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Added Basic Unit Tests for ReadClipper 

Tests some but not all functions
Some tests have been disabled because they are not working
This commit is contained in:
Roger Zurawicki 2011-11-13 22:27:49 -05:00
parent b7c33116af
commit 1202a809cb
1 changed files with 94 additions and 58 deletions
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152
public/java/test/org/broadinstitute/sting/utils/clipreads/ReadClipperUnitTest.java
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@ -30,9 +30,12 @@ import org.broadinstitute.sting.BaseTest;
import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils; import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord; import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.testng.Assert; import org.testng.Assert;
import org.testng.annotations.BeforeClass; import org.testng.annotations.BeforeTest;
import org.testng.annotations.Test; import org.testng.annotations.Test;
import java.util.LinkedList;
import java.util.List;
/** /**
* Created by IntelliJ IDEA. * Created by IntelliJ IDEA.
* User: roger * User: roger
@ -44,44 +47,57 @@ public class ReadClipperUnitTest extends BaseTest {
// TODO: Add error messages on failed tests // TODO: Add error messages on failed tests
//int debug = 0;
GATKSAMRecord read, expected; GATKSAMRecord read, expected;
ReadClipper readClipper; ReadClipper readClipper;
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
@BeforeClass // What the test read looks like
// Ref: 1 2 3 4 5 6 7 8
// Read: 0 1 2 3 - - - -
// -----------------------------
// Bases: A C T G - - - -
// Quals: ! + 5 ? - - - -
@BeforeTest
public void init() { public void init() {
SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(1, 1, 1000); SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(1, 1, 1000);
read = ArtificialSAMUtils.createArtificialRead(header, "read1", 0, 1, BASES.length()); read = ArtificialSAMUtils.createArtificialRead(header, "read1", 0, 1, BASES.length());
read.setReadUnmappedFlag(true);
read.setReadBases(new String(BASES).getBytes()); read.setReadBases(new String(BASES).getBytes());
read.setBaseQualityString(new String(QUALS)); read.setBaseQualityString(new String(QUALS));
readClipper = new ReadClipper(read); readClipper = new ReadClipper(read);
//logger.warn(read.getCigarString());
} }
@Test ( enabled = false ) @Test ( enabled = true )
public void testHardClipBothEndsByReferenceCoordinates() { public void testHardClipBothEndsByReferenceCoordinates() {
init();
logger.warn("Executing testHardClipBothEndsByReferenceCoordinates"); logger.warn("Executing testHardClipBothEndsByReferenceCoordinates");
//int debug = 1;
//Clip whole read //Clip whole read
Assert.assertEquals(readClipper.hardClipBothEndsByReferenceCoordinates(0,0), new GATKSAMRecord(read.getHeader())); Assert.assertEquals(readClipper.hardClipBothEndsByReferenceCoordinates(1,1), new GATKSAMRecord(read.getHeader()));
//clip 1 base //clip 1 base
expected = readClipper.hardClipBothEndsByReferenceCoordinates(0,3); expected = readClipper.hardClipBothEndsByReferenceCoordinates(1,4);
Assert.assertEquals(expected.getReadBases(), BASES.substring(1,3).getBytes()); Assert.assertEquals(expected.getReadBases(), BASES.substring(1,3).getBytes());
Assert.assertEquals(expected.getBaseQualityString(), QUALS.substring(1,3)); Assert.assertEquals(expected.getBaseQualityString(), QUALS.substring(1,3));
Assert.assertEquals(expected.getCigarString(), "1H2M1H"); Assert.assertEquals(expected.getCigarString(), "1H2M1H");
} }
@Test ( enabled = false ) @Test ( enabled = false ) // TODO This fails at hardClipCigar and returns a NullPointerException
public void testHardClipByReadCoordinates() { public void testHardClipByReadCoordinates() {
init();
logger.warn("Executing testHardClipByReadCoordinates"); logger.warn("Executing testHardClipByReadCoordinates");
//Clip whole read //Clip whole read
Assert.assertEquals(readClipper.hardClipByReadCoordinates(0,3), new GATKSAMRecord(read.getHeader())); Assert.assertEquals(readClipper.hardClipByReadCoordinates(0,3), new GATKSAMRecord(read.getHeader()));
//clip 1 base at start //clip 1 base at start
System.out.println(readClipper.read.getCigarString());
expected = readClipper.hardClipByReadCoordinates(0,0); expected = readClipper.hardClipByReadCoordinates(0,0);
Assert.assertEquals(expected.getReadBases(), BASES.substring(1,4).getBytes()); Assert.assertEquals(expected.getReadBases(), BASES.substring(1,4).getBytes());
