Package gorsat.process

Class HailInputSource

  • All Implemented Interfaces:
    java.lang.AutoCloseable, java.util.Iterator<org.gorpipe.gor.model.Row>
    public class HailInputSource
extends org.gorpipe.model.gor.iterators.RowSource

    • Nested Class Summary

      • Nested classes/interfaces inherited from class org.gorpipe.gor.model.GenomicIterator

        org.gorpipe.gor.model.GenomicIterator.ChromoLookup

    • Constructor Summary

      Constructors 
      Constructor Description
      HailInputSource​(java.lang.String[] iargs)  

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      void close()  
      boolean hasNext()  
      org.gorpipe.gor.model.Row next()  
      void setPosition​(java.lang.String seekChr, int seekPos)  
      void write​(java.lang.String parquetPath)  

      • Methods inherited from class org.gorpipe.model.gor.iterators.RowSource

        bufferSize, bufferSize_$eq, getAvgBasesPerMilliSecond, getAvgBatchSize, getAvgRowsPerMilliSecond, getAvgSeekTimeMilliSecond, getBufferSize, getCurrentBatchLoc, getCurrentBatchRow, getCurrentBatchSize, getGorHeader, getParent, moveToPosition, moveToPosition$default$3, next, parent, parent_$eq, seek, setBufferSize, setParent, terminateReading

      • Methods inherited from class org.gorpipe.gor.model.GenomicIterator

        clone, decStat, filter, getColnum, getContext, getEx, getHeader, getLookup, getMonitor, getSourceName, incStat, init, initStats, isBuffered, isSourceAlreadyInserted, pushdownCalc, pushdownCmd, pushdownFilter, pushdownGor, pushdownSelect, pushdownTop, pushdownWrite, seek, select, selectHeader, setColnum, setContext, setEx, setHeader, setSourceAlreadyInserted, setSourceName

      • Methods inherited from class java.lang.Object

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

      • Methods inherited from interface java.util.Iterator

        forEachRemaining, remove

    • Constructor Detail

      • HailInputSource

        public HailInputSource​(java.lang.String[] iargs)

    • Method Detail

      • write

        public void write​(java.lang.String parquetPath)

      • close

        public void close()
        Specified by:
        close in interface java.lang.AutoCloseable
        Specified by:
        close in class org.gorpipe.model.gor.iterators.RowSource

      • hasNext

        public boolean hasNext()
        Specified by:
        hasNext in interface java.util.Iterator<org.gorpipe.gor.model.Row>
        Overrides:
        hasNext in class org.gorpipe.gor.model.GenomicIterator

      • next

        public org.gorpipe.gor.model.Row next()
        Specified by:
        next in interface java.util.Iterator<org.gorpipe.gor.model.Row>
        Overrides:
        next in class org.gorpipe.gor.model.GenomicIterator

      • setPosition

        public void setPosition​(java.lang.String seekChr,
                        int seekPos)
        Specified by:
        setPosition in class org.gorpipe.model.gor.iterators.RowSource