Package gorsat.external.plink

Class PlinkAdjustAdaptor

  • All Implemented Interfaces:
    java.lang.Cloneable, scala.Cloneable
    public class PlinkAdjustAdaptor
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
      PlinkAdjustAdaptor​(java.lang.String header, boolean sort)  
      PlinkAdjustAdaptor​(java.lang.String header, java.lang.String adjustColumns, boolean sort)  

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      void finish()  
      java.lang.String getHeader()  
      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_$eq, from, getName, init, isCloned, isCloned_$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

      • PlinkAdjustAdaptor

        public PlinkAdjustAdaptor​(java.lang.String header,
                          boolean sort)
                   throws java.io.IOException
        Throws:
        java.io.IOException

      • PlinkAdjustAdaptor

        public PlinkAdjustAdaptor​(java.lang.String header,
                          java.lang.String adjustColumns,
                          boolean sort)
                   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

      • getHeader

        public java.lang.String getHeader()
        Overrides:
        getHeader in class gorsat.Commands.Analysis

      • finish

        public void finish()
        Overrides:
        finish in class gorsat.Commands.Analysis