Merge pull request #6 from mikeyhuang/master

New updates

Author: mulinlab

.gitignore

@@ -0,0 +1,47 @@
+.gradle
+*.sw?
+.#*
+*#
+*~
+/build
+/code
+.metadata
+.factorypath
+.recommenders
+bin
+build
+lib/
+target
+
+# eclipse ignore
+.settings/
+.project
+.classpath
+
+# idea ignore
+.idea/
+*.ipr
+*.iml
+*.iws
+
+
+.factorypath
+.springBeans
+interpolated*.xml
+dependency-reduced-pom.xml
+build.log
+_site/
+.*.md.html
+manifest.yml
+MANIFEST.MF
+settings.xml
+activemq-data
+overridedb.*
+
+.DS_Store
+.factorypath
+dump.rdb
+transaction-logs
+
+out/
+src/test/resources/

build.gradle

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+plugins {
+    id 'java'
+    id 'application'
+    id 'maven'
+    id 'maven-publish'
+}
+
+group 'com.mulinlab'
+version '1.1-SNAPSHOT'
+
+// jdk版本
+sourceCompatibility = 1.8
+targetCompatibility = 1.8
+// java编译的时候缺省状态下会因为中文字符而失败
+[compileJava, compileTestJava]*.options*.encoding = 'UTF-8'
+
+repositories {
+    mavenLocal()
+    mavenCentral()
+}
+publishing {
+    publications {
+        mavenJava(MavenPublication) {
+            from components.java
+            afterEvaluate {
+                artifactId = jar.baseName
+            }
+        }
+    }
+}
+
+dependencies {
+    compile('com.intel.gkl:gkl:0.8.6') {
+        exclude module: 'htsjdk'
+    }
+
+    compile 'com.github.samtools:htsjdk:2.20.3'
+    compile 'net.sf.jopt-simple:jopt-simple:5.0.3'
+    compile 'org.apache.commons:commons-lang3:3.4'
+    compileOnly 'org.apache.logging.log4j:log4j-api:2.3'
+    compileOnly 'org.apache.logging.log4j:log4j-core:2.3'
+//    compile 'org.apache.logging.log4j:log4j-api:2.3'
+//    compile 'org.apache.logging.log4j:log4j-core:2.3'
+    compile group: 'commons-io', name: 'commons-io', version: '2.6'
+    compile group: 'org.broadinstitute', name: 'barclay', version: '2.1.0'
+    compile group: 'de.charite.compbio', name: 'jannovar-core', version: '0.34'
+    compile group: 'de.charite.compbio', name: 'jannovar-stats', version: '0.33'
+    compile group: 'com.fasterxml.jackson.core', name: 'jackson-annotations', version: '2.10.0'
+    testCompile group: 'junit', name: 'junit', version: '4.12'
+}
+
+application {
+    mainClassName = 'org.mulinlab.varnote.cmdline.VarNoteCommandLine'
+}
+
+configurations.all {
+    exclude group: "org.slf4j", module: "slf4j-log4j12"
+    exclude group: "log4j", module: "log4j"
+}
+
+jar {
+    manifest {
+        attributes("Implementation-Title": "VarNote",
+                "Implementation-Version": version,
+                'Main-Class': 'org.mulinlab.varnote.cmdline.VarNoteCommandLine')
+    }
+
+    from {
+        configurations.compile.collect { it.isDirectory() ? it : zipTree(it) }
+    }
+    exclude 'log4j.properties'
+    exclude '**/*.SF'
+    exclude '**/*.RSA'
+//    exclude 'log4j2.xml'
+}
+
+
+tasks.withType(Javadoc) {
+    options.addStringOption('Xdoclint:none')
+}
+
+task sourcesJar(type: Jar, dependsOn: classes) {
+    classifier = 'sources'
+    from sourceSets.main.allSource
+}
+
+task javadocJar(type: Jar, dependsOn: javadoc) {
+    classifier = 'javadoc'
+    from javadoc.destinationDir
+}
+
+javadoc {
+    options.addStringOption('Xdoclint:none', '-quiet')
+    source = sourceSets.main.allJava
+    include '**/*.java'
+}
+
+artifacts {
+    archives jar
+}
+

gradle/wrapper/gradle-wrapper.jar

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+#Sat Sep 21 11:53:32 CST 2019
+distributionBase=GRADLE_USER_HOME
+distributionPath=wrapper/dists
+zipStoreBase=GRADLE_USER_HOME
+zipStorePath=wrapper/dists
+distributionUrl=https\://services.gradle.org/distributions/gradle-4.10-all.zip