heuermh / adam-plugins

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

GitHub

adam-plugins


NOTE: The ADAM plugin API was removed in https://github.com/bigdatagenomics/adam/pull/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

To build

$ mvn install

Running adam-plugins using adam-submit

$ 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)