From 5e3010fc83f15a32bdac9704543544a529de0172 Mon Sep 17 00:00:00 2001
From: JuanfeSanahuja <juanfe.sanahuja@zettagenomics.com>
Date: Thu, 7 Mar 2024 16:47:28 +0100
Subject: [PATCH 1/4] Prepare new development branch release-3.0.x

---
 biodata-external/pom.xml | 2 +-
 biodata-formats/pom.xml  | 2 +-
 biodata-models/pom.xml   | 2 +-
 biodata-tools/pom.xml    | 2 +-
 pom.xml                  | 4 ++--
 5 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/biodata-external/pom.xml b/biodata-external/pom.xml
index bf843117..b4501e0a 100644
--- a/biodata-external/pom.xml
+++ b/biodata-external/pom.xml
@@ -6,7 +6,7 @@
     <parent>
         <artifactId>biodata</artifactId>
         <groupId>org.opencb.biodata</groupId>
-        <version>3.0.0</version>
+        <version>3.1.0-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 
diff --git a/biodata-formats/pom.xml b/biodata-formats/pom.xml
index aaf09fd8..f562bcdf 100644
--- a/biodata-formats/pom.xml
+++ b/biodata-formats/pom.xml
@@ -22,7 +22,7 @@
     <parent>
         <groupId>org.opencb.biodata</groupId>
         <artifactId>biodata</artifactId>
-        <version>3.0.0</version>
+        <version>3.1.0-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 
diff --git a/biodata-models/pom.xml b/biodata-models/pom.xml
index aa53fa2c..f5dbb058 100644
--- a/biodata-models/pom.xml
+++ b/biodata-models/pom.xml
@@ -22,7 +22,7 @@
     <parent>
         <groupId>org.opencb.biodata</groupId>
         <artifactId>biodata</artifactId>
-        <version>3.0.0</version>
+        <version>3.1.0-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 
diff --git a/biodata-tools/pom.xml b/biodata-tools/pom.xml
index 29615312..2e7806d2 100644
--- a/biodata-tools/pom.xml
+++ b/biodata-tools/pom.xml
@@ -22,7 +22,7 @@
     <parent>
         <groupId>org.opencb.biodata</groupId>
         <artifactId>biodata</artifactId>
-        <version>3.0.0</version>
+        <version>3.1.0-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 
diff --git a/pom.xml b/pom.xml
index 61383366..de858078 100644
--- a/pom.xml
+++ b/pom.xml
@@ -22,7 +22,7 @@
 
     <groupId>org.opencb.biodata</groupId>
     <artifactId>biodata</artifactId>
-    <version>3.0.0</version>
+    <version>3.1.0-SNAPSHOT</version>
     <packaging>pom</packaging>
 
     <name>Biodata</name>
@@ -38,7 +38,7 @@
 
     <properties>
         <!-- All dependency versions must be defined here -->
-        <java-common-libs.version>5.0.0</java-common-libs.version>
+        <java-common-libs.version>5.1.0-SNAPSHOT</java-common-libs.version>
 
         <jackson.version>2.14.3</jackson.version>
         <collections.version>4.4</collections.version>

From 96c9e00c9ddb646f647bd29dbd74d6f61edd79ee Mon Sep 17 00:00:00 2001
From: JuanfeSanahuja <juanfe.sanahuja@zettagenomics.com>
Date: Tue, 26 Mar 2024 10:24:36 +0100
Subject: [PATCH 2/4] Create branch to test run.sh from opencga-enterprise
 #TASK-5605

---
 pom.xml | 5 -----
 1 file changed, 5 deletions(-)

diff --git a/pom.xml b/pom.xml
index de858078..c1ed8a30 100644
--- a/pom.xml
+++ b/pom.xml
@@ -230,11 +230,6 @@
                 <artifactId>commons-lang3</artifactId>
                 <version>${commons-lang.version}</version>
             </dependency>
-           <!-- <dependency>
-                <groupId>org.codehaus.jackson</groupId>
-                <artifactId>jackson-mapper-asl</artifactId>
-                <version>${jackson-mapper.version}</version>
-            </dependency>-->
             <dependency>
                 <groupId>org.apache.avro</groupId>
                 <artifactId>avro</artifactId>

From 6c7db0aee16a577682f56d24cdcd707287a5c012 Mon Sep 17 00:00:00 2001
From: JuanfeSanahuja <juanfe.sanahuja@zettagenomics.com>
Date: Wed, 10 Apr 2024 18:15:07 +0200
Subject: [PATCH 3/4] Temporaly fix test

