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Fun with varargs

This commit is contained in:
Joel Thibault 2012-12-18 13:38:10 -05:00
parent 1158c1529f
commit d69d1f8988
1 changed files with 16 additions and 17 deletions
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33
public/java/test/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegionsTest.java
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@ -239,19 +239,19 @@ public class TraverseActiveRegionsTest extends BaseTest {
ActiveRegion region; ActiveRegion region;
region = activeRegions.get(genomeLocParser.createGenomeLoc("1", 1, 999)); region = activeRegions.get(genomeLocParser.createGenomeLoc("1", 1, 999));
verifyReadMapping(region, new String[]{"simple", "overlap_equal", "overlap_unequal"}); verifyReadMapping(region, "simple", "overlap_equal", "overlap_unequal");
region = activeRegions.get(genomeLocParser.createGenomeLoc("1", 1000, 1999)); region = activeRegions.get(genomeLocParser.createGenomeLoc("1", 1000, 1999));
verifyReadMapping(region, new String[]{"boundary_unequal", "extended_and_np"}); verifyReadMapping(region, "boundary_unequal", "extended_and_np");
region = activeRegions.get(genomeLocParser.createGenomeLoc("1", 2000, 2999)); region = activeRegions.get(genomeLocParser.createGenomeLoc("1", 2000, 2999));
verifyReadMapping(region, new String[]{"boundary_equal"}); verifyReadMapping(region, "boundary_equal");
region = activeRegions.get(genomeLocParser.createGenomeLoc("1", 249250600, 249250621)); region = activeRegions.get(genomeLocParser.createGenomeLoc("1", 249250600, 249250621));
verifyReadMapping(region, new String[]{"end_of_chr1"}); verifyReadMapping(region, "end_of_chr1");
region = activeRegions.get(genomeLocParser.createGenomeLoc("20", 10000, 10100)); region = activeRegions.get(genomeLocParser.createGenomeLoc("20", 10000, 10100));
verifyReadMapping(region, new String[]{"simple20"}); verifyReadMapping(region, "simple20");
} }
@Test @Test
@ -278,19 +278,19 @@ public class TraverseActiveRegionsTest extends BaseTest {
ActiveRegion region; ActiveRegion region;
region = activeRegions.get(genomeLocParser.createGenomeLoc("1", 1, 999)); region = activeRegions.get(genomeLocParser.createGenomeLoc("1", 1, 999));
verifyReadMapping(region, new String[]{"simple", "overlap_equal", "overlap_unequal", "extended_and_np"}); verifyReadMapping(region, "simple", "overlap_equal", "overlap_unequal", "extended_and_np");
region = activeRegions.get(genomeLocParser.createGenomeLoc("1", 1000, 1999)); region = activeRegions.get(genomeLocParser.createGenomeLoc("1", 1000, 1999));
verifyReadMapping(region, new String[]{"boundary_equal", "boundary_unequal", "extended_and_np"}); verifyReadMapping(region, "boundary_equal", "boundary_unequal", "extended_and_np");
region = activeRegions.get(genomeLocParser.createGenomeLoc("1", 2000, 2999)); region = activeRegions.get(genomeLocParser.createGenomeLoc("1", 2000, 2999));
verifyReadMapping(region, new String[]{"boundary_equal", "boundary_unequal"}); verifyReadMapping(region, "boundary_equal", "boundary_unequal");
region = activeRegions.get(genomeLocParser.createGenomeLoc("1", 249250600, 249250621)); region = activeRegions.get(genomeLocParser.createGenomeLoc("1", 249250600, 249250621));
verifyReadMapping(region, new String[]{"end_of_chr1"}); verifyReadMapping(region, "end_of_chr1");
region = activeRegions.get(genomeLocParser.createGenomeLoc("20", 10000, 10100)); region = activeRegions.get(genomeLocParser.createGenomeLoc("20", 10000, 10100));
verifyReadMapping(region, new String[]{"simple20"}); verifyReadMapping(region, "simple20");
} }
@Test @Test
@ -317,21 +317,20 @@ public class TraverseActiveRegionsTest extends BaseTest {
Map<GenomeLoc, ActiveRegion> activeRegions = getActiveRegions(walker, intervals); Map<GenomeLoc, ActiveRegion> activeRegions = getActiveRegions(walker, intervals);
ActiveRegion region; ActiveRegion region;
region = activeRegions.get(genomeLocParser.createGenomeLoc("1", 1, 999)); region = activeRegions.get(genomeLocParser.createGenomeLoc("1", 1, 999));
verifyReadMapping(region, new String[]{"simple", "overlap_equal", "overlap_unequal", "extended_and_np"}); verifyReadMapping(region, "simple", "overlap_equal", "overlap_unequal", "extended_and_np");
region = activeRegions.get(genomeLocParser.createGenomeLoc("1", 1000, 1999)); region = activeRegions.get(genomeLocParser.createGenomeLoc("1", 1000, 1999));
verifyReadMapping(region, new String[]{"boundary_equal", "boundary_unequal", "extended_and_np"}); verifyReadMapping(region, "boundary_equal", "boundary_unequal", "extended_and_np");
region = activeRegions.get(genomeLocParser.createGenomeLoc("1", 2000, 2999)); region = activeRegions.get(genomeLocParser.createGenomeLoc("1", 2000, 2999));
verifyReadMapping(region, new String[]{"boundary_equal", "boundary_unequal", "extended_and_np"}); verifyReadMapping(region, "boundary_equal", "boundary_unequal", "extended_and_np");
region = activeRegions.get(genomeLocParser.createGenomeLoc("1", 249250600, 249250621)); region = activeRegions.get(genomeLocParser.createGenomeLoc("1", 249250600, 249250621));
verifyReadMapping(region, new String[]{"end_of_chr1"}); verifyReadMapping(region, "end_of_chr1");
region = activeRegions.get(genomeLocParser.createGenomeLoc("20", 10000, 10100)); region = activeRegions.get(genomeLocParser.createGenomeLoc("20", 10000, 10100));
verifyReadMapping(region, new String[]{"simple20"}); verifyReadMapping(region, "simple20");
} }
@Test @Test
@ -339,7 +338,7 @@ public class TraverseActiveRegionsTest extends BaseTest {
// TODO // TODO
} }
private void verifyReadMapping(ActiveRegion region, String[] reads) { private void verifyReadMapping(ActiveRegion region, String... reads) {
Collection<String> wantReads = new ArrayList<String>(Arrays.asList(reads)); Collection<String> wantReads = new ArrayList<String>(Arrays.asList(reads));
for (SAMRecord read : region.getReads()) { for (SAMRecord read : region.getReads()) {
String regionReadName = read.getReadName(); String regionReadName = read.getReadName();