Package gorsat.process

Class HailInputSource

java.lang.Object
org.gorpipe.gor.model.GenomicIterator
org.gorpipe.model.gor.iterators.RowSource
gorsat.process.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

    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_$eq, clone, getAvgBasesPerMilliSecond, getAvgBatchSize, getAvgRowsPerMilliSecond, getAvgSeekTimeMilliSecond, getBufferSize, getCurrentBatchLoc, getCurrentBatchRow, getCurrentBatchSize, getEx, getGorHeader, getParent, isBuffered, moveToPosition, moveToPosition$default$3, next, parent, parent_$eq, seek, setBufferSize, setEx, setParent, terminateReading

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

    decStat, filter, getColnum, getContext, getHeader, getLookup, getMonitor, getSourceName, incStat, init, initStats, isSourceAlreadyInserted, pushdownCalc, pushdownCmd, pushdownFilter, pushdownGor, pushdownSelect, pushdownTop, pushdownWrite, seek, select, selectHeader, setColnum, setContext, 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 Details

  • Method Details

    • 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)
      Overrides:
      setPosition in class org.gorpipe.model.gor.iterators.RowSource