zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Re-enabling the unit tests for reverse allele clipping

This commit is contained in:
Eric Banks 2012-07-29 22:24:56 -04:00
parent b07bf1950b
commit 7630c929a7
1 changed files with 48 additions and 0 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

48
public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUtilsUnitTest.java
View File

@ -655,4 +655,52 @@ public class VariantContextUtilsUnitTest extends BaseTest {
// test alleles are equal
Assert.assertEquals(VariantContextUtils.isTandemRepeat(cfg.vc, cfg.ref.getBytes()), cfg.isTrueRepeat);
}
// --------------------------------------------------------------------------------
//
// basic allele clipping test
//
// --------------------------------------------------------------------------------
private class ReverseClippingPositionTestProvider extends TestDataProvider {
final String ref;
final List<Allele> alleles = new ArrayList<Allele>();
final int expectedClip;
private ReverseClippingPositionTestProvider(final int expectedClip, final String ref, final String... alleles) {
super(ReverseClippingPositionTestProvider.class);
this.ref = ref;
for ( final String allele : alleles )
this.alleles.add(Allele.create(allele));
this.expectedClip = expectedClip;
}
@Override
public String toString() {
return String.format("ref=%s allele=%s reverse clip %d", ref, alleles, expectedClip);
}
}
@DataProvider(name = "ReverseClippingPositionTestProvider")
public Object[][] makeReverseClippingPositionTestProvider() {
// pair clipping
new ReverseClippingPositionTestProvider(0, "ATT", "CCG");
new ReverseClippingPositionTestProvider(1, "ATT", "CCT");
new ReverseClippingPositionTestProvider(2, "ATT", "CTT");
new ReverseClippingPositionTestProvider(2, "ATT", "ATT"); // cannot completely clip allele
// triplets
new ReverseClippingPositionTestProvider(0, "ATT", "CTT", "CGG");
new ReverseClippingPositionTestProvider(1, "ATT", "CTT", "CGT"); // the T can go
new ReverseClippingPositionTestProvider(2, "ATT", "CTT", "CTT"); // both Ts can go
return ReverseClippingPositionTestProvider.getTests(ReverseClippingPositionTestProvider.class);
}
@Test(dataProvider = "ReverseClippingPositionTestProvider")
public void testReverseClippingPositionTestProvider(ReverseClippingPositionTestProvider cfg) {
int result = VariantContextUtils.computeReverseClipping(cfg.alleles, cfg.ref.getBytes(), 0, false);
Assert.assertEquals(result, cfg.expectedClip);
}
}