SamFileIterator (SnpEff 5.2 API)

java.lang.Object

org.snpeff.fileIterator.FileIterator<SamEntry>

org.snpeff.fileIterator.SamFileIterator

All Implemented Interfaces:: Iterable<SamEntry>, Iterator<SamEntry>

public class SamFileIterator extends FileIterator<SamEntry>

Reads a SAM file Note: This is a very 'rustic' reader (we should use Picard's API instead)

Author:: pcingola

Field Summary

Fields

Modifier and Type

Field

Description

static boolean

debug

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

Constructors

Constructor

Description

SamFileIterator(String samFileName)
Method Summary

Modifier and Type

Method

Description

SamHeader

getHeaders()

Iterator<SamEntry>

iterator()

protected SamEntry

readNext()

Read a sequence from the file

Methods inherited from class org.snpeff.fileIterator.FileIterator
close, countNewLineChars, getFilePointer, getLine, getLineNum, guessNewLineChars, hasNext, hasSeek, init, isDebug, 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

Field Details
- debug
  
  public static boolean debug
Constructor Details
- SamFileIterator
  
  public SamFileIterator(String samFileName)
Method Details
- getHeaders
  
  public SamHeader getHeaders()
- iterator
  
  public Iterator<SamEntry> iterator()
  
  Specified by:
  
  iterator in interface Iterable<SamEntry>
  
  Overrides:
  
  iterator in class FileIterator<SamEntry>
- readNext
  
  protected SamEntry readNext()
  
  Read a sequence from the file
  
  Specified by:
  
  readNext in class FileIterator<SamEntry>
  
  Returns: