Package gorsat.external.plink

Class PlinkVcfProcessAdaptor

java.lang.Object

gorsat.Commands.Processor

gorsat.Commands.Analysis

gorsat.external.plink.PlinkProcessAdaptor

gorsat.external.plink.PlinkVcfProcessAdaptor

All Implemented Interfaces:

java.lang.Cloneable, scala.Cloneable

public class PlinkVcfProcessAdaptor
extends PlinkProcessAdaptor

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
PlinkVcfProcessAdaptor(org.gorpipe.gor.session.GorSession session, PlinkArguments plinkArguments, int refIdx, int altIdx, int rsIdx, int valueIdx, boolean hc, float th, boolean vcf, java.lang.String header, java.lang.String expectedHeader)

Method Summary

Modifier and Type	Method	Description
void	setup()

Methods inherited from class gorsat.external.plink.PlinkProcessAdaptor

finish, process

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, 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 Detail

PlinkVcfProcessAdaptor

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

Throws:

java.io.IOException

Method Detail

setup

public void setup()

Overrides:

setup in class PlinkProcessAdaptor