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Made all class methods private in the ReadClipper 

* ReadClipperUnitTest now uses static methods
 * Haplotype caller now uses static methods
 * Exon Junction Genotyper now uses static methods
This commit is contained in:
Mauricio Carneiro 2011-12-27 01:29:13 -05:00
parent ce493bf257
commit 17bfe48d5e
3 changed files with 24 additions and 27 deletions
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3
public/java/src/org/broadinstitute/sting/gatk/walkers/ClipReadsWalker.java
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@ -43,7 +43,6 @@ 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;
import java.io.File;
import java.io.PrintStream;
@ -300,7 +299,7 @@ public class ClipReadsWalker extends ReadWalker<ClipReadsWalker.ReadClipperWithD
public ReadClipperWithData map(ReferenceContext ref, GATKSAMRecord read, ReadMetaDataTracker metaDataTracker) {
if ( onlyDoRead == null || read.getReadName().equals(onlyDoRead) ) {
if ( clippingRepresentation == ClippingRepresentation.HARDCLIP_BASES )
read = (new ReadClipper(read)).revertSoftClippedBases();
read = ReadClipper.revertSoftClippedBases(read);
ReadClipperWithData clipper = new ReadClipperWithData(read, sequencesToClip);
//

18
public/java/src/org/broadinstitute/sting/utils/clipping/ReadClipper.java
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@ -151,7 +151,7 @@ public class ReadClipper {
* @return a new read, without the left tail.
*/
@Requires("!read.getReadUnmappedFlag()") // can't handle unmapped reads, as we're using reference coordinates to clip
public GATKSAMRecord hardClipByReferenceCoordinatesLeftTail(int refStop) {
private GATKSAMRecord hardClipByReferenceCoordinatesLeftTail(int refStop) {
return hardClipByReferenceCoordinates(-1, refStop);
}
public static GATKSAMRecord hardClipByReferenceCoordinatesLeftTail(GATKSAMRecord read, int refStop) {
@ -168,7 +168,7 @@ public class ReadClipper {
* @return a new read, without the right tail.
*/
@Requires("!read.getReadUnmappedFlag()") // can't handle unmapped reads, as we're using reference coordinates to clip
public GATKSAMRecord hardClipByReferenceCoordinatesRightTail(int refStart) {
private GATKSAMRecord hardClipByReferenceCoordinatesRightTail(int refStart) {
return hardClipByReferenceCoordinates(refStart, -1);
}
public static GATKSAMRecord hardClipByReferenceCoordinatesRightTail(GATKSAMRecord read, int refStart) {
@ -184,7 +184,7 @@ public class ReadClipper {
*/
@Requires({"start >= 0 && stop <= read.getReadLength() - 1", // start and stop have to be within the read
"start == 0 || stop == read.getReadLength() - 1"}) // cannot clip the middle of the read
public GATKSAMRecord hardClipByReadCoordinates(int start, int stop) {
private GATKSAMRecord hardClipByReadCoordinates(int start, int stop) {
if (read.isEmpty() || (start == 0 && stop == read.getReadLength() - 1))
return new GATKSAMRecord(read.getHeader());
@ -208,7 +208,7 @@ public class ReadClipper {
@Requires({"left <= right", // tails cannot overlap
"left >= read.getAlignmentStart()", // coordinate has to be within the mapped read
"right <= read.getAlignmentEnd()"}) // coordinate has to be within the mapped read
public GATKSAMRecord hardClipBothEndsByReferenceCoordinates(int left, int right) {
private GATKSAMRecord hardClipBothEndsByReferenceCoordinates(int left, int right) {
if (read.isEmpty() || left == right)
return new GATKSAMRecord(read.getHeader());
GATKSAMRecord leftTailRead = hardClipByReferenceCoordinates(right, -1);
@ -235,7 +235,7 @@ public class ReadClipper {
* @param lowQual every base quality lower than or equal to this in the tail of the read will be hard clipped
* @return a new read without low quality tails
*/
public GATKSAMRecord hardClipLowQualEnds(byte lowQual) {
private GATKSAMRecord hardClipLowQualEnds(byte lowQual) {
if (read.isEmpty())
return read;
@ -269,7 +269,7 @@ public class ReadClipper {
*
* @return a new read without the soft clipped bases
*/
public GATKSAMRecord hardClipSoftClippedBases () {
private GATKSAMRecord hardClipSoftClippedBases () {
if (read.isEmpty())
return read;
@ -314,7 +314,7 @@ public class ReadClipper {
*
* @return a new read without adaptor sequence
*/
public GATKSAMRecord hardClipAdaptorSequence () {
