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GELOG / adam-ibs

Ports the IBS/MDS/IBD functionality of Plink to Spark / ADAM
Apache License 2.0
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Adam IBS

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This project ports the IBS/MDS/IBD functionality of PLink to Spark / ADAM.

Getting started

Checkout our wiki

Requirements

JDK 1.7

Scala 2.10.x

Project organisation

adam-ibs is composed of modules adam-ibs-core and adam-ibs-data.

adam-ibs-data define the used avro data model. This module needs to be builded in order to be used in adam-ibs-core module as a .jar dependence.

adam-ibs-core include logic and lci and uses adam-ibs-data jar dependency.

Build

The project can be built by executing "mvn clean compile install" from the root folder or in two following steps :

  1. In adam-ibs-data folder : maven clean compile install

    • You will obtain both adam-ibs-data-0.1.0.jar which is used as maven dependency in adam-ibs-core.

  2. In adam-ibs-code folder : maven clean compile install

    • You will obtain 2 jar files :
    • adam-ibs-core-0.1.0.jar -> jar file containing adam-ibs-core code
    • adam-ibs-core-0.1.0-jar-with-dependencies.jar -> jar file containing adam-ibs-core code with all dependencies.

Execute from shell

From adam-ibs-core folder :

Help :

adam-ibs-core$ java -jar target/adam-ibs-core-0.1.0-jar-with-dependencies.jar -h
21:01:07.849 [main] [INFO ] [c.e.m.c.Main$] : Begin with arguments : -h 
    --file  <name>   Specify .ped + .map filename prefix (default 'plink')
    --genome         Calculate IBS distances between all individuals [needs
                   --file and --out]
    --make-bed       Create a new binary fileset. Specify .ped and .map files [required --file and --out]
    --out  <name>    Specify the output filename
    --show-parquet   Show Schema and data sample stored in a parquet file [required --file]
-h, --help  <arg>    Show help message

Execute with spark-submit :

spark-1.4.1/bin$ ./spark-submit --master local /home/ikizema/DEV/mgl804/adam-ibs/adam-ibs-core/target/adam-ibs-core-0.1.0-jar-with-dependencies.jar --file /home/ikizema/DEV/mgl804/adam-ibs/DATA/avro/test.makeBed.parquet --show-parquet

Execute from IDEA IDE

CLI parser is integrated to code.

  1. View CLI options (--help) : image image

  2. Exemple : Execute --make-bed on --file and get a parquet output file --out image