picard.illumina.parser.readers

Class FilterFileReader

java.lang.Object

picard.illumina.parser.readers.FilterFileReader

All Implemented Interfaces:

java.util.Iterator<java.lang.Boolean>

public class FilterFileReader
extends java.lang.Object
implements java.util.Iterator<java.lang.Boolean>

Illumina uses an algorithm described in "Theory of RTA" that determines whether or not a cluster passes filter("PF") or not. These values are written as sequential bytes to Filter Files. The structure of a filter file is as follows: Bytes 0-3 : 0 Bytes 4-7 : unsigned int version Bytes 8-11 : unsigned int numClusters

Field Summary

Fields

Modifier and Type	Field and Description
static int	EXPECTED_VERSION Expected Version
long	numClusters The number of cluster's pf values stored in this file
int	version Version number found in the FilterFile, this should equal 3

Constructor Summary

Constructors

Constructor and Description
FilterFileReader(java.io.File file)

Method Summary

Modifier and Type	Method and Description
boolean	hasNext()
java.lang.Boolean	next()
void	remove()
void	skipRecords(int numToSkip)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface java.util.Iterator

forEachRemaining

Field Detail

EXPECTED_VERSION

public static final int EXPECTED_VERSION

Expected Version

See Also:

Constant Field Values

version

public final int version

Version number found in the FilterFile, this should equal 3

numClusters

public final long numClusters

The number of cluster's pf values stored in this file

Constructor Detail

FilterFileReader

public FilterFileReader(java.io.File file)

Method Detail

hasNext

public boolean hasNext()

Specified by:

hasNext in interface java.util.Iterator<java.lang.Boolean>

next

public java.lang.Boolean next()

Specified by:

next in interface java.util.Iterator<java.lang.Boolean>

skipRecords

public void skipRecords(int numToSkip)

remove

public void remove()

Specified by:

remove in interface java.util.Iterator<java.lang.Boolean>