private GATKSAMRecord hardClipAdaptorSequence () {
final Integer adaptorBoundary = ReadUtils.getAdaptorBoundary(read);
if (adaptorBoundary == null || !ReadUtils.isInsideRead(read, adaptorBoundary))
@ -332,7 +332,7 @@ public class ReadClipper {
*
* @return a new read without leading insertions
*/
public GATKSAMRecord hardClipLeadingInsertions() {
private GATKSAMRecord hardClipLeadingInsertions() {
if (read.isEmpty())
return read;
@ -357,7 +357,7 @@ public class ReadClipper {
*
* @return a new read with every soft clip turned into a match
*/
public GATKSAMRecord revertSoftClippedBases() {
private GATKSAMRecord revertSoftClippedBases() {
this.addOp(new ClippingOp(0, 0)); // UNSOFTCLIP_BASES doesn't need coordinates
return this.clipRead(ClippingRepresentation.REVERT_SOFTCLIPPED_BASES);
}

30
public/java/test/org/broadinstitute/sting/utils/clipping/ReadClipperUnitTest.java
View File

@ -60,7 +60,7 @@ public class ReadClipperUnitTest extends BaseTest {
int alnEnd = read.getAlignmentEnd();
int readLength = alnStart - alnEnd;
for (int i=0; i<readLength/2; i++) {
GATKSAMRecord clippedRead = (new ReadClipper(read)).hardClipBothEndsByReferenceCoordinates(alnStart + i, alnEnd - i);
GATKSAMRecord clippedRead = ReadClipper.hardClipBothEndsByReferenceCoordinates(read, alnStart + i, alnEnd - i);
Assert.assertTrue(clippedRead.getAlignmentStart() >= alnStart + i, String.format("Clipped alignment start is less than original read (minus %d): %s -> %s", i, read.getCigarString(), clippedRead.getCigarString()));
Assert.assertTrue(clippedRead.getAlignmentEnd() <= alnEnd + i, String.format("Clipped alignment end is greater than original read (minus %d): %s -> %s", i, read.getCigarString(), clippedRead.getCigarString()));
}
@ -73,10 +73,10 @@ public class ReadClipperUnitTest extends BaseTest {
GATKSAMRecord read = ReadClipperTestUtils.makeReadFromCigar(cigar);
int readLength = read.getReadLength();
for (int i=0; i<readLength; i++) {
GATKSAMRecord clipLeft = (new ReadClipper(read)).hardClipByReadCoordinates(0, i);
GATKSAMRecord clipLeft = ReadClipper.hardClipByReadCoordinates(read, 0, i);
Assert.assertTrue(clipLeft.getReadLength() <= readLength - i, String.format("Clipped read length is greater than original read length (minus %d): %s -> %s", i, read.getCigarString(), clipLeft.getCigarString()));
GATKSAMRecord clipRight = (new ReadClipper(read)).hardClipByReadCoordinates(i, readLength-1);
GATKSAMRecord clipRight = ReadClipper.hardClipByReadCoordinates(read, i, readLength-1);
Assert.assertTrue(clipRight.getReadLength() <= i, String.format("Clipped read length is greater than original read length (minus %d): %s -> %s", i, read.getCigarString(), clipRight.getCigarString()));
}
}
@ -112,7 +112,7 @@ public class ReadClipperUnitTest extends BaseTest {
int alnEnd = read.getAlignmentEnd();
if (read.getSoftStart() == alnStart) { // we can't test left clipping if the read has hanging soft clips on the left side
for (int i=alnStart; i<=alnEnd; i++) {
GATKSAMRecord clipLeft = (new ReadClipper(read)).hardClipByReferenceCoordinates(alnStart, i);
GATKSAMRecord clipLeft = ReadClipper.hardClipByReferenceCoordinatesLeftTail(read, i);
if (!clipLeft.isEmpty())
Assert.assertTrue(clipLeft.getAlignmentStart() >= i + 1, String.format("Clipped alignment start (%d) is less the expected (%d): %s -> %s", clipLeft.getAlignmentStart(), i + 1, read.getCigarString(), clipLeft.getCigarString()));
}
@ -126,9 +126,9 @@ public class ReadClipperUnitTest extends BaseTest {
GATKSAMRecord read = ReadClipperTestUtils.makeReadFromCigar(cigar);
int alnStart = read.getAlignmentStart();
int alnEnd = read.getAlignmentEnd();
if (read.getSoftEnd() == alnEnd) { // we can't test right clipping if the read has hanging soft clips on the right side
if (read.getSoftEnd() == alnEnd) { // we can't test right clipping if the read has hanging soft clips on the right side
for (int i=alnStart; i<=alnEnd; i++) {
GATKSAMRecord clipRight = (new ReadClipper(read)).hardClipByReferenceCoordinates(i, alnEnd);
GATKSAMRecord clipRight = ReadClipper.hardClipByReferenceCoordinatesRightTail(read, i);
if (!clipRight.isEmpty() && clipRight.getAlignmentStart() <= clipRight.getAlignmentEnd()) // alnStart > alnEnd if the entire read is a soft clip now. We can't test those.
