From ae660ddb746cc7931015dbeb4f4c220e611bcf33 Mon Sep 17 00:00:00 2001 From: Louis Bergelson Date: Mon, 11 Mar 2019 13:29:21 -0400 Subject: [PATCH] Adding back a removed method * Adding back an accidentally removed an overload of IntervalList.getUniqueIntervals(). * This fixes a compatibility problem revealed in the pre-release checks. --- src/main/java/htsjdk/samtools/util/IntervalList.java | 12 +++++++++++- 1 file changed, 11 insertions(+), 1 deletion(-) diff --git a/src/main/java/htsjdk/samtools/util/IntervalList.java b/src/main/java/htsjdk/samtools/util/IntervalList.java index 8b555b5142..47b3a1189c 100644 --- a/src/main/java/htsjdk/samtools/util/IntervalList.java +++ b/src/main/java/htsjdk/samtools/util/IntervalList.java @@ -257,10 +257,20 @@ public static List getUniqueIntervals(final IntervalList list, final b /** * Merges list of intervals and reduces them like htsjdk.samtools.util.IntervalList#getUniqueIntervals() * - * @param combineAbuttingIntervals If true, intervals that are abutting will be combined into one interval. * @param concatenateNames If false, the merged interval has the name of the earlier interval. This keeps name shorter. * @param enforceSameStrands enforce that merged intervals have the same strand, otherwise ignore. */ + public static List getUniqueIntervals(final IntervalList list, final boolean concatenateNames, final boolean enforceSameStrands) { + return getUniqueIntervals(list, true, concatenateNames, enforceSameStrands); + } + + /** + * Merges list of intervals and reduces them like htsjdk.samtools.util.IntervalList#getUniqueIntervals() + * + * @param combineAbuttingIntervals If true, intervals that are abutting will be combined into one interval. + * @param concatenateNames If false, the merged interval has the name of the earlier interval. This keeps name shorter. + * @param enforceSameStrands enforce that merged intervals have the same strand, otherwise ignore. + */ public static List getUniqueIntervals(final IntervalList list, final boolean combineAbuttingIntervals, final boolean concatenateNames, final boolean enforceSameStrands) { final List intervals;