Merge pull request #160 from PolinaBevad/add_java_11_support

Add Java 11 support

Author: pcingola

.travis.yml

@@ -8,9 +8,10 @@ cache:
     - $HOME/.gradle/wrapper/
 jdk:
   - oraclejdk8
-  - oraclejdk10
+  - oraclejdk11
   - openjdk8
   - openjdk10
+  - openjdk11
 script:
   - ./gradlew test jacocoTestReport
   - ./gradlew installDist

VarDict

@@ -27,12 +27,8 @@ dependencies {
     compile('com.github.samtools:htsjdk:2.8.0') {
         transitive = false
     }
-    // https://mvnrepository.com/artifact/org.powermock/powermock-module-junit4
-    testCompile group: 'org.powermock', name: 'powermock-api-mockito2', version: '2.0.0-beta.5'
-    testCompile group: 'org.powermock', name: 'powermock-module-testng', version: '2.0.0-beta.5'
+    testCompile 'org.mockito:mockito-core:2.23.0'
     testCompile 'org.testng:testng:6.9.13.6'
-    testCompile 'net.bytebuddy:byte-buddy:1.8.3'
-    testCompile 'net.bytebuddy:byte-buddy-agent:1.8.3'
 }
 
 mainClassName = "com.astrazeneca.vardict.Main"
@@ -74,4 +70,7 @@ jar {
     }
 }
 
+jacoco {
+    toolVersion = "0.8.2"
+}
 applicationDistribution.from('VarDict/teststrandbias.R','VarDict/testsomatic.R','VarDict/var2vcf_valid.pl','VarDict/var2vcf_paired.pl').into('bin')

build.gradle

@@ -3,4 +3,4 @@ distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-4.8-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-4.10.2-bin.zip

gradle/wrapper/gradle-wrapper.properties

@@ -28,7 +28,11 @@ public static void main(String[] args) throws ParseException, IOException {
             if (cmd.getOptions().length == 0 || cmd.hasOption("H")) {
                 help(options);
             }
-            new Main().run(cmd);
+            Configuration conf = new Main().run(cmd);
+
+            ReferenceResource referenceResource = new ReferenceResource();
+            VarDict varDict = new VarDict(conf, referenceResource);
+            varDict.start();
         } catch (MissingOptionException e) {
             List<?> missingOptions = e.getMissingOptions();
             System.err.print("Missing required option(s): ");
@@ -45,7 +49,7 @@ public static void main(String[] args) throws ParseException, IOException {
         }
     }
 
-    private void run(CommandLine cmd) throws ParseException, IOException {
+    public Configuration run(CommandLine cmd) throws ParseException, IOException {
         Configuration conf = new Configuration();
 
         // -v is not used
@@ -150,8 +154,7 @@ private void run(CommandLine cmd) throws ParseException, IOException {
         conf.threads = Math.max(readThreadsCount(cmd), 1);
         conf.referenceExtension = getIntValue(cmd, "Y", 1200);
 
-        VarDict.start(conf);
-
+        return conf;
     }
 
     private int readThreadsCount(CommandLine cmd) throws ParseException {
@@ -183,7 +186,7 @@ private static int getColumnValue(CommandLine cmd, String opt, int defaultValue)
     }
 
     @SuppressWarnings("static-access")
-    private static Options buildOptions() {
+    public static Options buildOptions() {
         Options options = new Options();
         options.addOption("H", "?", false, "Print this help page");
         options.addOption("h", "header", false, "Print a header row describing columns");

src/main/java/com/astrazeneca/vardict/Main.java

@@ -36,7 +36,7 @@ synchronized private static IndexedFastaSequenceFile fetchFasta(String file) {
      * @param end end position of region
      * @return array of nucleotide bases in the region of fasta
      */
-    public static String[] retrieveSubSeq(String fasta, String chr, int start, int end) {
+    public String[] retrieveSubSeq(String fasta, String chr, int start, int end) {
         IndexedFastaSequenceFile idx = fetchFasta(fasta);
         ReferenceSequence seq = idx.getSubsequenceAt(chr, start, end);
         byte[] bases = seq.getBases();
@@ -50,7 +50,7 @@ public static String[] retrieveSubSeq(String fasta, String chr, int start, int e
      * @param conf Vardict Configuration
      * @return reference object contains sequence map: key - position, value - base and seed map
      */
-    public static Reference getREF(Region region, Map<String, Integer> chrs, Configuration conf) {
+    public Reference getREF(Region region, Map<String, Integer> chrs, Configuration conf) {
         Reference ref = new Reference();
         return getREF(region, chrs, conf, conf.referenceExtension, ref);
     }
@@ -64,7 +64,7 @@ public static Reference getREF(Region region, Map<String, Integer> chrs, Configu
      * @param ref reference
      * @return reference object contains sequence map: key - position, value - base and seed map
      */
-    public static Reference getREF(Region region, Map<String, Integer> chrs, Configuration conf, int extension, Reference ref) {
+    public Reference getREF(Region region, Map<String, Integer> chrs, Configuration conf, int extension, Reference ref) {
         int sequenceStart = region.start - conf.numberNucleotideToExtend - extension < 1 ? 1
                 : region.start - conf.numberNucleotideToExtend - extension;
         int len = chrs.containsKey(region.chr) ? chrs.get(region.chr) : 0;
@@ -98,7 +98,6 @@ public static Reference getREF(Region region, Map<String, Integer> chrs, Configu
 
             keySequence = substr(exon, i, Configuration.SEED_2);
             ref = addPositionsToSeedSequence(ref, sequenceStart, i, keySequence);
-
         }
 
         if (conf.y) {
@@ -116,7 +115,7 @@ public static Reference getREF(Region region, Map<String, Integer> chrs, Configu
      * @param keySequence sequence length of SEED_1 parameter from chromosome
      * @return updated Reference
      */
-    public static Reference addPositionsToSeedSequence(Reference ref, int sequenceStart, int i, String keySequence) {
+    private static Reference addPositionsToSeedSequence(Reference ref, int sequenceStart, int i, String keySequence) {
         List<Integer> seedPositions = ref.seed.getOrDefault(keySequence, new ArrayList<>());
         seedPositions.add(i + sequenceStart);
         ref.seed.put(keySequence, seedPositions);