org.snpeff.ped.PedFileIterator

public class PedFileIterator extends FileIterator<PedEntry>

PED file iterator (PED file from PLINK) Reference: http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml

Field Summary

Fields inherited from class org.snpeff.fileIterator.FileIterator
autoClose, countNewLineChars, debug, fileName, fileSize, line, lineNum, next, nextLine, reader, verbose
Constructor Summary

Constructors

Constructor

Description

PedFileIterator(String fileName, String mapFileName)
Method Summary

Modifier and Type

Method

Description

PlinkMap

getPlinkMap()

protected PedEntry

readNext()

Read next element

Methods inherited from class org.snpeff.fileIterator.FileIterator
close, countNewLineChars, getFilePointer, getLine, getLineNum, guessNewLineChars, hasNext, hasSeek, init, isDebug, iterator, load, next, readLine, ready, remove, seek, setAutoClose, setDebug, setVerbose, toString

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface java.lang.Iterable
forEach, spliterator

Methods inherited from interface java.util.Iterator
forEachRemaining

Constructor Details
- PedFileIterator
  
  public PedFileIterator(String fileName, String mapFileName)
Method Details
- getPlinkMap
  
  public PlinkMap getPlinkMap()
- readNext
  
  protected PedEntry readNext()
  
  Description copied from class: FileIterator
  
  Read next element
  
  Specified by:
  
  readNext in class FileIterator<PedEntry>

Class PedFileIterator

Field Summary