diff --git a/build.gradle b/build.gradle index 9e8f35154..25ca0c80a 100644 --- a/build.gradle +++ b/build.gradle @@ -136,7 +136,7 @@ task testSRA(type: Test) { task wrapper(type: Wrapper) { description = "Regenerate the gradle wrapper" - gradleVersion = '2.13' + gradleVersion = '3.2.1' } // This is a hack to disable the java 8 default javadoc lint until we fix the html formatting diff --git a/gradle/wrapper/gradle-wrapper.jar b/gradle/wrapper/gradle-wrapper.jar index ca78035ef..6ffa23784 100644 Binary files a/gradle/wrapper/gradle-wrapper.jar and b/gradle/wrapper/gradle-wrapper.jar differ diff --git a/gradle/wrapper/gradle-wrapper.properties b/gradle/wrapper/gradle-wrapper.properties index aad2b2428..7aff310b7 100644 --- a/gradle/wrapper/gradle-wrapper.properties +++ b/gradle/wrapper/gradle-wrapper.properties @@ -1,6 +1,6 @@ -#Fri May 13 14:00:35 EDT 2016 +#Tue Nov 29 15:10:15 EST 2016 distributionBase=GRADLE_USER_HOME distributionPath=wrapper/dists zipStoreBase=GRADLE_USER_HOME zipStorePath=wrapper/dists -distributionUrl=https\://services.gradle.org/distributions/gradle-2.13-bin.zip +distributionUrl=https\://services.gradle.org/distributions/gradle-3.2.1-bin.zip diff --git a/gradlew b/gradlew index 27309d923..9aa616c27 100755 --- a/gradlew +++ b/gradlew @@ -161,4 +161,9 @@ function splitJvmOpts() { eval splitJvmOpts $DEFAULT_JVM_OPTS $JAVA_OPTS $GRADLE_OPTS JVM_OPTS[${#JVM_OPTS[*]}]="-Dorg.gradle.appname=$APP_BASE_NAME" +# by default we should be in the correct project dir, but when run from Finder on Mac, the cwd is wrong +if [[ "$(uname)" == "Darwin" ]] && [[ "$HOME" == "$PWD" ]]; then + cd "$(dirname "$0")" +fi + exec "$JAVACMD" "${JVM_OPTS[@]}" -classpath "$CLASSPATH" org.gradle.wrapper.GradleWrapperMain "$@" diff --git a/settings.gradle b/settings.gradle new file mode 100644 index 000000000..95584da4a --- /dev/null +++ b/settings.gradle @@ -0,0 +1 @@ +rootProject.name = "htsjdk" diff --git a/src/main/java/htsjdk/samtools/util/SamLocusIterator.java b/src/main/java/htsjdk/samtools/util/SamLocusIterator.java index 7a60756d6..dc6745f5d 100644 --- a/src/main/java/htsjdk/samtools/util/SamLocusIterator.java +++ b/src/main/java/htsjdk/samtools/util/SamLocusIterator.java @@ -268,13 +268,13 @@ public void addInserted(final SAMRecord read, int firstPosition) { public List getInsertedInRecord() { return (insertedInRecord == null) ? Collections.emptyList() : Collections.unmodifiableList(insertedInRecord); } - - /** - * @return the number of records overlapping the position, with deletions included if they are being tracked. + + /** + * @return the number of records overlapping the position, with deletions included if they are being tracked. */ @Override - public int size() { - return super.size() + ((deletedInRecord == null) ? 0 : deletedInRecord.size()); + public int size() { + return super.size() + ((deletedInRecord == null) ? 0 : deletedInRecord.size()); } @@ -284,7 +284,7 @@ public int size() { */ @Override public boolean isEmpty() { - return getRecordAndPositions().isEmpty() && + return getRecordAndOffsets().isEmpty() && (deletedInRecord == null || deletedInRecord.isEmpty()) && (insertedInRecord == null || insertedInRecord.isEmpty()); } diff --git a/src/test/java/htsjdk/samtools/util/SamLocusIteratorTest.java b/src/test/java/htsjdk/samtools/util/SamLocusIteratorTest.java index 262b7c93f..5bcea40df 100644 --- a/src/test/java/htsjdk/samtools/util/SamLocusIteratorTest.java +++ b/src/test/java/htsjdk/samtools/util/SamLocusIteratorTest.java @@ -61,7 +61,7 @@ public void testBasicIterator() { int pos = startPosition; for (final SamLocusIterator.LocusInfo li : sli) { Assert.assertEquals(li.getPosition(), pos++); - Assert.assertEquals(li.getRecordAndPositions().size(), coverage); + Assert.assertEquals(li.getRecordAndOffsets().size(), coverage); Assert.assertEquals(li.size(), coverage); // make sure that we are not accumulating indels Assert.assertEquals(li.getDeletedInRecord().size(), 0); @@ -86,7 +86,7 @@ public void testMissingQualityString() { int pos = 165; for (final SamLocusIterator.LocusInfo li : sli) { Assert.assertEquals(li.getPosition(), pos++); - Assert.assertEquals(li.getRecordAndPositions().size(), 2); + Assert.assertEquals(li.getRecordAndOffsets().size(), 2); Assert.assertEquals(li.size(), 2); } } @@ -123,7 +123,7 @@ public void testEmitUncoveredLoci() { } else { expectedReads = 0; } - Assert.assertEquals(li.getRecordAndPositions().size(), expectedReads); + Assert.assertEquals(li.getRecordAndOffsets().size(), expectedReads); Assert.assertEquals(li.size(), expectedReads); // make sure that we are not accumulating indels Assert.assertEquals(li.getDeletedInRecord().size(), 0); @@ -161,7 +161,7 @@ public void testQualityFilter() { // make sure we accumulated depth coverage for even positions, coverage/2 for odd positions int pos = startPosition; for (final SamLocusIterator.LocusInfo li : sli) { - Assert.assertEquals(li.getRecordAndPositions().size(), (pos % 2 == 0) ? coverage / 2 : coverage); + Assert.assertEquals(li.getRecordAndOffsets().size(), (pos % 2 == 0) ? coverage / 2 : coverage); Assert.assertEquals(li.size(), (pos % 2 == 0) ? coverage / 2 : coverage); Assert.assertEquals(li.getPosition(), pos++); // make sure that we are not accumulating indels @@ -200,7 +200,7 @@ public void testSimpleDeletion() { Assert.assertEquals(li.getPosition(), pos++); if (isDeletedPosition) { // make sure there are no reads without indels - Assert.assertEquals(li.getRecordAndPositions().size(), 0); + Assert.assertEquals(li.getRecordAndOffsets().size(), 0); Assert.assertEquals(li.size(), coverage); // should include deletions // make sure that we are accumulating indels @@ -208,7 +208,7 @@ public void testSimpleDeletion() { Assert.assertEquals(li.getInsertedInRecord().size(), 0); } else { // make sure we are accumulating normal coverage - Assert.assertEquals(li.getRecordAndPositions().size(), coverage); + Assert.assertEquals(li.getRecordAndOffsets().size(), coverage); Assert.assertEquals(li.size(), coverage); // make sure that we are not accumulating indels @@ -241,7 +241,7 @@ public void testSimpleInsertion() { for (final SamLocusIterator.LocusInfo li : sli) { Assert.assertEquals(li.getPosition(), pos++); // make sure we are accumulating normal coverage - Assert.assertEquals(li.getRecordAndPositions().size(), coverage); + Assert.assertEquals(li.getRecordAndOffsets().size(), coverage); Assert.assertEquals(li.size(), coverage); // make sure that we are not accumulating deletions @@ -278,7 +278,7 @@ public void testStartWithInsertion() { for (final SamLocusIterator.LocusInfo li : sli) { Assert.assertEquals(li.getPosition(), pos); // accumulation of coverage - Assert.assertEquals(li.getRecordAndPositions().size(), (indelPosition) ? 0 : coverage); + Assert.assertEquals(li.getRecordAndOffsets().size(), (indelPosition) ? 0 : coverage); Assert.assertEquals(li.size(), (indelPosition) ? 0 : coverage); // no accumulation of deletions @@ -319,7 +319,7 @@ public void testStartWithSoftClipAndInsertion() { for (final SamLocusIterator.LocusInfo li : sli) { Assert.assertEquals(li.getPosition(), pos); // accumulation of coverage - Assert.assertEquals(li.getRecordAndPositions().size(), (indelPosition) ? 0 : coverage); + Assert.assertEquals(li.getRecordAndOffsets().size(), (indelPosition) ? 0 : coverage); Assert.assertEquals(li.size(), (indelPosition) ? 0 : coverage); // no accumulation of deletions Assert.assertEquals(li.getDeletedInRecord().size(), 0); @@ -364,7 +364,7 @@ public void testNBeforeInsertion() { } Assert.assertEquals(li.getPosition(), pos); // accumulation of coverage - Assert.assertEquals(li.getRecordAndPositions().size(), (pos == endN) ? 0 : coverage); + Assert.assertEquals(li.getRecordAndOffsets().size(), (pos == endN) ? 0 : coverage); Assert.assertEquals(li.size(), (pos == endN) ? 