https://github.com/heuermh/adam-examples

Examples in Java and Scala for ADAM: Genomic Data System. Apache 2 licensed.
https://github.com/heuermh/adam-examples

Last synced: 9 days ago
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Examples in Java and Scala for ADAM: Genomic Data System. Apache 2 licensed.

• Host: GitHub
• URL: https://github.com/heuermh/adam-examples
• Owner: heuermh
• License: apache-2.0
• Created: 2015-10-16T23:02:54.000Z (about 9 years ago)
• Default Branch: master
• Last Pushed: 2023-04-21T20:47:44.000Z (over 1 year ago)
• Last Synced: 2024-06-30T21:52:03.322Z (4 months ago)
• Language: Java
• Size: 110 KB
• Stars: 4
• Watchers: 4
• Forks: 2
• Open Issues: 1
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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adam-examples

=============

[![Build Status](https://travis-ci.org/heuermh/adam-examples.svg?branch=master)](https://travis-ci.org/heuermh/adam-examples)

[![Maven Central](https://img.shields.io/maven-central/v/com.github.heuermh.adamexamples/adam-examples_2.12.svg?maxAge=600)](http://search.maven.org/#search%7Cga%7C1%7Ccom.github.heuermh.adamexamples)

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 2.12.15 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

### Running adam-examples using ```spark-submit```

    $ 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)