Examples in Java and Scala for ADAM: Genomic Data System. Apache 2 licensed.
Install
- JDK 1.8 or later, http://openjdk.java.net
- Scala 2.12.15 or later, http://www.scala-lang.org
- Apache Maven 3.3.1 or later, http://maven.apache.org
- Apache Spark 3.2.0 or later, http://spark.apache.org
- ADAM: Genomic Data System 0.37.0 or later, https://github.com/bigdatagenomics/adam
To build
$ mvn install
$ spark-submit \
--master local[4] \
--class com.github.heuermh.adam.examples.CountAlignments \
target/adam-examples_2.12-${ADAM_VERSION}.jar \
src/test/resources/small.sam
(1,20)
$ spark-submit \
--master local[4] \
--class com.github.heuermh.adam.examples.CountAlignmentsPerRead \
target/adam-examples_2.12-${ADAM_VERSION}.jar \
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:1:5469106:true,1)
(simread:1:186794283:true,1)
(simread:1:189606653:true,1)
(simread:1:101556378:false,1)
(simread:1:37577445:false,1)
(simread:1:89554252:false,1)
(simread:1:153978724:false,1)
(simread:1:169801933:true,1)