0 : coverage); // no accumulation of deletions Assert.assertEquals(li.getDeletedInRecord().size(), 0); @@ -416,7 +416,7 @@ public void testNBeforeDeletion() { final boolean insideDeletion = incIndels && (pos >= startDel && pos <= endDel); Assert.assertEquals(li.getPosition(), pos); // accumulation of coverage - Assert.assertEquals(li.getRecordAndPositions().size(), (insideDeletion) ? 0 : coverage); + Assert.assertEquals(li.getRecordAndOffsets().size(), (insideDeletion) ? 0 : coverage); Assert.assertEquals(li.size(), coverage); // either will be all deletions, or all non-deletions, but always of size `coverage`. // accumulation of deletions Assert.assertEquals(li.getDeletedInRecord().size(), (insideDeletion) ? coverage : 0); @@ -506,18 +506,18 @@ public void testSimpleGappedAlignment() { if (inDelRange) { // check the coverage for insertion and normal records Assert.assertEquals(li.getDeletedInRecord().size(), coverage); - Assert.assertEquals(li.getRecordAndPositions().size(), 0); + Assert.assertEquals(li.getRecordAndOffsets().size(), 0); Assert.assertEquals(li.size(), coverage); // includes deletions // check the offset for the deletion Assert.assertEquals(li.getDeletedInRecord().get(0).getOffset(), expectedReadOffsets[i]); Assert.assertEquals(li.getDeletedInRecord().get(1).getOffset(), expectedReadOffsets[i]); } else { // if it is not a deletion, perform the same test as before - Assert.assertEquals(li.getRecordAndPositions().size(), coverage); + Assert.assertEquals(li.getRecordAndOffsets().size(), coverage); Assert.assertEquals(li.size(), coverage); // Assert.assertEquals(li.getDeletedInRecord().size(), 0); - Assert.assertEquals(li.getRecordAndPositions().get(0).getOffset(), expectedReadOffsets[i]); - Assert.assertEquals(li.getRecordAndPositions().get(1).getOffset(), expectedReadOffsets[i]); + Assert.assertEquals(li.getRecordAndOffsets().get(0).getOffset(), expectedReadOffsets[i]); + Assert.assertEquals(li.getRecordAndOffsets().get(1).getOffset(), expectedReadOffsets[i]); } ++i; } @@ -576,12 +576,12 @@ public void testOverlappingGappedAlignmentsWithoutIndels() { i = 0; for (final SamLocusIterator.LocusInfo li : sli) { - Assert.assertEquals(li.getRecordAndPositions().size(), expectedDepths[i]); + Assert.assertEquals(li.getRecordAndOffsets().size(), expectedDepths[i]); Assert.assertEquals(li.size(), expectedDepths[i]); Assert.assertEquals(li.getPosition(), expectedReferencePositions[i]); - Assert.assertEquals(li.getRecordAndPositions().size(), expectedReadOffsets[i].length); + Assert.assertEquals(li.getRecordAndOffsets().size(), expectedReadOffsets[i].length); for (int j = 0; j < expectedReadOffsets[i].length; ++j) { - Assert.assertEquals(li.getRecordAndPositions().get(j).getOffset(), expectedReadOffsets[i][j]); + Assert.assertEquals(li.getRecordAndOffsets().get(j).getOffset(), expectedReadOffsets[i][j]); } // make sure that we are not accumulating indels Assert.assertEquals(li.getDeletedInRecord().size(), 0); @@ -652,12 +652,12 @@ public void testOverlappingGappedAlignmentsWithIndels() { i = 0; for (final SamLocusIterator.LocusInfo li : sli) { // checking the same as without indels - Assert.assertEquals(li.getRecordAndPositions().size(), expectedDepths[i]); + Assert.assertEquals(li.getRecordAndOffsets().size(), expectedDepths[i]); Assert.assertEquals(li.size(), expectedDepths[i] + expectedDelDepths[i]); // include deletions Assert.assertEquals(li.getPosition(), expectedReferencePositions[i]); - Assert.assertEquals(li.getRecordAndPositions().size(), expectedReadOffsets[i].length); + Assert.assertEquals(li.getRecordAndOffsets().size(), expectedReadOffsets[i].length); for (int j = 0; j < expectedReadOffsets[i].length; ++j) { - Assert.assertEquals(li.getRecordAndPositions().get(j).getOffset(), expectedReadOffsets[i][j]); + Assert.assertEquals(li.getRecordAndOffsets().get(j).getOffset(), expectedReadOffsets[i][j]); } // check the deletions Assert.assertEquals(li.getDeletedInRecord().size(), expectedDelDepths[i]); @@ -670,4 +670,4 @@ public void testOverlappingGappedAlignmentsWithIndels() { } } -} \ No newline at end of file +}