From bf6a3a65320cf5d1fa9aed9f3db5154579921443 Mon Sep 17 00:00:00 2001 From: Roger Zurawicki Date: Sun, 2 Oct 2011 22:33:46 -0400 Subject: [PATCH] Added framework to do batch CigarClip Testing *NOTE: This commit has not been compiled! --- .../sting/utils/clipreads/ReadClipperUnitTest.java | 14 ++++++++++++++ 1 file changed, 14 insertions(+) diff --git a/public/java/test/org/broadinstitute/sting/utils/clipreads/ReadClipperUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/clipreads/ReadClipperUnitTest.java index 1415379db..38eee762a 100644 --- a/public/java/test/org/broadinstitute/sting/utils/clipreads/ReadClipperUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/utils/clipreads/ReadClipperUnitTest.java @@ -62,6 +62,20 @@ public class ReadClipperUnitTest extends BaseTest { 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 public void testHardClipBothEndsByReferenceCoordinates() { logger.warn("Executing testHardClipBothEndsByReferenceCoordinates");