diff --git a/src/main/java/picard/sam/markduplicates/MarkDuplicates.java b/src/main/java/picard/sam/markduplicates/MarkDuplicates.java index 51a744fe76..b1ad890eae 100644 --- a/src/main/java/picard/sam/markduplicates/MarkDuplicates.java +++ b/src/main/java/picard/sam/markduplicates/MarkDuplicates.java @@ -613,7 +613,6 @@ private void buildSortedReadEndLists(final boolean useBarcodes) { } pairedEnds.score += calcHelper.getReadDuplicateScore(rec, pairedEnds); - this.pairSort.add(pairedEnds); } } @@ -808,8 +807,7 @@ protected void handleChunk(List nextChunk) { } } - protected boolean areComparableForDuplicates(final ReadEndsForMarkDuplicates lhs, final ReadEndsForMarkDuplicates rhs, - final boolean compareRead2, final boolean useBarcodes) { + protected boolean areComparableForDuplicates(final ReadEndsForMarkDuplicates lhs, final ReadEndsForMarkDuplicates rhs, final boolean compareRead2, final boolean useBarcodes) { boolean areComparable = lhs.libraryId == rhs.libraryId; if (useBarcodes && areComparable) { // areComparable is useful here to avoid the casts below @@ -822,7 +820,7 @@ protected boolean areComparableForDuplicates(final ReadEndsForMarkDuplicates lhs if (areComparable) { areComparable = lhs.read1ReferenceIndex == rhs.read1ReferenceIndex && - lhs.read1Coordinate==rhs.read1Coordinate && + lhs.read1Coordinate == rhs.read1Coordinate && lhs.orientation == rhs.orientation; }