Package gorsat.external.plink

Class PlinkProcessAdaptor

java.lang.Object
gorsat.Commands.Processor
gorsat.Commands.Analysis
gorsat.external.plink.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

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