Package gorsat.process

Class NordIterator

java.lang.Object
org.gorpipe.gor.model.GenomicIteratorBase
gorsat.process.NordIterator
All Implemented Interfaces:
AutoCloseable, Iterator<org.gorpipe.gor.model.Row>, org.gorpipe.gor.model.GenomicIterator, org.gorpipe.gor.model.RowSourceStats
public class NordIterator extends org.gorpipe.gor.model.GenomicIteratorBase

Iterator to access data from a nor dictionary file.

Nor dictionary file is a file to tag mapping where the iterator represents the data as a continuous stream. The nor dictionary iterator supports filtering from an input filter array. An empty filter array indicates no filter. Results from the nor dictionary iterator contains the original source plus a source column which contains the originating tag for the row. Filters can be silenced and a custom source column name can be applied. All files in the nor dictionary are relative to the dictionary file unless a full path is specified.

Nor dictionary supports header which starts with #. All lines starting with # are ignored from the dictionary. All header entries starting with ##[key]=[value] are treated as key value pairs. Nord files support the 'Source' keyword for naming the source column. If no Source reference is set in the nor dictionary file or no source is set with the -s option, the source column is not shown.

Example of a nor dictionary:

##Source=phenotype

#Source\tTag\n

./nor/file1.tsv\tPatient_1\n

./nor/file2.tsv\tPatient_2\n

./nor/file3.tsv\tPatient_3\n

#./nor/file4.tsv\tPatient_4\n -> Ignored

Nor dictionaries do not support bucketization as there only one file open at a time.

  • Field Summary

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

    statsSenderAnnotation, statsSenderName

  • Constructor Summary

    Constructors
    Constructor
    Description
    NordIterator(String nordFile, boolean useFilter, String[] filterEntries, String sourceColumnName, boolean ignoreMissingEntries, boolean forceReadOfHeader)
    Nor dictionary constructor.

  • Method Summary

    Modifier and Type
    Method
    Description
    void
    close()
     
    boolean
    hasNext()
     
    void
    init(org.gorpipe.gor.session.GorSession session)
     
    org.gorpipe.gor.model.Row
    next()
     
    boolean
    seek(String seekChr, int seekPos)
     

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

    clone, decStat, getBufferSize, getContext, getHeader, getSourceName, getTypes, incStat, 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

    • NordIterator

      public NordIterator(String nordFile, boolean useFilter, String[] filterEntries, String sourceColumnName, boolean ignoreMissingEntries, boolean forceReadOfHeader)
      Nor dictionary constructor. Creates an instance of nor dictionary iterator, see class description.
      Parameters:
      nordFile - Nor dictionary file path
      filterEntries - Array of tags to be inclusively filtered.
      sourceColumnName - Name of the ouput source column
      ignoreMissingEntries - Indicates if missing entries should be ignored or not. Not ignoring missing entries will throw a parsing exception.
      forceReadOfHeader - Force the read of headers in the source files.

  • Method Details

    • close

      public void close()

    • hasNext

      public boolean hasNext()

    • next

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

    • seek

      public boolean seek(String seekChr, int seekPos)

    • init

      public void init(org.gorpipe.gor.session.GorSession session)
      Specified by:
      init in interface org.gorpipe.gor.model.GenomicIterator
      Overrides:
      init in class org.gorpipe.gor.model.GenomicIteratorBase