From 116c923d4dd52e988e74a2012de513b15e2d5371 Mon Sep 17 00:00:00 2001
From: Tom White <tom.e.white@gmail.com>
Date: Mon, 28 Jan 2019 14:52:31 +0000
Subject: [PATCH 1/4] Test on Java 11

---
 .travis.yml                         | 13 ++++++++----
 pom.xml                             | 31 ++++++++++++++++++++++++++---
 src/build/conf/spotbugs-exclude.xml | 15 ++++++++++++++
 3 files changed, 52 insertions(+), 7 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index 82618d2..b43228d 100755
--- a/.travis.yml
+++ b/.travis.yml
@@ -1,12 +1,17 @@
 language: java
 sudo: required
-jdk:
-  - oraclejdk8
-  - openjdk8
+matrix:
+  include:
+    - jdk: oraclejdk8
+      env: JAVA_RELEASE=8 JAVA_VERSION=1.8 SCALA_VERSION=2.11
+    - jdk: openjdk8
+      env: JAVA_RELEASE=8 JAVA_VERSION=1.8 SCALA_VERSION=2.11
+    - jdk: openjdk11
+      env: JAVA_RELEASE=11 JAVA_VERSION=11 SCALA_VERSION=2.12
 env:
   - NO_GCE_CHECK=true
 script:
-  - mvn -B verify -Ddisq.test.real.world.files.dir=$TRAVIS_BUILD_DIR/gatk/src/test/resources/large -Ddisq.test.real.world.files.ref=$TRAVIS_BUILD_DIR/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta -Ddisq.samtools.bin=/usr/bin/samtools -Ddisq.bcftools.bin=/usr/bin/bcftools
+  - mvn -B verify -Djava.release=$JAVA_RELEASE -Djava.version=$JAVA_VERSION -Dscala.version=$SCALA_VERSION -Ddisq.test.real.world.files.dir=$TRAVIS_BUILD_DIR/gatk/src/test/resources/large -Ddisq.test.real.world.files.ref=$TRAVIS_BUILD_DIR/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta -Ddisq.samtools.bin=/usr/bin/samtools -Ddisq.bcftools.bin=/usr/bin/bcftools
 cache:
   directories:
     - $HOME/.m2
diff --git a/pom.xml b/pom.xml
index 0fbe8e1..ed9fe71 100644
--- a/pom.xml
+++ b/pom.xml
@@ -30,15 +30,17 @@
     </developers>
 
     <properties>
-        <maven.compiler.target>1.8</maven.compiler.target>
-        <maven.compiler.source>1.8</maven.compiler.source>
+        <java.release>8</java.release>
+        <java.version>1.8</java.version>
+        <maven.compiler.target>${java.version}</maven.compiler.target>
+        <maven.compiler.source>${java.version}</maven.compiler.source>
         <htsjdk.version>2.19.0</htsjdk.version>
         <hadoop.version>2.7.5</hadoop.version>
         <mockito.version>2.22.0</mockito.version>
         <kryo-serializers.version>0.42</kryo-serializers.version>
         <slf4j.version>1.7.25</slf4j.version>
         <scala.version>2.11</scala.version>
-        <spark.version>2.3.2</spark.version>
+        <spark.version>2.4.3</spark.version>
     </properties>
 
     <dependencies>
@@ -161,6 +163,11 @@
 
     <build>
         <plugins>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-compiler-plugin</artifactId>
+                <version>3.8.0</version>
+            </plugin>
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-enforcer-plugin</artifactId>
@@ -338,6 +345,24 @@
     </distributionManagement>
 
     <profiles>
+        <profile>
+            <id>java11</id>
+            <activation>
+                <jdk>11</jdk>
+            </activation>
+            <build>
+                <plugins>
+                    <plugin>
+                        <groupId>org.apache.maven.plugins</groupId>
+                        <artifactId>maven-compiler-plugin</artifactId>
+                        <version>3.8.0</version>
+                        <configuration>
+                            <release>${java.release}</release>
+                        </configuration>
+                    </plugin>
+                </plugins>
+            </build>
+        </profile>
         <profile>
             <id>release</id>
             <build>
diff --git a/src/build/conf/spotbugs-exclude.xml b/src/build/conf/spotbugs-exclude.xml
index 97f9adc..8e3defd 100644
--- a/src/build/conf/spotbugs-exclude.xml
+++ b/src/build/conf/spotbugs-exclude.xml
@@ -1,5 +1,20 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <FindBugsFilter>
+    <Match>
+        <!-- Java 11 false positive -->
+        <!-- https://github.com/spotbugs/spotbugs/issues/756 -->
+        <Bug pattern="RCN_REDUNDANT_NULLCHECK_WOULD_HAVE_BEEN_A_NPE" />
+    </Match>
+    <Match>
+        <!-- Java 11 false positive -->
+        <!-- https://github.com/spotbugs/spotbugs/issues/756 -->
+        <Or>
+            <Bug pattern="NP_LOAD_OF_KNOWN_NULL_VALUE" />
+            <Bug pattern="RCN_REDUNDANT_NULLCHECK_OF_NONNULL_VALUE" />
+            <Bug pattern="RCN_REDUNDANT_NULLCHECK_OF_NULL_VALUE" />
+        </Or>
+        <Class name="org.disq_bio.disq.impl.formats.cram.CramSource"/>
+    </Match>
     <Match>
         <Class name="org.disq_bio.disq.impl.file.SeekableByteChannelPrefetcher"/>
     </Match>

