adam-plugins

External plugins in Java and Scala for ADAM: Genomic Data System. Apache 2 licensed.

###Hacking adam-plugins

Install

• JDK 1.7 or later, http://openjdk.java.net
• Scala 2.10.4 or later, http://www.scala-lang.org
• Apache Maven 3.2.3 or later, http://maven.apache.org
• ADAM: Genomic Data System 0.14.0 or later, https://github.com/bigdatagenomics/adam

To build

$ mvn install

To add the plugins in this repository to the ADAM command line, add the jar to $CLASSPATH_PREFIX

$ cp target/adam-plugins-0.14.1-SNAPSHOT.jar $ADAM_DIR
$ cd $ADAM_DIR
$ CLASSPATH_PREFIX=adam-plugins-0.14.1-SNAPSHOT.jar sh adam-cli/target/appassembler/bin/adam

####Examples

$ CLASSPATH_PREFIX=adam-plugins-0.14.1-SNAPSHOT.jar \
        sh adam-cli/target/appassembler/bin/adam \
        plugin com.github.heuermh.adam.plugins.CountAlignments \
        adam-core/src/test/resources/small.sam
 
(1,20)


$ CLASSPATH_PREFIX=adam-plugins-0.14.1-SNAPSHOT.jar \
        sh adam-cli/target/appassembler/bin/adam \
        plugin com.github.heuermh.adam.plugins.CountAlignmentsPerRead \
        adam-core/src/test/resources/small.sam
 
(simread:1:237728409:true,1)
(simread:1:195211965:false,1)
(simread:1:163841413:false,1)
(simread:1:231911906:false,1)
(simread:1:26472783:false,1)
(simread:1:165341382:true,1)
(simread:1:240344442:true,1)
(simread:1:50683371:false,1)
(simread:1:240997787:true,1)
(simread:1:14397233:false,1)
(simread:1:207027738:true,1)
(simread:1:20101800:true,1)
(simread:1:101556378:false,1)
(simread:1:37577445:false,1)
(simread:1:189606653:true,1)
(simread:1:5469106:true,1)
(simread:1:186794283:true,1)
(simread:1:89554252:false,1)
(simread:1:153978724:false,1)
(simread:1:169801933:true,1)