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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 3.2.0 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-<version>-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>