Upgrade to htsjdk 3.0.0. (#1812)

* Fix code GenotypeConcordance code that is sensitive to Allele ordering in sets. * Upgrade to htsjdk 3.0.0.
broadinstitute · Jun 8, 2022 · 09183c8 · 09183c8
1 parent fc91208
commit 09183c8
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Showing 3 changed files with 4 additions and 3 deletions.
diff --git a/build.gradle b/build.gradle
@@ -65,7 +65,7 @@ def ensureBuildPrerequisites(buildPrerequisitesMessage) {
 
 ensureBuildPrerequisites(buildPrerequisitesMessage)
 
-final htsjdkVersion = System.getProperty('htsjdk.version', '2.24.1')
+final htsjdkVersion = System.getProperty('htsjdk.version', '3.0.0')
 final googleNio = 'com.google.cloud:google-cloud-nio:0.123.25'
 
 // Get the jdk files we need to run javaDoc. We need to use these during compile, testCompile,

diff --git a/src/main/java/picard/vcf/GenotypeConcordance.java b/src/main/java/picard/vcf/GenotypeConcordance.java
@@ -71,6 +71,7 @@
 import java.util.HashMap;
 import java.util.HashSet;
 import java.util.Iterator;
+import java.util.LinkedHashSet;
 import java.util.List;
 import java.util.Map;
 import java.util.Optional;
@@ -534,7 +535,7 @@ private void writeVcfTuple(final VcfTuple tuple, final VariantContextWriter writ
             final List<Allele> callAlleles  = alleles.callAlleles();
 
             // Get the alleles present at this site for both samples to use for the output variant context, but remove no calls.
-            final Set<Allele> siteAlleles = new HashSet<>();
+            final Set<Allele> siteAlleles = new LinkedHashSet<>();
             siteAlleles.addAll(allAlleles);
             siteAlleles.remove(Allele.NO_CALL);
 

diff --git a/testdata/picard/vcf/spanningDeletionCallset_vs_spanningDeletionTruth.vcf b/testdata/picard/vcf/spanningDeletionCallset_vs_spanningDeletionTruth.vcf
@@ -90,5 +90,5 @@
 ##source=htsbox-pileup-r315
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	call	truth
 chr1	18359359	.	A	G,*	30	.	CONC_ST=TP	GT:AD	2|1:0,1,1	2|1:0,1,1
-chr1	18359383	.	AAAGGAAGG	GAAGGAAGG,A,*,AAAGGAAGGAAGG	216.73	.	CONC_ST=FP,FN	GT:AD:DP:GQ:MBQ:MFRL:MMQ:MPOS:PL	2/4:0,5,3:8:76:30,30:0,418,443:60,60:13,18:254,76,159,185,0,175	3|1:0,1,1
+chr1	18359383	.	AAAGGAAGG	*,GAAGGAAGG,A,AAAGGAAGGAAGG	216.73	.	CONC_ST=FP,FN	GT:AD:DP:GQ:MBQ:MFRL:MMQ:MPOS:PL	3/4:0,5,3:8:76:30,30:0,418,443:60,60:13,18:254,76,159,185,0,175	1|2:0,1,1
 chrX	27587985	.	AATATATAT	A,*	6939.56	.	CONC_ST=FP,FN	GT:AD:DP:GQ:PL	0/2:16,16,0,0:32:99:522,0,592,571,640,1210,571,640,1210,1210	1/1:0,20