Assert.assertEquals(expected.getBaseQualityString(), QUALS.substring(1,4)); Assert.assertEquals(expected.getBaseQualityString(), QUALS.substring(1,4));
@ -107,83 +123,101 @@ public class ReadClipperUnitTest extends BaseTest {
} }
@Test ( enabled = false ) public void testIfEqual( GATKSAMRecord read, byte[] readBases, String baseQuals, String cigar) {
Assert.assertEquals(read.getReadBases(), readBases);
Assert.assertEquals(read.getBaseQualityString(), baseQuals);
Assert.assertEquals(read.getCigarString(), cigar);
}
public class testParameter {
int inputStart;
int inputStop;
int substringStart;
int substringStop;
String cigar;
public testParameter(int InputStart, int InputStop, int SubstringStart, int SubstringStop, String Cigar) {
inputStart = InputStart;
inputStop = InputStop;
substringStart = SubstringStart;
substringStop = SubstringStop;
cigar = Cigar;
}
}
@Test ( enabled = true )
public void testHardClipByReferenceCoordinates() { public void testHardClipByReferenceCoordinates() {
logger.warn("Executing testHardClipByReferenceCoordinates"); logger.warn("Executing testHardClipByReferenceCoordinates");
//logger.warn(debug);
//Clip whole read //Clip whole read
Assert.assertEquals(readClipper.hardClipByReferenceCoordinates(1,4), new GATKSAMRecord(read.getHeader())); Assert.assertEquals(readClipper.hardClipByReferenceCoordinates(1,4), new GATKSAMRecord(read.getHeader()));
//clip 1 base at start List<testParameter> testList = new LinkedList<testParameter>();
expected = readClipper.hardClipByReferenceCoordinates(-1,1); testList.add(new testParameter(-1,1,1,4,"1H3M"));//clip 1 base at start
Assert.assertEquals(expected.getReadBases(), BASES.substring(1,4).getBytes()); testList.add(new testParameter(4,-1,0,3,"3M1H"));//clip 1 base at end
Assert.assertEquals(expected.getBaseQualityString(), QUALS.substring(1,4)); testList.add(new testParameter(-1,2,2,4,"2H2M"));//clip 2 bases at start
Assert.assertEquals(expected.getCigarString(), "1H3M"); testList.add(new testParameter(3,-1,0,2,"2M2H"));//clip 2 bases at end
//clip 1 base at end for ( testParameter p : testList ) {
expected = readClipper.hardClipByReferenceCoordinates(3,-1); init();
Assert.assertEquals(expected.getReadBases(), BASES.substring(0,3).getBytes()); //logger.warn("Testing Parameters: " + p.inputStart+","+p.inputStop+","+p.substringStart+","+p.substringStop+","+p.cigar);
Assert.assertEquals(expected.getBaseQualityString(), QUALS.substring(0,3)); testIfEqual( readClipper.hardClipByReferenceCoordinates(p.inputStart,p.inputStop),
Assert.assertEquals(expected.getCigarString(), "3M1H"); BASES.substring(p.substringStart,p.substringStop).getBytes(),
QUALS.substring(p.substringStart,p.substringStop),
//clip 2 bases at start p.cigar );
expected = readClipper.hardClipByReferenceCoordinates(-1,2); }
Assert.assertEquals(expected.getReadBases(), BASES.substring(2,4).getBytes());
Assert.assertEquals(expected.getBaseQualityString(), QUALS.substring(2,4));
Assert.assertEquals(expected.getCigarString(), "2H2M");
//clip 2 bases at end
expected = readClipper.hardClipByReferenceCoordinates(2,-1);
Assert.assertEquals(expected.getReadBases(), BASES.substring(0,2).getBytes());
Assert.assertEquals(expected.getBaseQualityString(), QUALS.substring(0,2));
Assert.assertEquals(expected.getCigarString(), "2M2H");
} }
@Test ( enabled = false ) @Test ( enabled = true )
public void testHardClipByReferenceCoordinatesLeftTail() { public void testHardClipByReferenceCoordinatesLeftTail() {
init();
logger.warn("Executing testHardClipByReferenceCoordinatesLeftTail"); logger.warn("Executing testHardClipByReferenceCoordinatesLeftTail");
//Clip whole read //Clip whole read
Assert.assertEquals(readClipper.hardClipByReferenceCoordinatesLeftTail(4), new GATKSAMRecord(read.getHeader())); Assert.assertEquals(readClipper.hardClipByReferenceCoordinatesLeftTail(4), new GATKSAMRecord(read.getHeader()));
//clip 1 base at start List<testParameter> testList = new LinkedList<testParameter>();
expected = readClipper.hardClipByReferenceCoordinatesLeftTail(1); testList.add(new testParameter(1,-1,1,4,"1H3M"));//clip 1 base at start
Assert.assertEquals(expected.getReadBases(), BASES.substring(1,4).getBytes()); testList.add(new testParameter(2,-1,2,4,"2H2M"));//clip 2 bases at start
Assert.assertEquals(expected.getBaseQualityString(), QUALS.substring(1,4));
Assert.assertEquals(expected.getCigarString(), "1H3M");
//clip 2 bases at start for ( testParameter p : testList ) {
expected = readClipper.hardClipByReferenceCoordinatesLeftTail(2); init();
