Shekharrajak / adam-examples

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

adam-examples

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

Hacking adam-examples

Install

• JDK 1.8 or later, http://openjdk.java.net
• Scala 2.11.12 or later, http://www.scala-lang.org
• Apache Maven 3.3.1 or later, http://maven.apache.org
• Apache Spark 2.3.2 or later, http://spark.apache.org
• ADAM: Genomic Data System 0.26.0-SNAPSHOT or later, https://github.com/bigdatagenomics/adam

To build

$ mvn install

Running adam-examples using spark-submit

$ spark-submit \
  --master local[4] \
  --class com.github.heuermh.adam.examples.CountAlignments \
  target/adam-examples_2.11-0.26.0-SNAPSHOT.jar \
  src/test/resources/small.sam

(1,20)


$ spark-submit \
  --master local[4] \
  --class com.github.heuermh.adam.examples.CountAlignmentsPerRead \
  target/adam-examples_2.11-0.26.0-SNAPSHOT.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)