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Remove ClippingOp UnitTests 

* all testing functionality is in the ReadClipperUnitTest, no need to double test.
* class and package naming cleanup
This commit is contained in:
Mauricio Carneiro 2011-12-18 12:26:06 -05:00
parent 1ead00cac5
commit 5b678e3b94
7 changed files with 23 additions and 88 deletions
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6
public/java/src/org/broadinstitute/sting/gatk/walkers/ClipReadsWalker.java
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@ -38,9 +38,9 @@ import org.broadinstitute.sting.gatk.io.StingSAMFileWriter;
import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.clipreads.ClippingOp;
import org.broadinstitute.sting.utils.clipreads.ClippingRepresentation;
import org.broadinstitute.sting.utils.clipreads.ReadClipper;
import org.broadinstitute.sting.utils.clipping.ClippingOp;
import org.broadinstitute.sting.utils.clipping.ClippingRepresentation;
import org.broadinstitute.sting.utils.clipping.ReadClipper;
import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.sting.utils.sam.ReadUtils;

2
public/java/src/org/broadinstitute/sting/utils/clipreads/ClippingOp.java → public/java/src/org/broadinstitute/sting/utils/clipping/ClippingOp.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.utils.clipreads;
package org.broadinstitute.sting.utils.clipping;
import com.google.java.contract.Requires;
import net.sf.samtools.Cigar;

2
public/java/src/org/broadinstitute/sting/utils/clipreads/ClippingRepresentation.java → public/java/src/org/broadinstitute/sting/utils/clipping/ClippingRepresentation.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.utils.clipreads;
package org.broadinstitute.sting.utils.clipping;
/**
* How should we represent a clipped bases in a read?

2
public/java/src/org/broadinstitute/sting/utils/clipreads/ReadClipper.java → public/java/src/org/broadinstitute/sting/utils/clipping/ReadClipper.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.utils.clipreads;
package org.broadinstitute.sting.utils.clipping;
import com.google.java.contract.Requires;
import net.sf.samtools.CigarElement;

8
public/java/test/org/broadinstitute/sting/utils/clipreads/ClipReadsTestUtils.java → public/java/test/org/broadinstitute/sting/utils/clipping/ReadClipperTestUtils.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.utils.clipreads;
package org.broadinstitute.sting.utils.clipping;
import net.sf.samtools.Cigar;
import net.sf.samtools.CigarElement;
@ -8,7 +8,9 @@ import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.testng.Assert;
import java.util.*;
import java.util.LinkedList;
import java.util.List;
import java.util.Stack;
/**
* Created by IntelliJ IDEA.
@ -17,7 +19,7 @@ import java.util.*;
* Time: 6:45 AM
* To change this template use File | Settings | File Templates.
*/
public class ClipReadsTestUtils {
public class ReadClipperTestUtils {
//Should contain all the utils needed for tests to mass produce
//reads, cigars, and other needed classes

