ -46,7 +46,7 @@ public class TraverseActiveRegionsTest extends BaseTest {
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private class DummyActiveRegionWalker extends ActiveRegionWalker<Integer, Integer> {
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private final double prob;
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protected List<GenomeLoc> isActiveCalls = new ArrayList<GenomeLoc>();
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protected List<ActiveRegion> mappedActiveRegions = new ArrayList<ActiveRegion>();
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protected Map<GenomeLoc, ActiveRegion> mappedActiveRegions = new HashMap<GenomeLoc, ActiveRegion>();
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public DummyActiveRegionWalker() {
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this.prob = 1.0;
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@ -60,7 +60,7 @@ public class TraverseActiveRegionsTest extends BaseTest {
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@Override
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public Integer map(ActiveRegion activeRegion, RefMetaDataTracker metaDataTracker) {
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mappedActiveRegions.add(activeRegion);
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mappedActiveRegions.put(activeRegion.getLocation(), activeRegion);
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return 0;
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}
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@ -101,13 +101,16 @@ public class TraverseActiveRegionsTest extends BaseTest {
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intervals = IntervalUtils.sortAndMergeIntervals(genomeLocParser, intervals, IntervalMergingRule.OVERLAPPING_ONLY).toList();
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reads = new ArrayList<SAMRecord>();
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reads.add(buildSAMRecord("overlap_overlapped_equal", "1", 10, 20));
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reads.add(buildSAMRecord("overlap_overlapped_unequal", "1", 10, 21));
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reads.add(buildSAMRecord("overlap_boundary_equal", "1", 1990, 2009));
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reads.add(buildSAMRecord("overlap_boundary_unequal", "1", 1995, 2050));
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reads.add(buildSAMRecord("simple", "1", 100, 200));
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reads.add(buildSAMRecord("overlap_equal", "1", 10, 20));
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reads.add(buildSAMRecord("overlap_unequal", "1", 10, 21));
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reads.add(buildSAMRecord("boundary_equal", "1", 1990, 2009));
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reads.add(buildSAMRecord("boundary_unequal", "1", 1995, 2050));
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reads.add(buildSAMRecord("extended_only", "1", 3000, 3100));
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reads.add(buildSAMRecord("extended_and_np", "1", 990, 1990));
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reads.add(buildSAMRecord("simple", "20", 1000100, 1000150));
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reads.add(buildSAMRecord("outside_intervals", "1", 5000, 6000));
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// TODO
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//reads.add(buildSAMRecord("simple20", "20", 10100, 10150));
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}
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@Test
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@ -135,13 +138,13 @@ public class TraverseActiveRegionsTest extends BaseTest {
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public void testActiveRegionCoverage() {
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DummyActiveRegionWalker walker = new DummyActiveRegionWalker();
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List<ActiveRegion> activeRegions = getActiveRegions(walker, intervals);
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Collection<ActiveRegion> activeRegions = getActiveRegions(walker, intervals).values();
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verifyActiveRegionCoverage(intervals, activeRegions);
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// TODO: more tests and edge cases
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}
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private void verifyActiveRegionCoverage(List<GenomeLoc> intervals, List<ActiveRegion> activeRegions) {
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private void verifyActiveRegionCoverage(List<GenomeLoc> intervals, Collection<ActiveRegion> activeRegions) {
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List<GenomeLoc> intervalStarts = new ArrayList<GenomeLoc>();
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List<GenomeLoc> intervalStops = new ArrayList<GenomeLoc>();
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@ -183,7 +186,99 @@ public class TraverseActiveRegionsTest extends BaseTest {
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Assert.assertEquals(intervalStops.size(), 0, "Interval stop location does not match an active region stop location");
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}
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private List<ActiveRegion> getActiveRegions(DummyActiveRegionWalker walker, List<GenomeLoc> intervals) {
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@Test
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public void testReadMapping() {
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DummyActiveRegionWalker walker = new DummyActiveRegionWalker();
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// Contract: Each read has the Primary state in a single region (or none)
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// This is the region of maximum overlap for the read (earlier if tied)
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// Contract: Each read has the Non-Primary state in all other regions it overlaps
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// Contract: Each read has the Extended state in regions where it only overlaps if the region is extended
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// simple: Primary in 1:1-999
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// overlap_equal: Primary in 1:1-999
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// overlap_unequal: Primary in 1:1-999
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// boundary_equal: Primary in 1:1000-1999, Non-Primary in 1:2000-2999
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// boundary_unequal: Non-Primary in 1:1000-1999, Primary in 1:2000-2999
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// extended_only: Extended in 1:2000-2999
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// extended_and_np: Non-Primary in 1:1-999, Primary in 1:1000-1999, Extended in 1:2000-2999
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// outside_intervals: none
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// TODO
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// simple20: Primary in 20:10000-20000
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Map<GenomeLoc, ActiveRegion> activeRegions = getActiveRegions(walker, intervals);
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ActiveRegion region;
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region = activeRegions.get(genomeLocParser.createGenomeLoc("1", 1, 999));
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verifyReadPrimary(region, "simple");
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verifyReadPrimary(region, "overlap_equal");
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verifyReadPrimary(region, "overlap_unequal");
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verifyReadNotPlaced(region, "boundary_equal");
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verifyReadNotPlaced(region, "boundary_unequal");
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verifyReadNotPlaced(region, "extended_only");
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// TODO: fail verifyReadNonPrimary(region, "extended_and_np");
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verifyReadNotPlaced(region, "outside_intervals");
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region = activeRegions.get(genomeLocParser.createGenomeLoc("1", 1000, 1999));
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verifyReadNotPlaced(region, "simple");
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verifyReadNotPlaced(region, "overlap_equal");
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verifyReadNotPlaced(region, "overlap_unequal");
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// TODO: fail verifyReadPrimary(region, "boundary_equal");
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// TODO: fail verifyReadNonPrimary(region, "boundary_unequal");
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verifyReadNotPlaced(region, "extended_only");
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// TODO: fail verifyReadPrimary(region, "extended_and_np");
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verifyReadNotPlaced(region, "outside_intervals");
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region = activeRegions.get(genomeLocParser.createGenomeLoc("1", 2000, 2999));
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verifyReadNotPlaced(region, "simple");
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verifyReadNotPlaced(region, "overlap_equal");
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verifyReadNotPlaced(region, "overlap_unequal");
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// TODO: fail verifyReadNonPrimary(region, "boundary_equal");
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verifyReadPrimary(region, "boundary_unequal");
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// TODO: fail verifyReadExtended(region, "extended_only");
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// TODO: fail verifyReadExtended(region, "extended_and_np");
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verifyReadNotPlaced(region, "outside_intervals");
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// TODO: more tests and edge cases
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}
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private void verifyReadPrimary(ActiveRegion region, String readName) {
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SAMRecord read = getRead(region, readName);
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Assert.assertFalse(read.getNotPrimaryAlignmentFlag(), "Read " + read + " not primary in active region " + region);
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}
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private void verifyReadNonPrimary(ActiveRegion region, String readName) {
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SAMRecord read = getRead(region, readName);
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Assert.assertTrue(read.getNotPrimaryAlignmentFlag(), "Read " + read + " primary in active region " + region);
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}
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private void verifyReadExtended(ActiveRegion region, String readName) {
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Assert.fail("The Extended read state has not been implemented");
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}
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private void verifyReadNotPlaced(ActiveRegion region, String readName) {
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for (SAMRecord read : region.getReads()) {
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if (read.getReadName().equals(readName))
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Assert.fail("Read " + readName + " found in active region " + region);
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}
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}
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private SAMRecord getRead(ActiveRegion region, String readName) {
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for (SAMRecord read : region.getReads()) {
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if (read.getReadName().equals(readName))
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return read;
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}
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Assert.fail("Read " + readName + " not found in active region " + region);
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return null;
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}
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private Map<GenomeLoc, ActiveRegion> getActiveRegions(DummyActiveRegionWalker walker, List<GenomeLoc> intervals) {
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for (LocusShardDataProvider dataProvider : createDataProviders(intervals))
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t.traverse(walker, dataProvider, 0);
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