VarDictJava inherited Perl version static procedural structure. In this release huge refactoring was provided. At the top level refactoring includes following steps:

Scopes decomposition
Method decomposition
Data aggregation
Global scope extraction
Entities extraction
Data flow rerouting
Extraction of Modules entities
Pipeline organisation
Extraction of Modes entities

 Also, custom htsjdk version was applied in the VarDict release 2.0, it includes new cache feature for bam-files.

Author: Nikolai Karulin

Readme.md

@@ -18,7 +18,7 @@ Original coded by Zhongwu Lai 2014.
 VarDictJava can run in single sample (see Single sample mode section), paired sample (see Paired variant calling section), or amplicon bias aware modes. As input, VarDictJava takes reference genomes in FASTA format, aligned reads in BAM format, and target regions in BED format.
 
 ##Requirements
-1. JDK 1.7 or later
+1. JDK 1.8 or later
 2. R language (uses /usr/bin/env R)
 3. Perl (uses /usr/bin/env perl)
 4. Internet connection to download dependencies using gradle.
@@ -50,7 +50,6 @@ To generate Javadoc, in the build/docs/javadoc folder, run the following command
 ./gradlew clean javadoc
 ```
 
-
 ###Single sample mode
 
 To run VarDictJava in single sample mode, use a BAM file specified without the `|` symbol and perform Steps 3 and 4 (see the Program workflow section) using `teststrandbias.R` and `var2vcf_valid.pl.`
@@ -103,7 +102,11 @@ The VarDictJava program follows the workflow:
 4.	Transform the intermediate tabular format to VCF. Output the variants with filtering and statistical data.  
      **Note**: Use the Perl scripts `var2vcf_valid.pl` or `var2vcf_paired.pl` for this step.
 
+###BAM caching
 
+For enabling bam caching feature append the VARDICT_OPT parameter with:
+-Dsamjdk.bam_caching=true
+-Dsamjdk.cache_size=[value] (default value = 128, measured in MB).
 
 ##Program Options
 
@@ -220,6 +223,7 @@ The VarDictJava program follows the workflow:
 18. PStd - flag for read position standard deviation
 19. QMean - mean base quality
 20. QStd - flag for base quality standard deviation
+21. Mapq - Mean mapping quality
 23. QRATIO - ratio of high quality reads to low-quality reads
 24. HIFREQ - variant frequency for high-quality reads
 25. EXTRAFR - Adjusted AF for indels due to local realignment

VarDictDescription.docx

@@ -1,16 +1,34 @@
-apply plugin: 'java'
-apply plugin:'application'
+plugins {
+    id 'java'
+    id 'application'
+    id 'jacoco'
+    id "org.sonarqube" version "2.2"
+}
 
-version = '1.4.8'
+version = '2.0b'
 
 
 repositories { 
-    mavenCentral() 
+    mavenCentral()
+    jcenter()
+    //for building custom htsjdk with bam caching from our fork repo
+    maven { url "https://jitpack.io" }
 }
 
 targetCompatibility = "1.8"
 sourceCompatibility = "1.8"
 
+sourceSets {
+    integrationTest {
+        java {
+            compileClasspath += main.output + test.output
+            runtimeClasspath += main.output + test.output
+            srcDir file('src/integration-test/java')
+        }
+        resources.srcDir file('src/integration-test/resources')
+    }
+}
+
 
 afterEvaluate {
     if(project.hasProperty("hprof")) {
@@ -20,13 +38,22 @@ afterEvaluate {
     }
 }
 
+configurations {
+    integrationTestCompile.extendsFrom testCompile
+    integrationTestRuntime.extendsFrom testRuntime
+}
+
 dependencies {
     compile 'commons-cli:commons-cli:1.2' 
     compile 'com.edropple.jregex:jregex:1.2_01'
-    compile('com.github.samtools:htsjdk:2.8.0') {
-        transitive = false
-    }
-    testCompile 'junit:junit:4.8.2'
+    compile 'com.github.EpamLifeSciencesTeam:htsjdk:epam-ls_BAM_cache-SNAPSHOT'
+    // https://mvnrepository.com/artifact/org.powermock/powermock-module-junit4
+    testCompile group: 'org.powermock', name: 'powermock-api-mockito', version: '1.6.6'
+    testCompile group: 'org.powermock', name: 'powermock-module-testng', version: '1.6.6'
