Package gorsat.process

Class HailInputSource

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

    • Field Summary

      • Fields inherited from class org.gorpipe.gor.model.GenomicIteratorBase

        statsSenderAnnotation, statsSenderName

    • 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()  
      boolean seek​(java.lang.String chr, int pos)  
      void write​(java.lang.String parquetPath)  

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

        clone, decStat, getBufferSize, getContext, getHeader, getSourceName, getTypes, incStat, init, initStats, isSourceAlreadyInserted, setBufferSize, setContext, setHeader, setSourceAlreadyInserted, setSourceName, setTypes

      • Methods inherited from class java.lang.Object

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

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

        filter, getMonitor, isBuffered, moveToPosition, moveToPosition, pushdownCalc, pushdownCmd, pushdownFilter, pushdownGor, pushdownSelect, pushdownTop, pushdownWrite, seek, select, setRequestedRange

      • Methods inherited from interface java.util.Iterator

        forEachRemaining, remove

      • Methods inherited from interface org.gorpipe.gor.model.RowSourceStats

        getAvgBasesPerMilliSecond, getAvgBatchSize, getAvgRowsPerMilliSecond, getAvgSeekTimeMilliSecond, getCurrentBatchLoc, getCurrentBatchRow, getCurrentBatchSize

    • Constructor Detail

      • HailInputSource

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

    • Method Detail

      • write

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

      • seek

        public boolean seek​(java.lang.String chr,
                    int pos)

      • close

        public void close()

      • hasNext

        public boolean hasNext()

      • next

        public org.gorpipe.gor.model.Row next()