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Added unit test to catch Ryan's exception 

Unit test to catch the special case that broke the clipping op, fixed in the previous commit.
This commit is contained in:
Mauricio Carneiro 2011-12-14 16:52:43 -05:00
parent 128bdf9c09
commit 50dee86d7f
2 changed files with 26 additions and 30 deletions
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12
public/java/test/org/broadinstitute/sting/utils/clipreads/ClipReadsTestUtils.java
View File

@ -24,6 +24,18 @@ public class ClipReadsTestUtils {
final static String BASES = "ACTG"; final static String BASES = "ACTG";
final static String QUALS = "!+5?"; //ASCII values = 33,43,53,63 final static String QUALS = "!+5?"; //ASCII values = 33,43,53,63
public static void assertEqualReads(GATKSAMRecord actual, GATKSAMRecord expected) {
// If they're both not empty, test their contents
if(!actual.isEmpty() && !expected.isEmpty()) {
Assert.assertEquals(actual.getReadBases(), expected.getReadBases());
Assert.assertEquals(actual.getBaseQualities(), expected.getBaseQualities());
Assert.assertEquals(actual.getCigarString(), expected.getCigarString());
}
// Otherwise test if they're both empty
else
Assert.assertEquals(actual.isEmpty(), expected.isEmpty());
}
public static void testBaseQualCigar(GATKSAMRecord read, byte[] readBases, byte[] baseQuals, String cigar) { public static void testBaseQualCigar(GATKSAMRecord read, byte[] readBases, byte[] baseQuals, String cigar) {
// Because quals to char start at 33 for visibility // Because quals to char start at 33 for visibility
baseQuals = subtractToArray(baseQuals, 33); baseQuals = subtractToArray(baseQuals, 33);

44
public/java/test/org/broadinstitute/sting/utils/clipreads/ReadClipperUnitTest.java
View File

@ -30,6 +30,7 @@ import net.sf.samtools.CigarElement;
import net.sf.samtools.CigarOperator; import net.sf.samtools.CigarOperator;
import net.sf.samtools.TextCigarCodec; import net.sf.samtools.TextCigarCodec;
import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.BaseTest;
import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord; import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.sting.utils.sam.ReadUtils; import org.broadinstitute.sting.utils.sam.ReadUtils;
import org.testng.Assert; import org.testng.Assert;
@ -230,42 +231,25 @@ public class ReadClipperUnitTest extends BaseTest {
@Test(enabled = true) @Test(enabled = true)
public void testHardClipLowQualEnds() { public void testHardClipLowQualEnds() {
// Needs a thorough redesign
logger.warn("Executing testHardClipLowQualEnds"); logger.warn("Executing testHardClipLowQualEnds");
//Clip whole read // Testing clipping that ends inside an insertion
Assert.assertEquals(readClipper.hardClipLowQualEnds((byte) 64), new GATKSAMRecord(readClipper.read.getHeader())); final byte[] BASES = {'A','C','G','T','A','C','G','T'};
final byte[] QUALS = {2, 2, 2, 2, 20, 20, 20, 2};
final String CIGAR = "1S1M5I1S";
List<TestParameter> testList = new LinkedList<TestParameter>(); final byte[] CLIPPED_BASES = {};
testList.add(new TestParameter(1, -1, 1, 4, "1H3M"));//clip 1 base at start final byte[] CLIPPED_QUALS = {};
testList.add(new TestParameter(11, -1, 2, 4, "2H2M"));//clip 2 bases at start final String CLIPPED_CIGAR = "";
for (TestParameter p : testList) {
init();
//logger.warn("Testing Parameters: " + p.inputStart+","+p.substringStart+","+p.substringStop+","+p.cigar);
ClipReadsTestUtils.testBaseQualCigar(readClipper.hardClipLowQualEnds((byte) p.inputStart),
ClipReadsTestUtils.BASES.substring(p.substringStart, p.substringStop).getBytes(),
ClipReadsTestUtils.QUALS.substring(p.substringStart, p.substringStop).getBytes(),
p.cigar);
}
/* todo find a better way to test lowqual tail clipping on both sides
// Reverse Quals sequence
readClipper.getRead().setBaseQualityString("?5+!"); // 63,53,43,33
testList = new LinkedList<testParameter>(); GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(BASES, QUALS, CIGAR);
testList.add(new testParameter(1,-1,0,3,"3M1H"));//clip 1 base at end GATKSAMRecord expected = ArtificialSAMUtils.createArtificialRead(CLIPPED_BASES, CLIPPED_QUALS, CLIPPED_CIGAR);
testList.add(new testParameter(11,-1,0,2,"2M2H"));//clip 2 bases at end
ReadClipper lowQualClipper = new ReadClipper(read);
ClipReadsTestUtils.assertEqualReads(lowQualClipper.hardClipLowQualEnds((byte) 2), expected);
for ( testParameter p : testList ) {
init();
readClipper.getRead().setBaseQualityString("?5+!"); // 63,53,43,33
//logger.warn("Testing Parameters: " + p.inputStart+","+p.substringStart+","+p.substringStop+","+p.cigar);
testBaseQualCigar( readClipper.hardClipLowQualEnds( (byte)p.inputStart ),
BASES.substring(p.substringStart,p.substringStop).getBytes(),
QUALS.substring(p.substringStart,p.substringStop),
p.cigar );
}
*/
} }
@Test(enabled = false) @Test(enabled = false)