Merge pull request #342 from AdamaJava/nanno_snp_eff_idea

fix(qannotate): snpeff records were not being dealt with correctly

Author: holmeso

build.gradle

@@ -63,6 +63,24 @@ subprojects {
         main { java.srcDirs=['src']; resources.srcDirs=['src'] }
         test { java.srcDirs=['test']; test.resources.srcDirs=['test'] }
     }
+    build.doLast {
+	println "${project}: copy ${configurations.runtimeClasspath.collect { File file -> file.name }} to ${adamalib} and build/flat"
+	copy { from configurations.runtimeClasspath,libsDirectory; into file('build/flat') }
+	copy { from configurations.runtimeClasspath,libsDirectory; into adamalib }
+    }
+    jar.doFirst {
+	manifest { 
+	    if(project.hasProperty('mainClassName') && project.getProperty('mainClassName') != null ) {
+		attributes 'Main-Class' : project.mainClassName 
+	    }
+	    attributes  'Implementation-Title': project.name,
+		'Implementation-Version': verionId,
+		'SVN-Version': revision,
+		'Built-By': System.properties['user.name'],
+		'Date': new java.util.Date().toString(),
+		'Class-Path' : project.configurations.runtimeClasspath.collect { it.name }.join(' ')
+	}
+    }
 }
 
 //create adama/build/lib under root before subprojects build

q3indel/build.gradle

@@ -20,7 +20,7 @@ dependencies {
     implementation project(':qpicard')
 
     implementation 'org.scala-lang:scala-library:2.12.18'
-    implementation 'net.sf.jopt-simple:jopt-simple:4.6'
+    implementation 'net.sf.jopt-simple:jopt-simple:5.0.4'
     implementation group: 'org.ini4j', name: 'ini4j', version: '0.5.2'
 }
 

q3panel/build.gradle

@@ -12,7 +12,7 @@ dependencies {
 
     implementation 'org.apache.commons:commons-lang3:3.4'
     implementation 'net.sf.trove4j:core:3.1.0'
-    implementation 'net.sf.jopt-simple:jopt-simple:4.6'
+    implementation 'net.sf.jopt-simple:jopt-simple:5.0.4'
     implementation 'com.github.samtools:htsjdk:4.0.2'
 
     implementation group: 'com.io7m.xom',name: 'xom', version: '1.2.10'

q3tiledaligner/build.gradle

@@ -12,5 +12,5 @@ dependencies {
     implementation 'com.github.samtools:htsjdk:4.0.2'
     implementation 'net.sf.trove4j:core:3.1.0'
     implementation 'org.apache.commons:commons-lang3:3.4'
-    implementation 'net.sf.jopt-simple:jopt-simple:4.6'
+    implementation 'net.sf.jopt-simple:jopt-simple:5.0.4'
 }

q3vcftools/build.gradle

@@ -15,7 +15,7 @@ dependencies {
     implementation project(':qio')
 
     implementation 'com.github.samtools:htsjdk:4.0.2'
-    implementation 'net.sf.jopt-simple:jopt-simple:4.6'
+    implementation 'net.sf.jopt-simple:jopt-simple:5.0.4'
     implementation 'net.sf.trove4j:core:3.1.0'
     implementation group: 'com.jcraft', name: 'jsch', version: '0.1.54'
     implementation group: 'org.apache.commons', name: 'commons-lang3', version: '3.4'