---
 .../org/opencb/biodata/tools/variant/VcfManagerTest.java   | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/biodata-tools/src/test/java/org/opencb/biodata/tools/variant/VcfManagerTest.java b/biodata-tools/src/test/java/org/opencb/biodata/tools/variant/VcfManagerTest.java
index 1a4ac4c3..f75a2ae9 100644
--- a/biodata-tools/src/test/java/org/opencb/biodata/tools/variant/VcfManagerTest.java
+++ b/biodata-tools/src/test/java/org/opencb/biodata/tools/variant/VcfManagerTest.java
@@ -1,6 +1,7 @@
 package org.opencb.biodata.tools.variant;
 
 import htsjdk.variant.variantcontext.VariantContext;
+import org.junit.BeforeClass;
 import org.junit.Test;
 import org.opencb.biodata.models.core.Region;
 import org.opencb.biodata.models.variant.Variant;
@@ -13,6 +14,7 @@
 import java.nio.file.Path;
 import java.nio.file.Paths;
 import java.util.List;
+import java.util.Locale;
 
 import static org.junit.Assert.assertEquals;
 
@@ -22,6 +24,11 @@
 public class VcfManagerTest {
     String filename = "/ibs.vcf";
 
+    @BeforeClass
+    public static void setUp(){
+        Locale.setDefault(new Locale("en", "EN"));
+    }
+
     private Path index(VcfManager vcfManager) throws IOException {
         return vcfManager.createIndex();
     }

From 146f1b1afd30b8101f87c8183a84e94f4da2fbdb Mon Sep 17 00:00:00 2001
From: JuanfeSanahuja <juanfe.sanahuja@zettagenomics.com>
Date: Mon, 20 May 2024 15:37:02 +0200
Subject: [PATCH 4/4] Prepare release 3.1.0

---
 biodata-external/pom.xml | 2 +-
 biodata-formats/pom.xml  | 2 +-
 biodata-models/pom.xml   | 2 +-
 biodata-tools/pom.xml    | 2 +-
 pom.xml                  | 4 ++--
 5 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/biodata-external/pom.xml b/biodata-external/pom.xml
index b4501e0a..46b50c19 100644
--- a/biodata-external/pom.xml
+++ b/biodata-external/pom.xml
@@ -6,7 +6,7 @@
     <parent>
         <artifactId>biodata</artifactId>
         <groupId>org.opencb.biodata</groupId>
-        <version>3.1.0-SNAPSHOT</version>
+        <version>3.1.0</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 
diff --git a/biodata-formats/pom.xml b/biodata-formats/pom.xml
index f562bcdf..167e16df 100644
--- a/biodata-formats/pom.xml
+++ b/biodata-formats/pom.xml
@@ -22,7 +22,7 @@
     <parent>
         <groupId>org.opencb.biodata</groupId>
         <artifactId>biodata</artifactId>
-        <version>3.1.0-SNAPSHOT</version>
+        <version>3.1.0</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 
diff --git a/biodata-models/pom.xml b/biodata-models/pom.xml
index f5dbb058..fce0a389 100644
--- a/biodata-models/pom.xml
+++ b/biodata-models/pom.xml
@@ -22,7 +22,7 @@
     <parent>
         <groupId>org.opencb.biodata</groupId>
         <artifactId>biodata</artifactId>
-        <version>3.1.0-SNAPSHOT</version>
+        <version>3.1.0</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 
diff --git a/biodata-tools/pom.xml b/biodata-tools/pom.xml
index 2e7806d2..142deb3e 100644
--- a/biodata-tools/pom.xml
+++ b/biodata-tools/pom.xml
@@ -22,7 +22,7 @@
     <parent>
         <groupId>org.opencb.biodata</groupId>
         <artifactId>biodata</artifactId>
-        <version>3.1.0-SNAPSHOT</version>
+        <version>3.1.0</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 
diff --git a/pom.xml b/pom.xml
index c1ed8a30..8ae4a43a 100644
--- a/pom.xml
+++ b/pom.xml
@@ -22,7 +22,7 @@
 
     <groupId>org.opencb.biodata</groupId>
     <artifactId>biodata</artifactId>
-    <version>3.1.0-SNAPSHOT</version>
+    <version>3.1.0</version>
     <packaging>pom</packaging>
 
     <name>Biodata</name>
@@ -38,7 +38,7 @@
 
     <properties>
         <!-- All dependency versions must be defined here -->
-        <java-common-libs.version>5.1.0-SNAPSHOT</java-common-libs.version>
+        <java-common-libs.version>5.1.0</java-common-libs.version>
 
         <jackson.version>2.14.3</jackson.version>
         <collections.version>4.4</collections.version>