Package gorsat.external.plink

Class PlinkProcessAdaptor

java.lang.Object

gorsat.Commands.Processor

gorsat.Commands.Analysis

gorsat.external.plink.PlinkProcessAdaptor

All Implemented Interfaces:

Cloneable, scala.Cloneable

Direct Known Subclasses:

PlinkVcfProcessAdaptor

public class PlinkProcessAdaptor
extends gorsat.Commands.Analysis

This analysis class collects gor or vcf lines and writes them in batches to a temporary vcf files read by plink2 process

Constructor Summary

Constructors

Constructor	Description
PlinkProcessAdaptor(org.gorpipe.gor.session.GorSession session, PlinkArguments plinkArguments, int refIdx, int altIdx, int rsIdx, int valueIdx, boolean hc, float th, boolean vcf, String header)

Method Summary

Modifier and Type	Method	Description
void	finish()
void	process(org.gorpipe.gor.model.Row row)
void	setup()

Methods inherited from class gorsat.Commands.Analysis

$bar, $bar, alreadyFinished, alreadyFinished_$eq, clone, cloned, cloned_$eq, from, getHeader, getName, init, isCloned, isCloned_$eq, isInErrorState, isInErrorState_$eq, isTypeInformationMaintained, isTypeInformationNeeded, nextProcessor, nextProcessor_$eq, pipeFrom, pipeFrom_$eq, pipeTo, pipeTo_$eq, reportWantsNoMore, reset, rowHeader, rowHeader_$eq, securedFinish, securedSetup, setContext, setRowHeader, statsAdd, statsCollector, statsDec, statsInc, statsSenderAnnotation, statsSenderAnnotation_$eq, statsSenderId, statsSenderId_$eq, statsSenderName, statsSenderName_$eq, toString

Methods inherited from class gorsat.Commands.Processor

rs, rs_$eq, wantsNoMore, wantsNoMore_$eq

Methods inherited from class java.lang.Object

equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Details

PlinkProcessAdaptor

public PlinkProcessAdaptor(org.gorpipe.gor.session.GorSession session,
 PlinkArguments plinkArguments,
 int refIdx,
 int altIdx,
 int rsIdx,
 int valueIdx,
 boolean hc,
 float th,
 boolean vcf,
 String header)
                    throws IOException

Throws:

IOException

Method Details

setup

public void setup()

Overrides:

setup in class gorsat.Commands.Analysis

process

public void process(org.gorpipe.gor.model.Row row)

Overrides:

process in class gorsat.Commands.Analysis

finish

public void finish()

Overrides:

finish in class gorsat.Commands.Analysis