From 3a0406493998809a9dcddf987d5c55a310101ac9 Mon Sep 17 00:00:00 2001
From: Tom White <tom.e.white@gmail.com>
Date: Mon, 10 Jun 2019 10:31:56 +0100
Subject: [PATCH 2/4] NO_GCE_CHECK=true

---
 .travis.yml | 8 +++-----
 1 file changed, 3 insertions(+), 5 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index b43228d..bfeb9b6 100755
--- a/.travis.yml
+++ b/.travis.yml
@@ -3,13 +3,11 @@ sudo: required
 matrix:
   include:
     - jdk: oraclejdk8
-      env: JAVA_RELEASE=8 JAVA_VERSION=1.8 SCALA_VERSION=2.11
+      env: JAVA_RELEASE=8 JAVA_VERSION=1.8 SCALA_VERSION=2.11 NO_GCE_CHECK=true
     - jdk: openjdk8
-      env: JAVA_RELEASE=8 JAVA_VERSION=1.8 SCALA_VERSION=2.11
+      env: JAVA_RELEASE=8 JAVA_VERSION=1.8 SCALA_VERSION=2.11 NO_GCE_CHECK=true
     - jdk: openjdk11
-      env: JAVA_RELEASE=11 JAVA_VERSION=11 SCALA_VERSION=2.12
-env:
-  - NO_GCE_CHECK=true
+      env: JAVA_RELEASE=11 JAVA_VERSION=11 SCALA_VERSION=2.12 NO_GCE_CHECK=true
 script:
   - mvn -B verify -Djava.release=$JAVA_RELEASE -Djava.version=$JAVA_VERSION -Dscala.version=$SCALA_VERSION -Ddisq.test.real.world.files.dir=$TRAVIS_BUILD_DIR/gatk/src/test/resources/large -Ddisq.test.real.world.files.ref=$TRAVIS_BUILD_DIR/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta -Ddisq.samtools.bin=/usr/bin/samtools -Ddisq.bcftools.bin=/usr/bin/bcftools
 cache:

From 0f646f483b1bd5ee1df2321c5e30b9080368953f Mon Sep 17 00:00:00 2001
From: Tom White <tom.e.white@gmail.com>
Date: Tue, 2 Jul 2019 10:02:22 +0100
Subject: [PATCH 3/4] Revert "NO_GCE_CHECK=true"

This reverts commit 3a0406493998809a9dcddf987d5c55a310101ac9.
---
 .travis.yml | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index bfeb9b6..b43228d 100755
--- a/.travis.yml
+++ b/.travis.yml
@@ -3,11 +3,13 @@ sudo: required
 matrix:
   include:
     - jdk: oraclejdk8
-      env: JAVA_RELEASE=8 JAVA_VERSION=1.8 SCALA_VERSION=2.11 NO_GCE_CHECK=true
+      env: JAVA_RELEASE=8 JAVA_VERSION=1.8 SCALA_VERSION=2.11
     - jdk: openjdk8
-      env: JAVA_RELEASE=8 JAVA_VERSION=1.8 SCALA_VERSION=2.11 NO_GCE_CHECK=true
+      env: JAVA_RELEASE=8 JAVA_VERSION=1.8 SCALA_VERSION=2.11
     - jdk: openjdk11
-      env: JAVA_RELEASE=11 JAVA_VERSION=11 SCALA_VERSION=2.12 NO_GCE_CHECK=true
+      env: JAVA_RELEASE=11 JAVA_VERSION=11 SCALA_VERSION=2.12
+env:
+  - NO_GCE_CHECK=true
 script:
   - mvn -B verify -Djava.release=$JAVA_RELEASE -Djava.version=$JAVA_VERSION -Dscala.version=$SCALA_VERSION -Ddisq.test.real.world.files.dir=$TRAVIS_BUILD_DIR/gatk/src/test/resources/large -Ddisq.test.real.world.files.ref=$TRAVIS_BUILD_DIR/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta -Ddisq.samtools.bin=/usr/bin/samtools -Ddisq.bcftools.bin=/usr/bin/bcftools
 cache:

From 8b113bf3fb769f892e1dd43db8da56fdba550ee2 Mon Sep 17 00:00:00 2001
From: Tom White <tom.e.white@gmail.com>
Date: Tue, 2 Jul 2019 10:02:45 +0100
Subject: [PATCH 4/4] Global NO_GCE_CHECK=true

---
 .travis.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.travis.yml b/.travis.yml
index b43228d..32b6aad 100755
--- a/.travis.yml
+++ b/.travis.yml
@@ -9,7 +9,8 @@ matrix:
     - jdk: openjdk11
       env: JAVA_RELEASE=11 JAVA_VERSION=11 SCALA_VERSION=2.12
 env:
-  - NO_GCE_CHECK=true
+  global:
+    - NO_GCE_CHECK=true
 script:
   - mvn -B verify -Djava.release=$JAVA_RELEASE -Djava.version=$JAVA_VERSION -Dscala.version=$SCALA_VERSION -Ddisq.test.real.world.files.dir=$TRAVIS_BUILD_DIR/gatk/src/test/resources/large -Ddisq.test.real.world.files.ref=$TRAVIS_BUILD_DIR/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta -Ddisq.samtools.bin=/usr/bin/samtools -Ddisq.bcftools.bin=/usr/bin/bcftools
 cache: