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Refactor region/read comparisons

This commit is contained in:
Joel Thibault 2012-12-18 10:35:07 -05:00
parent c86f5e46b0
commit 1158c1529f
1 changed files with 22 additions and 162 deletions
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184
public/java/test/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegionsTest.java
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@ -239,64 +239,19 @@ public class TraverseActiveRegionsTest extends BaseTest {
ActiveRegion region;
region = activeRegions.get(genomeLocParser.createGenomeLoc("1", 1, 999));
getRead(region, "simple");
getRead(region, "overlap_equal");
getRead(region, "overlap_unequal");
verifyReadNotPlaced(region, "boundary_equal");
verifyReadNotPlaced(region, "boundary_unequal");
verifyReadNotPlaced(region, "extended_and_np");
verifyReadNotPlaced(region, "outside_intervals");
verifyReadNotPlaced(region, "end_of_chr1");
verifyReadNotPlaced(region, "simple20");
verifyReadMapping(region, new String[]{"simple", "overlap_equal", "overlap_unequal"});
region = activeRegions.get(genomeLocParser.createGenomeLoc("1", 1000, 1999));
verifyReadNotPlaced(region, "simple");
verifyReadNotPlaced(region, "overlap_equal");
verifyReadNotPlaced(region, "overlap_unequal");
verifyReadNotPlaced(region, "boundary_equal");
getRead(region, "boundary_unequal");
getRead(region, "extended_and_np");
verifyReadNotPlaced(region, "outside_intervals");
verifyReadNotPlaced(region, "end_of_chr1");
verifyReadNotPlaced(region, "simple20");
verifyReadMapping(region, new String[]{"boundary_unequal", "extended_and_np"});
region = activeRegions.get(genomeLocParser.createGenomeLoc("1", 2000, 2999));
verifyReadNotPlaced(region, "simple");
verifyReadNotPlaced(region, "overlap_equal");
verifyReadNotPlaced(region, "overlap_unequal");
getRead(region, "boundary_equal");
verifyReadNotPlaced(region, "boundary_unequal");
verifyReadNotPlaced(region, "extended_and_np");
verifyReadNotPlaced(region, "outside_intervals");
verifyReadNotPlaced(region, "end_of_chr1");
verifyReadNotPlaced(region, "simple20");
verifyReadMapping(region, new String[]{"boundary_equal"});
region = activeRegions.get(genomeLocParser.createGenomeLoc("1", 249250600, 249250621));
verifyReadNotPlaced(region, "simple");
verifyReadNotPlaced(region, "overlap_equal");
verifyReadNotPlaced(region, "overlap_unequal");
verifyReadNotPlaced(region, "boundary_equal");
verifyReadNotPlaced(region, "boundary_unequal");
verifyReadNotPlaced(region, "extended_and_np");
verifyReadNotPlaced(region, "outside_intervals");
getRead(region, "end_of_chr1");
verifyReadNotPlaced(region, "simple20");
verifyReadMapping(region, new String[]{"end_of_chr1"});
region = activeRegions.get(genomeLocParser.createGenomeLoc("20", 10000, 10100));
verifyReadNotPlaced(region, "simple");
verifyReadNotPlaced(region, "overlap_equal");
verifyReadNotPlaced(region, "overlap_unequal");
verifyReadNotPlaced(region, "boundary_equal");
verifyReadNotPlaced(region, "boundary_unequal");
verifyReadNotPlaced(region, "extended_and_np");
verifyReadNotPlaced(region, "outside_intervals");
verifyReadNotPlaced(region, "end_of_chr1");
getRead(region, "simple20");
verifyReadMapping(region, new String[]{"simple20"});
}
@Test
@ -323,64 +278,19 @@ public class TraverseActiveRegionsTest extends BaseTest {
ActiveRegion region;
region = activeRegions.get(genomeLocParser.createGenomeLoc("1", 1, 999));
getRead(region, "simple");
getRead(region, "overlap_equal");
getRead(region, "overlap_unequal");
verifyReadNotPlaced(region, "boundary_equal");
verifyReadNotPlaced(region, "boundary_unequal");
getRead(region, "extended_and_np");
verifyReadNotPlaced(region, "outside_intervals");
verifyReadNotPlaced(region, "end_of_chr1");
verifyReadNotPlaced(region, "simple20");
verifyReadMapping(region, new String[]{"simple", "overlap_equal", "overlap_unequal", "extended_and_np"});
region = activeRegions.get(genomeLocParser.createGenomeLoc("1", 1000, 1999));
verifyReadNotPlaced(region, "simple");
verifyReadNotPlaced(region, "overlap_equal");
verifyReadNotPlaced(region, "overlap_unequal");
getRead(region, "boundary_equal");
getRead(region, "boundary_unequal");
getRead(region, "extended_and_np");
verifyReadNotPlaced(region, "outside_intervals");
verifyReadNotPlaced(region, "end_of_chr1");
verifyReadNotPlaced(region, "simple20");
verifyReadMapping(region, new String[]{"boundary_equal", "boundary_unequal", "extended_and_np"});
region = activeRegions.get(genomeLocParser.createGenomeLoc("1", 2000, 2999));
verifyReadNotPlaced(region, "simple");
verifyReadNotPlaced(region, "overlap_equal");
verifyReadNotPlaced(region, "overlap_unequal");
getRead(region, "boundary_equal");
getRead(region, "boundary_unequal");
verifyReadNotPlaced(region, "extended_and_np");
verifyReadNotPlaced(region, "outside_intervals");
verifyReadNotPlaced(region, "end_of_chr1");
verifyReadNotPlaced(region, "simple20");
verifyReadMapping(region, new String[]{"boundary_equal", "boundary_unequal"});
region = activeRegions.get(genomeLocParser.createGenomeLoc("1", 249250600, 249250621));
verifyReadNotPlaced(region, "simple");
verifyReadNotPlaced(region, "overlap_equal");
verifyReadNotPlaced(region, "overlap_unequal");
verifyReadNotPlaced(region, "boundary_equal");
verifyReadNotPlaced(region, "boundary_unequal");
verifyReadNotPlaced(region, "extended_and_np");
verifyReadNotPlaced(region, "outside_intervals");
getRead(region, "end_of_chr1");
verifyReadNotPlaced(region, "simple20");
verifyReadMapping(region, new String[]{"end_of_chr1"});
region = activeRegions.get(genomeLocParser.createGenomeLoc("20", 10000, 10100));
verifyReadNotPlaced(region, "simple");
verifyReadNotPlaced(region, "overlap_equal");
verifyReadNotPlaced(region, "overlap_unequal");
verifyReadNotPlaced(region, "boundary_equal");
verifyReadNotPlaced(region, "boundary_unequal");
verifyReadNotPlaced(region, "extended_and_np");
verifyReadNotPlaced(region, "outside_intervals");
verifyReadNotPlaced(region, "end_of_chr1");
getRead(region, "simple20");
verifyReadMapping(region, new String[]{"simple20"});
}
@Test
@ -407,65 +317,21 @@ public class TraverseActiveRegionsTest extends BaseTest {
Map<GenomeLoc, ActiveRegion> activeRegions = getActiveRegions(walker, intervals);
ActiveRegion region;
region = activeRegions.get(genomeLocParser.createGenomeLoc("1", 1, 999));
getRead(region, "simple");
getRead(region, "overlap_equal");
getRead(region, "overlap_unequal");
verifyReadNotPlaced(region, "boundary_equal");
verifyReadNotPlaced(region, "boundary_unequal");
getRead(region, "extended_and_np");
verifyReadNotPlaced(region, "outside_intervals");
verifyReadNotPlaced(region, "end_of_chr1");
verifyReadNotPlaced(region, "simple20");
region = activeRegions.get(genomeLocParser.createGenomeLoc("1", 1, 999));