Assert.assertTrue(clipRight.getAlignmentEnd() <= i - 1, String.format("Clipped alignment end (%d) is greater than expected (%d): %s -> %s", clipRight.getAlignmentEnd(), i - 1, read.getCigarString(), clipRight.getCigarString()));
}
@ -154,7 +154,7 @@ public class ReadClipperUnitTest extends BaseTest {
for (int addLeft = 0; addLeft < nLowQualBases; addLeft++)
quals[addLeft] = LOW_QUAL;
read.setBaseQualities(quals);
GATKSAMRecord clipLeft = (new ReadClipper(read)).hardClipLowQualEnds(LOW_QUAL);
GATKSAMRecord clipLeft = ReadClipper.hardClipLowQualEnds(read, LOW_QUAL);
// Tests
@ -162,14 +162,14 @@ public class ReadClipperUnitTest extends BaseTest {
assertNoLowQualBases(clipLeft, LOW_QUAL);
// Can't run this test with the current contract of no hanging insertions
//Assert.assertEquals(clipLeft.getReadLength(), readLength - nLowQualBases, String.format("Clipped read size (%d) is different than the number high qual bases (%d) -- Cigars: %s -> %s", clipLeft.getReadLength(), readLength - nLowQualBases, read.getCigarString(), clipLeft.getCigarString()));
// Assert.assertEquals(clipLeft.getReadLength(), readLength - nLowQualBases, String.format("Clipped read size (%d) is different than the number high qual bases (%d) -- Cigars: %s -> %s", clipLeft.getReadLength(), readLength - nLowQualBases, read.getCigarString(), clipLeft.getCigarString()));
// create a read with nLowQualBases in the right tail
Utils.fillArrayWithByte(quals, HIGH_QUAL);
for (int addRight = 0; addRight < nLowQualBases; addRight++)
quals[readLength - addRight - 1] = LOW_QUAL;
read.setBaseQualities(quals);
GATKSAMRecord clipRight = (new ReadClipper(read)).hardClipLowQualEnds(LOW_QUAL);
GATKSAMRecord clipRight = ReadClipper.hardClipLowQualEnds(read, LOW_QUAL);
// Tests
@ -187,7 +187,7 @@ public class ReadClipperUnitTest extends BaseTest {
quals[readLength - addBoth - 1] = LOW_QUAL;
}
read.setBaseQualities(quals);
GATKSAMRecord clipBoth = (new ReadClipper(read)).hardClipLowQualEnds(LOW_QUAL);
GATKSAMRecord clipBoth = ReadClipper.hardClipLowQualEnds(read, LOW_QUAL);
// Tests
@ -214,8 +214,7 @@ public class ReadClipperUnitTest extends BaseTest {
GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(BASES, QUALS, CIGAR);
GATKSAMRecord expected = ArtificialSAMUtils.createArtificialRead(CLIPPED_BASES, CLIPPED_QUALS, CLIPPED_CIGAR);
ReadClipper lowQualClipper = new ReadClipper(read);
ReadClipperTestUtils.assertEqualReads(lowQualClipper.hardClipLowQualEnds((byte) 2), expected);
ReadClipperTestUtils.assertEqualReads(ReadClipper.hardClipLowQualEnds(read, (byte) 2), expected);
}
@Test(enabled = true)
@ -224,8 +223,7 @@ public class ReadClipperUnitTest extends BaseTest {
// Generate a list of cigars to test
for (Cigar cigar : cigarList) {
GATKSAMRecord read = ReadClipperTestUtils.makeReadFromCigar(cigar);
ReadClipper readClipper = new ReadClipper(read);
GATKSAMRecord clippedRead = readClipper.hardClipSoftClippedBases();
GATKSAMRecord clippedRead = ReadClipper.hardClipSoftClippedBases(read);
int sumHardClips = 0;
int sumMatches = 0;
@ -276,7 +274,7 @@ public class ReadClipperUnitTest extends BaseTest {
for (Cigar cigar : cigarList) {
if (startsWithInsertion(cigar)) {
GATKSAMRecord read = ReadClipperTestUtils.makeReadFromCigar(cigar);
GATKSAMRecord clippedRead = (new ReadClipper(read)).hardClipLeadingInsertions();
GATKSAMRecord clippedRead = ReadClipper.hardClipLeadingInsertions(read);
int expectedLength = read.getReadLength() - leadingCigarElementLength(read.getCigar(), CigarOperator.INSERTION);
if (cigarHasElementsDifferentThanInsertionsAndHardClips(read.getCigar()))
@ -300,7 +298,7 @@ public class ReadClipperUnitTest extends BaseTest {
final int tailSoftClips = leadingCigarElementLength(ReadClipperTestUtils.invertCigar(cigar), CigarOperator.SOFT_CLIP);
final GATKSAMRecord read = ReadClipperTestUtils.makeReadFromCigar(cigar);
final GATKSAMRecord unclipped = (new ReadClipper(read)).revertSoftClippedBases();
final GATKSAMRecord unclipped = ReadClipper.revertSoftClippedBases(read);
if ( leadingSoftClips > 0 || tailSoftClips > 0) {
final int expectedStart = read.getAlignmentStart() - leadingSoftClips;