From 1d86bcea0e082418edadd5ac7627f24638c51878 Mon Sep 17 00:00:00 2001 From: Nils Homer Date: Thu, 18 May 2017 12:36:44 -0700 Subject: [PATCH 1/2] Adding the COVERED action to interval list tools. Find only intervals in INPUT that have any overlap with SECOND_INPUT --- src/main/java/picard/util/IntervalListTools.java | 12 +++++++----- 1 file changed, 7 insertions(+), 5 deletions(-) diff --git a/src/main/java/picard/util/IntervalListTools.java b/src/main/java/picard/util/IntervalListTools.java index f3aeca7c6..e2370c3d6 100644 --- a/src/main/java/picard/util/IntervalListTools.java +++ b/src/main/java/picard/util/IntervalListTools.java @@ -3,11 +3,7 @@ import htsjdk.samtools.SAMException; import htsjdk.samtools.SAMFileHeader; import htsjdk.samtools.SAMProgramRecord; -import htsjdk.samtools.util.CollectionUtil; -import htsjdk.samtools.util.IOUtil; -import htsjdk.samtools.util.Interval; -import htsjdk.samtools.util.IntervalList; -import htsjdk.samtools.util.Log; +import htsjdk.samtools.util.*; import htsjdk.variant.vcf.VCFFileReader; import picard.PicardException; import picard.cmdline.CommandLineParser; @@ -148,6 +144,12 @@ IntervalList act(final List list1, final List list2) IntervalList act(final List list1, final List list2) { return IntervalList.difference(list1, list2); } + }, + OVERLAPS("Find only intervals in INPUT that have any overlap with SECOND_INPUT") { + @Override + IntervalList act(final List list1, final List list2) { + return IntervalList.overlaps(list1, list2); + } }; String helpdoc; From cc1fed15fbb09595a49ae82c5b30833c27d2fd95 Mon Sep 17 00:00:00 2001 From: Nils Homer Date: Thu, 8 Jun 2017 10:46:30 -0700 Subject: [PATCH 2/2] Update htsjdk to 2.10.1 --- build.gradle | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/build.gradle b/build.gradle index 6e12edd5d..10447e69d 100644 --- a/build.gradle +++ b/build.gradle @@ -47,7 +47,7 @@ jacoco { toolVersion = "0.7.5.201505241946" } -final htsjdkVersion = System.getProperty('htsjdk.version', '2.10.0') +final htsjdkVersion = System.getProperty('htsjdk.version', '2.10.1') dependencies { compile 'com.google.guava:guava:15.0'