+    testCompile'org.testng:testng:6.9.13.6'
+
+    integrationTestCompile 'org.testng:testng:6.9.13.6'
+
 }
 
 mainClassName = "com.astrazeneca.vardict.Main"
@@ -50,7 +77,39 @@ javadoc {
     exclude '**/ConcurrentHashSet*'
     exclude '**/Utils*'
     exclude '**/Tuple*'
-    exclude '**/Main*'
 }
 
 
+task integrationTest(type: Test) {
+    testClassesDir = sourceSets.integrationTest.output.classesDir
+    classpath = sourceSets.integrationTest.runtimeClasspath
+    useTestNG()
+}
+
+task integrationTestCoverageReport(type:JacocoReport) {
+    dependsOn integrationTest
+    executionData integrationTest
+    sourceSets sourceSets.main
+}
+
+test {
+    // enable TestNG support (default is JUnit)
+    useTestNG()
+
+    // show standard out and standard error of the test JVM(s) on the console
+    testLogging.showStandardStreams = true
+
+    // set JVM arguments for the test JVM(s)
+    jvmArgs '-XX:MaxPermSize=256m'
+
+    // listen to events in the test execution lifecycle
+    beforeTest { descriptor ->
+        logger.lifecycle("Running test: " + descriptor)
+    }
+
+    // listen to standard out and standard error of the test JVM(s)
+    onOutput { descriptor, event ->
+        logger.lifecycle("Test: " + descriptor + " produced standard out/err: " + event.message )
+    }
+}
+

VarDict_Getting_Started_Guide_1_2.docx

@@ -0,0 +1,38 @@
+package com.astrazeneca;
+
+import com.astrazeneca.vardict.Configuration;
+
+import java.io.PrintStream;
+import java.util.Map;
+
+public class GlobalReadOnlyScope {
+
+    private volatile static GlobalReadOnlyScope instance;
+
+    public static GlobalReadOnlyScope instance() {
+        return instance;
+    }
+
+    public static synchronized void init(Configuration conf, Map<String, Integer> chrLengths, String sample, String samplem, String ampliconBasedCalling) {
+        if (instance != null) {
+            throw new IllegalStateException("GlobalReadOnlyScope was already initialized. Must be initialized only once.");
+        }
+        instance = new GlobalReadOnlyScope(conf, chrLengths, sample, samplem, ampliconBasedCalling);
+    }
+
+    public final Configuration conf;
+    public final Map<String, Integer> chrLengths;
+    public final String sample;
+    public final String samplem;
+    public final String ampliconBasedCalling;
+    public final PrintStream out;
+
+    public GlobalReadOnlyScope(Configuration conf, Map<String, Integer> chrLengths, String sample, String samplem, String ampliconBasedCalling) {
+        this.conf = conf;
+        this.chrLengths = chrLengths;
+        this.sample = sample;
+        this.samplem = samplem;
+        this.ampliconBasedCalling = ampliconBasedCalling;
+        this.out = System.out;
+    }
+}

VarDict_Getting_Started_Guide_2.0b.docx

@@ -1,4 +1,4 @@
-package com.astrazeneca.vardict;
+package com.astrazeneca.utils;
 
 import java.util.Collection;
 import java.util.Iterator;

build.gradle

@@ -0,0 +1,10 @@
+package com.astrazeneca.utils;
+
+import java.util.concurrent.Executor;
+
+public class DirectThreadExecutor implements Executor {
+    @Override
+    public void execute(Runnable command) {
+        command.run();
+    }
+}

src/main/java/com/astrazeneca/GlobalReadOnlyScope.java

@@ -1,4 +1,4 @@
-package com.astrazeneca.vardict;
+package com.astrazeneca.utils;
 
 
 public final class Tuple {

src/main/java/com/astrazeneca/vardict/ConcurrentHashSet.java renamed to src/main/java/com/astrazeneca/utils/ConcurrentHashSet.java

@@ -1,4 +1,4 @@
-package com.astrazeneca.vardict;
+package com.astrazeneca.utils;
 
 import java.util.*;
 
@@ -139,4 +139,11 @@ public static List<String> globalFind(jregex.Pattern alignedLength, String strin
     }
 
 
+    public static boolean isEquals(Character ch1, Character ch2) {
+        if (ch1 == null && ch2 == null)
+            return true;
+        if (ch1 == null || ch2 == null)
+            return false;
+        return ch1.equals(ch2);
+    }
 }