verifyReadMapping(region, new String[]{"simple", "overlap_equal", "overlap_unequal", "extended_and_np"});
region = activeRegions.get(genomeLocParser.createGenomeLoc("1", 1000, 1999));
verifyReadNotPlaced(region, "simple");
verifyReadNotPlaced(region, "overlap_equal");
verifyReadNotPlaced(region, "overlap_unequal");
getRead(region, "boundary_equal");
getRead(region, "boundary_unequal");
getRead(region, "extended_and_np");
verifyReadNotPlaced(region, "outside_intervals");
verifyReadNotPlaced(region, "end_of_chr1");
verifyReadNotPlaced(region, "simple20");
verifyReadMapping(region, new String[]{"boundary_equal", "boundary_unequal", "extended_and_np"});
region = activeRegions.get(genomeLocParser.createGenomeLoc("1", 2000, 2999));
verifyReadNotPlaced(region, "simple");
verifyReadNotPlaced(region, "overlap_equal");
verifyReadNotPlaced(region, "overlap_unequal");
getRead(region, "boundary_equal");
getRead(region, "boundary_unequal");
getRead(region, "extended_and_np");
verifyReadNotPlaced(region, "outside_intervals");
verifyReadNotPlaced(region, "end_of_chr1");
verifyReadNotPlaced(region, "simple20");
verifyReadMapping(region, new String[]{"boundary_equal", "boundary_unequal", "extended_and_np"});
region = activeRegions.get(genomeLocParser.createGenomeLoc("1", 249250600, 249250621));
verifyReadNotPlaced(region, "simple");
verifyReadNotPlaced(region, "overlap_equal");
verifyReadNotPlaced(region, "overlap_unequal");
verifyReadNotPlaced(region, "boundary_equal");
verifyReadNotPlaced(region, "boundary_unequal");
verifyReadNotPlaced(region, "extended_and_np");
verifyReadNotPlaced(region, "outside_intervals");
getRead(region, "end_of_chr1");
verifyReadNotPlaced(region, "simple20");
verifyReadMapping(region, new String[]{"end_of_chr1"});
region = activeRegions.get(genomeLocParser.createGenomeLoc("20", 10000, 10100));
verifyReadNotPlaced(region, "simple");
verifyReadNotPlaced(region, "overlap_equal");
verifyReadNotPlaced(region, "overlap_unequal");
verifyReadNotPlaced(region, "boundary_equal");
verifyReadNotPlaced(region, "boundary_unequal");
verifyReadNotPlaced(region, "extended_and_np");
verifyReadNotPlaced(region, "outside_intervals");
verifyReadNotPlaced(region, "end_of_chr1");
getRead(region, "simple20");
verifyReadMapping(region, new String[]{"simple20"});
}
@Test
@ -473,21 +339,15 @@ public class TraverseActiveRegionsTest extends BaseTest {
// TODO
}
private void verifyReadNotPlaced(ActiveRegion region, String readName) {
private void verifyReadMapping(ActiveRegion region, String[] reads) {
Collection<String> wantReads = new ArrayList<String>(Arrays.asList(reads));
for (SAMRecord read : region.getReads()) {
if (read.getReadName().equals(readName))
Assert.fail("Read " + readName + " found in active region " + region);
}
}
private SAMRecord getRead(ActiveRegion region, String readName) {
for (SAMRecord read : region.getReads()) {
if (read.getReadName().equals(readName))
return read;
String regionReadName = read.getReadName();
Assert.assertTrue(wantReads.contains(regionReadName), "Read " + regionReadName + " assigned to active region " + region);
wantReads.remove(regionReadName);
}
Assert.fail("Read " + readName + " not assigned to active region " + region);
return null;
Assert.assertTrue(wantReads.isEmpty(), "Reads missing in active region " + region);
}
private Map<GenomeLoc, ActiveRegion> getActiveRegions(DummyActiveRegionWalker walker, List<GenomeLoc> intervals) {