NOTE: The ADAM plugin API was removed in bigdatagenomics/adam#1065.
This project will no longer be updated.
External plugins in Java and Scala for ADAM: Genomic Data System. Apache 2 licensed.
###Hacking adam-plugins
Install
- JDK 1.8 or later, http://openjdk.java.net
- Scala 2.10.5 or later, http://www.scala-lang.org
- Apache Maven 3.2.5 or later, http://maven.apache.org
- Apache Spark 1.6.1 or later, http://spark.apache.org
- ADAM: Genomic Data System 0.19.1-SNAPSHOT or later, https://github.com/bigdatagenomics/adam
To build
$ mvn install
$ cp target/adam-plugins_2.10-0.19.1-SNAPSHOT.jar $ADAM_DIR
$ cd $ADAM_DIR
To run the plugins in this repository via the ADAM command line, add the jar to the classpath with the Spark --jars argument.
Note the -- argument separator between Spark arguments and ADAM arguments.
Run plugins
$ ./bin/adam-submit \
--jars adam-plugins_2.10-0.19.1-SNAPSHOT.jar \
-- \
plugin com.github.heuermh.adam.plugins.CountAlignments \
adam-core/src/test/resources/small.sam
(1,20)
$ ./bin/adam-submit \
--jars adam-plugins_2.10-0.19.1-SNAPSHOT.jar \
-- \
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)