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Added framework to do batch CigarClip Testing 

*NOTE: This commit has not been compiled!
This commit is contained in:
Roger Zurawicki 2011-10-02 22:33:46 -04:00
parent fc86cd6fd8
commit bf6a3a6532
1 changed files with 14 additions and 0 deletions
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14
public/java/test/org/broadinstitute/sting/utils/clipreads/ReadClipperUnitTest.java
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@ -62,6 +62,20 @@ public class ReadClipperUnitTest extends BaseTest {
readClipper = new ReadClipper(read); readClipper = new ReadClipper(read);
} }
private void testHardClipCigarByReadCoordinate( SAMRecord read, String inputCigar, String expectedCigar, int expectedStart, int expectedStop) {
read.setCigar(TextCigarCodec.getSingleton().decode(inputCigar) );
SAMRecord clipped = readClipper.hardClipByReadCoordinates(expectedStart,expectedStop);
Assert.assertEquals(clipped.getCigarString(), expectedCigar, "Clipped Cigar string is different than expected");
}
/*
private void testReadBasesAndQuals(SAMRecord read, int expectedStart, int expectedStop) {
SAMRecord clipped = ReadUtils.hardClipBases(read, expectedStart, expectedStop - 1, null);
String expectedBases = BASES.substring(expectedStart, expectedStop);
String expectedQuals = QUALS.substring(expectedStart, expectedStop);
Assert.assertEquals(clipped.getReadBases(), expectedBases.getBytes(), "Clipped bases not those expected");
Assert.assertEquals(clipped.getBaseQualityString(), expectedQuals, "Clipped quals not those expected");
}
*/
@Test @Test
public void testHardClipBothEndsByReferenceCoordinates() { public void testHardClipBothEndsByReferenceCoordinates() {
logger.warn("Executing testHardClipBothEndsByReferenceCoordinates"); logger.warn("Executing testHardClipBothEndsByReferenceCoordinates");