Package gorsat.external.plink

Class PlinkProcessAdaptor

  • All Implemented Interfaces:
    java.lang.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, java.lang.String header)  

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      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, 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

      • 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,
                           java.lang.String header)
                    throws java.io.IOException
        Throws:
        java.io.IOException

    • Method Detail

      • 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