Release 3.5.1

hivdb · Sep 21, 2024 · 70c2444 · 70c2444
1 parent 8a2a862
commit 70c2444
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Showing 7 changed files with 8 additions and 7 deletions.
diff --git a/.latest-version b/.latest-version
@@ -1 +1 @@
-20240721011022
+20240921052047
diff --git a/build.gradle b/build.gradle
@@ -6,7 +6,7 @@ plugins {
 }
 
 group = 'edu.stanford.hivdb'
-version = '3.5.0'
+version = '3.5.1'
 
 sourceCompatibility = 15
 targetCompatibility = 15

diff --git a/hivfacts b/hivfacts
diff --git a/sierra-core b/sierra-core
diff --git a/sierra-tests/build.gradle b/sierra-tests/build.gradle
@@ -5,7 +5,7 @@ plugins {
 }
 
 group = 'edu.stanford.hivdb'
-version = '3.5.0'
+version = '3.5.1'
 
 description = """Sierra Unit Tests"""
 

diff --git a/sierra-tests/src/test/java/edu/stanford/hivdb/sequences/PostAlignAlignerTest.java b/sierra-tests/src/test/java/edu/stanford/hivdb/sequences/PostAlignAlignerTest.java
@@ -72,6 +72,7 @@ public void testSingleSequence() {
 			seqPR.getAlignedAAs()
 		);
 		AlignedGeneSeq<HIV> seqRT = alignedSeq.getAlignedGeneSequence(hiv.getGene("HIV1RT"));
+
 		assertEquals(1, seqRT.getFirstAA());
 		assertEquals(298, seqRT.getFirstNA());
 		assertEquals(230, seqRT.getLastAA());

diff --git a/src/main/resources/version.properties b/src/main/resources/version.properties
@@ -1,2 +1,2 @@
-version = 3.5.0
-versionDate = 2024-03-09
+version = 3.5.1
+versionDate = 2024-09-20
+1 −1		data/alignment-config_hiv1.yml
+1 −1		data/genotypes/genotype-references_hiv2.json
+1 −1		data/genotypes/genotype-references_hiv2.yml
+28 −3		hivfacts-java/src/main/java/edu/stanford/hivdb/hivfacts/HIVDefaultSequenceReadsValidator.java
+1 −1		hivfacts-java/src/main/java/edu/stanford/hivdb/hivfacts/hiv2/HIV2DefaultSequenceValidator.java
+1 −1		build.gradle
+12 −17		src/main/java/edu/stanford/hivdb/genotypes/Genotyper.java
+1 −0		src/main/java/edu/stanford/hivdb/seqreads/SequenceReads.java
+3 −3		src/main/java/edu/stanford/hivdb/seqreads/SequenceReadsAssembler.java
+4 −2		src/main/java/edu/stanford/hivdb/seqreads/SequenceReadsAssemblyRegion.java
+25 −5		src/main/java/edu/stanford/hivdb/sequences/AlignedGeneSeq.java
+7 −8		src/main/java/edu/stanford/hivdb/sequences/AlignedSequence.java
+3 −3		src/main/java/edu/stanford/hivdb/sequences/Aligner.java
+6 −5		src/main/java/edu/stanford/hivdb/sequences/SequenceAssembler.java
+13 −2		src/main/java/edu/stanford/hivdb/sequences/SequenceAssemblyRegion.java
+3 −9		src/main/java/edu/stanford/hivdb/utilities/FastaUtils.java
+9 −5		src/main/java/edu/stanford/hivdb/viruses/Assembler.java
+1 −1		src/main/java/edu/stanford/hivdb/viruses/AssemblyRegion.java