24
public/java/test/org/broadinstitute/sting/utils/clipreads/ReadClipperUnitTest.java → public/java/test/org/broadinstitute/sting/utils/clipping/ReadClipperUnitTest.java
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@ -23,7 +23,7 @@
* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.utils.clipreads;
package org.broadinstitute.sting.utils.clipping;
import net.sf.samtools.Cigar;
import net.sf.samtools.CigarElement;
@ -50,13 +50,13 @@ public class ReadClipperUnitTest extends BaseTest {
@BeforeClass
public void init() {
cigarList = ClipReadsTestUtils.generateCigarList(maximumCigarSize);
cigarList = ReadClipperTestUtils.generateCigarList(maximumCigarSize);
}
@Test(enabled = true)
public void testHardClipBothEndsByReferenceCoordinates() {
for (Cigar cigar : cigarList) {
GATKSAMRecord read = ClipReadsTestUtils.makeReadFromCigar(cigar);
GATKSAMRecord read = ReadClipperTestUtils.makeReadFromCigar(cigar);
int alnStart = read.getAlignmentStart();
int alnEnd = read.getAlignmentEnd();
int readLength = alnStart - alnEnd;
@ -71,7 +71,7 @@ public class ReadClipperUnitTest extends BaseTest {
@Test(enabled = true)
public void testHardClipByReadCoordinates() {
for (Cigar cigar : cigarList) {
GATKSAMRecord read = ClipReadsTestUtils.makeReadFromCigar(cigar);
GATKSAMRecord read = ReadClipperTestUtils.makeReadFromCigar(cigar);
int readLength = read.getReadLength();
for (int i=0; i<readLength; i++) {
GATKSAMRecord clipLeft = (new ReadClipper(read)).hardClipByReadCoordinates(0, i);
@ -86,7 +86,7 @@ public class ReadClipperUnitTest extends BaseTest {
@Test(enabled = true)
public void testHardClipByReferenceCoordinates() {
for (Cigar cigar : cigarList) {
GATKSAMRecord read = ClipReadsTestUtils.makeReadFromCigar(cigar);
GATKSAMRecord read = ReadClipperTestUtils.makeReadFromCigar(cigar);
int alnStart = read.getAlignmentStart();
int alnEnd = read.getAlignmentEnd();
for (int i=alnStart; i<=alnEnd; i++) {
@ -108,7 +108,7 @@ public class ReadClipperUnitTest extends BaseTest {
@Test(enabled = true)
public void testHardClipByReferenceCoordinatesLeftTail() {
for (Cigar cigar : cigarList) {
GATKSAMRecord read = ClipReadsTestUtils.makeReadFromCigar(cigar);
GATKSAMRecord read = ReadClipperTestUtils.makeReadFromCigar(cigar);
int alnStart = read.getAlignmentStart();
int alnEnd = read.getAlignmentEnd();
if (ReadUtils.getRefCoordSoftUnclippedStart(read) == alnStart) { // we can't test left clipping if the read has hanging soft clips on the left side
@ -124,7 +124,7 @@ public class ReadClipperUnitTest extends BaseTest {
@Test(enabled = true)
public void testHardClipByReferenceCoordinatesRightTail() {
for (Cigar cigar : cigarList) {
GATKSAMRecord read = ClipReadsTestUtils.makeReadFromCigar(cigar);
GATKSAMRecord read = ReadClipperTestUtils.makeReadFromCigar(cigar);
int alnStart = read.getAlignmentStart();
int alnEnd = read.getAlignmentEnd();
if (ReadUtils.getRefCoordSoftUnclippedEnd(read) == alnEnd) { // we can't test right clipping if the read has hanging soft clips on the right side
@ -144,7 +144,7 @@ public class ReadClipperUnitTest extends BaseTest {
// create a read for every cigar permutation
for (Cigar cigar : cigarList) {
GATKSAMRecord read = ClipReadsTestUtils.makeReadFromCigar(cigar);
GATKSAMRecord read = ReadClipperTestUtils.makeReadFromCigar(cigar);
int readLength = read.getReadLength();
byte [] quals = new byte[readLength];
@ -216,7 +216,7 @@ public class ReadClipperUnitTest extends BaseTest {
GATKSAMRecord expected = ArtificialSAMUtils.createArtificialRead(CLIPPED_BASES, CLIPPED_QUALS, CLIPPED_CIGAR);
ReadClipper lowQualClipper = new ReadClipper(read);
ClipReadsTestUtils.assertEqualReads(lowQualClipper.hardClipLowQualEnds((byte) 2), expected);
ReadClipperTestUtils.assertEqualReads(lowQualClipper.hardClipLowQualEnds((byte) 2), expected);
}
@Test(enabled = true)
@ -224,7 +224,7 @@ public class ReadClipperUnitTest extends BaseTest {
// Generate a list of cigars to test
for (Cigar cigar : cigarList) {
GATKSAMRecord read = ClipReadsTestUtils.makeReadFromCigar(cigar);
GATKSAMRecord read = ReadClipperTestUtils.makeReadFromCigar(cigar);
ReadClipper readClipper = new ReadClipper(read);
GATKSAMRecord clippedRead = readClipper.hardClipSoftClippedBases();
@ -276,12 +276,12 @@ public class ReadClipperUnitTest extends BaseTest {
public void testHardClipLeadingInsertions() {
for (Cigar cigar : cigarList) {
if (startsWithInsertion(cigar)) {
GATKSAMRecord read = ClipReadsTestUtils.makeReadFromCigar(cigar);
GATKSAMRecord read = ReadClipperTestUtils.makeReadFromCigar(cigar);
GATKSAMRecord clippedRead = (new ReadClipper(read)).hardClipLeadingInsertions();
int expectedLength = read.getReadLength() - leadingInsertionLength(read.getCigar());
if (cigarHasElementsDifferentThanInsertionsAndHardClips(read.getCigar()))
expectedLength -= leadingInsertionLength(ClipReadsTestUtils.invertCigar(read.getCigar()));
expectedLength -= leadingInsertionLength(ReadClipperTestUtils.invertCigar(read.getCigar()));
if (! clippedRead.isEmpty()) {
Assert.assertEquals(expectedLength, clippedRead.getReadLength(), String.format("%s -> %s", read.getCigarString(), clippedRead.getCigarString())); // check that everything else is still there

