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- responding to reviewer's comments.

This commit is contained in:
Yossi Farjoun 2017-06-28 16:40:55 -04:00
parent 741c544fbf
commit d535c377b5
2 changed files with 3 additions and 3 deletions
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2
public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/clipping/ReadClipper.java
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@ -395,7 +395,7 @@ public class ReadClipper {
/** /**
* Checks if a read contains adaptor sequences. If it does, hard clips them out. * Checks if a read contains adaptor sequences. If it does, hard clips them out.
* *
* Note: To see how a read is checked for adaptor sequence see ReadUtils.getAdaptorBoundary() * Note: To see how a read is checked for adaptor sequence see {@link ReadUtils::getAdaptorBoundary}
* *
* @return a new read without adaptor sequence * @return a new read without adaptor sequence
*/ */

4
public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ReadUtilsUnitTest.java
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@ -25,8 +25,8 @@
package org.broadinstitute.gatk.utils.sam; package org.broadinstitute.gatk.utils.sam;
import htsjdk.samtools.SAMReadGroupRecord;
import htsjdk.samtools.SAMFileHeader; import htsjdk.samtools.SAMFileHeader;
import htsjdk.samtools.SAMReadGroupRecord;
import htsjdk.samtools.reference.ReferenceSequenceFile; import htsjdk.samtools.reference.ReferenceSequenceFile;
import org.broadinstitute.gatk.utils.BaseTest; import org.broadinstitute.gatk.utils.BaseTest;
import org.broadinstitute.gatk.utils.BaseUtils; import org.broadinstitute.gatk.utils.BaseUtils;
@ -335,7 +335,7 @@ public class ReadUtilsUnitTest extends BaseTest {
} }
@Test(dataProvider = "HasWellDefinedFragmentSizeData") @Test(dataProvider = "HasWellDefinedFragmentSizeData")
private void testHasWellDefinedFragmentSize(final String name, final GATKSAMRecord read, final boolean expected) { public void testHasWellDefinedFragmentSize(final String name, final GATKSAMRecord read, final boolean expected) {
Assert.assertEquals(ReadUtils.hasWellDefinedFragmentSize(read), expected); Assert.assertEquals(ReadUtils.hasWellDefinedFragmentSize(read), expected);
} }