External plugins for ADAM: Genomic Data System
###Hacking adam-plugins
Install
- JDK 1.7 or later, http://openjdk.java.net
- Scala 2.10.3 or later, http://www.scala-lang.org
- Apache Maven 3.2.1 or later, http://maven.apache.org
- ADAM: Genomic Data System 0.9.0 or later, https://github.com/bigdatagenomics/adam
To build
$ mvn install
To add the plugins in this repository to the ADAM command line
$ cp target/adam-plugins-1.0-SNAPSHOT.jar $ADAM_DIR
$ cd $ADAM_DIR
$ java -classpath "adam-cli/target/adam-$VERSION.jar:adam-plugins-$VERSION.jar" \
org.bdgenomics.adam.cli.ADAMMain
####Examples
$ java -classpath adam-cli/target/adam-0.9.1-SNAPSHOT.jar:adam-plugins-1.0-SNAPSHOT.jar \
org.bdgenomics.adam.cli.ADAMMain \
plugin com.github.heuermh.adam.plugins.CountAlignments \
adam-core/src/test/resources/small.sam
(1,10)
(unmapped,10)
$ java -classpath adam-cli/target/adam-0.9.1-SNAPSHOT.jar:adam-plugins-1.0-SNAPSHOT.jar \
org.bdgenomics.adam.cli.ADAMMain \
plugin com.github.heuermh.adam.plugins.CountAlignmentsPerRead \
adam-core/src/test/resources/small.sam
(simread:1:89554252:false,1)
(simread:1:195211965:false,1)
(simread:1:101556378:false,1)
(simread:1:231911906:false,1)
(unmapped,10)
(simread:1:14397233:false,1)
(simread:1:153978724:false,1)
(simread:1:37577445:false,1)
(simread:1:26472783:false,1)
(simread:1:50683371:false,1)
(simread:1:163841413:false,1)