67
public/java/test/org/broadinstitute/sting/utils/clipreads/ClippingOpUnitTest.java
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@ -1,67 +0,0 @@
package org.broadinstitute.sting.utils.clipreads;
import org.broadinstitute.sting.BaseTest;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.testng.annotations.BeforeTest;
import org.testng.annotations.Test;
/**
* Created by IntelliJ IDEA.
* User: roger
* Date: 11/27/11
* Time: 5:17 AM
* To change this template use File | Settings | File Templates.
*/
public class ClippingOpUnitTest extends BaseTest {
ClippingOp clippingOp;
GATKSAMRecord read;
@BeforeTest
public void init() {
read = ClipReadsTestUtils.makeRead();
}
@Test
private void testHardClip() {
// List<TestParameter> testList = new LinkedList<TestParameter>();
// testList.add(new TestParameter(0, 0, 1, 4, "1H3M"));//clip 1 base at start
// testList.add(new TestParameter(3, 3, 0, 3, "3M1H"));//clip 1 base at end
// testList.add(new TestParameter(0, 1, 2, 4, "2H2M"));//clip 2 bases at start
// testList.add(new TestParameter(2, 3, 0, 2, "2M2H"));//clip 2 bases at end
// testList.add(new TestParameter(0, 2, 3, 4, "3H1M"));//clip 3 bases at start
// testList.add(new TestParameter(1, 3, 0, 1, "1M3H"));//clip 3 bases at end
//
// for (TestParameter p : testList) {
// init();
// clippingOp = new ClippingOp(p.inputStart, p.inputStop);
// logger.warn("Testing Parameters: " + p.inputStart + "," + p.inputStop + "," + p.substringStart + "," + p.substringStop + "," + p.cigar);
// ClipReadsTestUtils.testBaseQualCigar(clippingOp.apply(ClippingRepresentation.HARDCLIP_BASES, read),
// ClipReadsTestUtils.BASES.substring(p.substringStart, p.substringStop).getBytes(),
// ClipReadsTestUtils.QUALS.substring(p.substringStart, p.substringStop).getBytes(),
// p.cigar);
// }
}
@Test
private void testSoftClip() {
// List<TestParameter> testList = new LinkedList<TestParameter>();
// testList.add(new TestParameter(0, 0, -1, -1, "1S3M"));//clip 1 base at start
// testList.add(new TestParameter(3, 3, -1, -1, "3M1S"));//clip 1 base at end
// testList.add(new TestParameter(0, 1, -1, -1, "2S2M"));//clip 2 bases at start
// testList.add(new TestParameter(2, 3, -1, -1, "2M2S"));//clip 2 bases at end
// testList.add(new TestParameter(0, 2, -1, -1, "3S1M"));//clip 3 bases at start
// testList.add(new TestParameter(1, 3, -1, -1, "1M3S"));//clip 3 bases at end
//
// for (TestParameter p : testList) {
// init();
// clippingOp = new ClippingOp(p.inputStart, p.inputStop);
// logger.warn("Testing Parameters: " + p.inputStart + "," + p.inputStop + "," + p.cigar);
// ClipReadsTestUtils.testBaseQualCigar(clippingOp.apply(ClippingRepresentation.SOFTCLIP_BASES, read),
// ClipReadsTestUtils.BASES.getBytes(), ClipReadsTestUtils.QUALS.getBytes(), p.cigar);
// }
}
}