Package gorsat.process

Class HailInputSource

java.lang.Object
org.gorpipe.gor.model.GenomicIteratorBase
gorsat.process.HailInputSource
All Implemented Interfaces:
AutoCloseable, 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(String[] iargs)
     

  • Method Summary

    Modifier and Type
    Method
    Description
    void
    close()
     
    boolean
    hasNext()
     
    org.gorpipe.gor.model.Row
    next()
     
    boolean
    seek(String chr, int pos)
     
    void
    write(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 Details

    • HailInputSource

      public HailInputSource(String[] iargs)

  • Method Details

    • write

      public void write(String parquetPath)

    • seek

      public boolean seek(String chr, int pos)

    • close

      public void close()

    • hasNext

      public boolean hasNext()

    • next

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