Assert.assertEquals(expected.getReadBases(), BASES.substring(2,4).getBytes()); //logger.warn("Testing Parameters: " + p.inputStart+","+p.substringStart+","+p.substringStop+","+p.cigar);
Assert.assertEquals(expected.getBaseQualityString(), QUALS.substring(2,4)); testIfEqual( readClipper.hardClipByReferenceCoordinatesLeftTail(p.inputStart),
Assert.assertEquals(expected.getCigarString(), "2H2M"); BASES.substring(p.substringStart,p.substringStop).getBytes(),
QUALS.substring(p.substringStart,p.substringStop),
p.cigar );
}
} }
@Test ( enabled = false ) @Test ( enabled = true )
public void testHardClipByReferenceCoordinatesRightTail() { public void testHardClipByReferenceCoordinatesRightTail() {
init();
logger.warn("Executing testHardClipByReferenceCoordinatesRightTail"); logger.warn("Executing testHardClipByReferenceCoordinatesRightTail");
//Clip whole read //Clip whole read
Assert.assertEquals(readClipper.hardClipByReferenceCoordinatesRightTail(1), new GATKSAMRecord(read.getHeader())); Assert.assertEquals(readClipper.hardClipByReferenceCoordinatesRightTail(1), new GATKSAMRecord(read.getHeader()));
//clip 1 base at end List<testParameter> testList = new LinkedList<testParameter>();
expected = readClipper.hardClipByReferenceCoordinatesRightTail(3); testList.add(new testParameter(-1,4,0,3,"3M1H"));//clip 1 base at end
Assert.assertEquals(expected.getReadBases(), BASES.substring(0,3).getBytes()); testList.add(new testParameter(-1,3,0,2,"2M2H"));//clip 2 bases at end
Assert.assertEquals(expected.getBaseQualityString(), QUALS.substring(0,3));
Assert.assertEquals(expected.getCigarString(), "3M1H");
//clip 2 bases at end for ( testParameter p : testList ) {
expected = readClipper.hardClipByReferenceCoordinatesRightTail(2); init();
Assert.assertEquals(expected.getReadBases(), BASES.substring(0,2).getBytes()); //logger.warn("Testing Parameters: " + p.inputStop+","+p.substringStart+","+p.substringStop+","+p.cigar);
Assert.assertEquals(expected.getBaseQualityString(), QUALS.substring(0,2)); testIfEqual( readClipper.hardClipByReferenceCoordinatesRightTail(p.inputStop),
Assert.assertEquals(expected.getCigarString(), "2M2H"); BASES.substring(p.substringStart,p.substringStop).getBytes(),
QUALS.substring(p.substringStart,p.substringStop),
p.cigar );
}
} }
@Test ( enabled = false ) @Test ( enabled = false ) // TODO This function is returning null reads
public void testHardClipLowQualEnds() { public void testHardClipLowQualEnds() {
init();
logger.warn("Executing testHardClipByReferenceCoordinates"); logger.warn("Executing testHardClipByReferenceCoordinates");
@ -192,6 +226,7 @@ public class ReadClipperUnitTest extends BaseTest {
//clip 1 base at start //clip 1 base at start
expected = readClipper.hardClipLowQualEnds((byte)34); expected = readClipper.hardClipLowQualEnds((byte)34);
logger.warn(expected.getBaseQualities().toString()+","+expected.getBaseQualityString());
Assert.assertEquals(expected.getReadBases(), BASES.substring(1,4).getBytes()); Assert.assertEquals(expected.getReadBases(), BASES.substring(1,4).getBytes());
Assert.assertEquals(expected.getBaseQualityString(), QUALS.substring(1,4)); Assert.assertEquals(expected.getBaseQualityString(), QUALS.substring(1,4));
Assert.assertEquals(expected.getCigarString(), "1H3M"); Assert.assertEquals(expected.getCigarString(), "1H3M");
@ -203,10 +238,11 @@ public class ReadClipperUnitTest extends BaseTest {
Assert.assertEquals(expected.getCigarString(), "2H2M"); Assert.assertEquals(expected.getCigarString(), "2H2M");
// Reverse Quals sequence // Reverse Quals sequence
readClipper.getRead().setBaseQualityString("?5+!"); // 63,53,43,33 //readClipper.getRead().setBaseQualityString("?5+!"); // 63,53,43,33
//clip 1 base at end //clip 1 base at end
expected = readClipper.hardClipLowQualEnds((byte)34); expected = readClipper.hardClipLowQualEnds((byte)'!');
logger.warn(expected.getBaseQualities().toString()+","+expected.getBaseQualityString());
Assert.assertEquals(expected.getReadBases(), BASES.substring(0,3).getBytes()); Assert.assertEquals(expected.getReadBases(), BASES.substring(0,3).getBytes());
Assert.assertEquals(expected.getBaseQualityString(), QUALS.substring(0,3)); Assert.assertEquals(expected.getBaseQualityString(), QUALS.substring(0,3));
Assert.assertEquals(expected.getCigarString(), "3M1H"); Assert.assertEquals(expected.getCigarString(), "3M1H");
@ -220,4 +256,4 @@ public class ReadClipperUnitTest extends BaseTest {
// revert Qual sequence // revert Qual sequence
readClipper.getRead().setBaseQualityString(QUALS); readClipper.getRead().setBaseQualityString(QUALS);
} }
} }