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

Interactive explorer for ADAM genomics data models. Apache 2 licensed.
https://github.com/heuermh/adam-explorer

Last synced: 9 days ago
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Interactive explorer for ADAM genomics data models. Apache 2 licensed.

• Host: GitHub
• URL: https://github.com/heuermh/adam-explorer
• Owner: heuermh
• License: apache-2.0
• Created: 2019-01-29T19:20:57.000Z (almost 6 years ago)
• Default Branch: master
• Last Pushed: 2023-04-21T20:46:26.000Z (over 1 year ago)
• Last Synced: 2024-06-30T21:52:03.736Z (4 months ago)
• Language: Java
• Size: 916 KB
• Stars: 0
• Watchers: 2
• Forks: 0
• Open Issues: 2
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# adam-explorer

Interactive explorer for ADAM genomics data models.  Apache 2 licensed.

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

[![Maven Central](https://img.shields.io/maven-central/v/com.github.heuermh.adamexplorer/adam-explorer_2.12.svg?maxAge=600)](http://search.maven.org/#search%7Cga%7C1%7Ccom.github.heuermh.adamexplorer)

[![API Documentation](http://javadoc.io/badge/com.github.heuermh.adamexplorer/adam-explorer_2.12.svg?color=brightgreen&label=scaladoc)](http://javadoc.io/doc/com.github.heuermh.adamexplorer/adam-explorer)

### Hacking adam-explorer

Install

 * JDK 1.8 or later, http://openjdk.java.net

 * Apache Maven 3.3.9 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-explorer using ```spark-shell```

```

$ spark-shell \

    --conf spark.serializer=org.apache.spark.serializer.KryoSerializer \

    --conf spark.kryo.registrator=org.bdgenomics.adam.serialization.ADAMKryoRegistrator \

    --jars target/adam-explorer_2.12--SNAPSHOT.jar,$PATH_TO_ADAM_ASSEMBLY_JAR

...

Welcome to

      ____              __

     / __/__  ___ _____/ /__

    _\ \/ _ \/ _ `/ __/  '_/

   /___/ .__/\_,_/_/ /_/\_\   version 3.2.0

      /_/

Using Scala version 2.12.15 (Java HotSpot(TM) 64-Bit Server VM, Java 1.8.0_191)

Type in expressions to have them evaluated.

Type :help for more information.

scala> import org.bdgenomics.adam.ds.ADAMContext._

import org.bdgenomics.adam.ds.ADAMContext._

scala> import com.github.heuermh.adam.explorer.ADAMExplorer._

import com.github.heuermh.adam.explorer.ADAMExplorer._

scala> val alignments = sc.loadAlignments("sample.bam")

alignments: org.bdgenomics.adam.ds.read.AlignmentRecordRDD = RDDBoundAlignmentRecordRDD

with 85 reference sequences, 3 read groups, and 0 processing steps

scala> explore(alignments)

res0: Int = 0

scala>

```

![adam-explorer screenshot](https://github.com/heuermh/adam-explorer/raw/master/images/screen-shot.png)