adam-explorer_2.11

Interactive explorer for ADAM genomics data models.

License	Apache License
GroupId	com.github.heuermh.adamexplorer
ArtifactId	adam-explorer_2.11
Last Version	0.30.0
Release Date	Jan 31, 2020
Type	jar
Description	adam-explorer_2.11 Interactive explorer for ADAM genomics data models.
Project URL	http://github.com/heuermh/adam-explorer
Source Code Management	https://github.com/heuermh/adam-explorer.git

Download adam-explorer_2.11

Filename	Size
adam-explorer_2.11-0.30.0.pom
adam-explorer_2.11-0.30.0.jar	10 MB
adam-explorer_2.11-0.30.0-sources.jar	32 KB
adam-explorer_2.11-0.30.0-javadoc.jar	24 KB

How to add to project

Apache Maven

<!-- https://jarcasting.com/artifacts/com.github.heuermh.adamexplorer/adam-explorer_2.11/ -->
<dependency>
    <groupId>com.github.heuermh.adamexplorer</groupId>
    <artifactId>adam-explorer_2.11</artifactId>
    <version>0.30.0</version>
</dependency>

Gradle Groovy

// https://jarcasting.com/artifacts/com.github.heuermh.adamexplorer/adam-explorer_2.11/
implementation 'com.github.heuermh.adamexplorer:adam-explorer_2.11:0.30.0'

Gradle Kotlin

// https://jarcasting.com/artifacts/com.github.heuermh.adamexplorer/adam-explorer_2.11/
implementation ("com.github.heuermh.adamexplorer:adam-explorer_2.11:0.30.0")

Apache Buildr

'com.github.heuermh.adamexplorer:adam-explorer_2.11:jar:0.30.0'

Apache Ivy

<dependency org="com.github.heuermh.adamexplorer" name="adam-explorer_2.11" rev="0.30.0">
  <artifact name="adam-explorer_2.11" type="jar" />
</dependency>

Groovy Grape

@Grapes(
@Grab(group='com.github.heuermh.adamexplorer', module='adam-explorer_2.11', version='0.30.0')
)

Scala SBT

libraryDependencies += "com.github.heuermh.adamexplorer" % "adam-explorer_2.11" % "0.30.0"

Leiningen

[com.github.heuermh.adamexplorer/adam-explorer_2.11 "0.30.0"]

Dependencies

compile (3)

Group / Artifact	Type	Version
org.dishevelled : dsh-eventlist-view	jar	2.2
org.dishevelled : dsh-layout	jar	1.1
org.dishevelled : dsh-iconbundle-tango	jar	1.1

provided (2)

Group / Artifact	Type	Version
org.apache.spark : spark-core_2.11	jar	2.4.4
org.bdgenomics.adam : adam-core-spark2_2.11	jar	0.30.0

runtime (1)

Group / Artifact	Type	Version
org.apache.xmlgraphics : xmlgraphics-commons	jar	2.2

Project Modules

There are no modules declared in this project.

adam-explorer

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

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 3.0.1 or later, http://spark.apache.org
• ADAM: Genomic Data System 0.33.0 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-<version>-SNAPSHOT.jar,$PATH_TO_ADAM_ASSEMBLY_JAR

...
Welcome to
      ____              __
     / __/__  ___ _____/ /__
    _\ \/ _ \/ _ `/ __/  '_/
   /___/ .__/\_,_/_/ /_/\_\   version 3.0.1
      /_/

Using Scala version 2.12.8 (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.rdd.ADAMContext._
import org.bdgenomics.adam.rdd.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.rdd.read.AlignmentRecordRDD = RDDBoundAlignmentRecordRDD
with 85 reference sequences, 3 read groups, and 0 processing steps

scala> explore(alignments)
res0: Int = 0

scala>

Versions

Version
0.30.0 Jan 31, 2020
0.29.0 Sep 30, 2019
0.28.0 Jul 11, 2019