net.sf.snver.pileup.util
Class Filter

java.lang.Object
  net.sf.snver.pileup.util.Filter

public class Filter
extends java.lang.Object

Regional target object to filter result

Created by IntelliJ IDEA. User: weicheng hu Date: 10/28/11 Time: 10:54 AM

Constructor Summary

Filter()

Method Summary

void	add(java.lang.String name, int start, int end) Add a region to filter pool
boolean	filterOut(net.sf.samtools.SAMRecord record) Filter a SAMRecord
boolean	filterOut(java.lang.String name, int index) Filter a position
boolean	filterOut(java.lang.String name, int start, int end) Filter a chunk of position
int	size() Return filter pool size

Methods inherited from class java.lang.Object

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

Constructor Detail

Filter

public Filter()

Method Detail

add

public void add(java.lang.String name,
                int start,
                int end)

Add a region to filter pool

Parameters:

name - String

start - int

end - int

filterOut

public boolean filterOut(java.lang.String name,
                         int index)

Filter a position

Parameters:

name - String

index - int

Returns:

boolean

filterOut

public boolean filterOut(java.lang.String name,
                         int start,
                         int end)

Filter a chunk of position

Parameters:

name - String

start - int

end - int

Returns:

boolean

filterOut

public boolean filterOut(net.sf.samtools.SAMRecord record)

Filter a SAMRecord

Parameters:

record - SAMRecord

Returns:

boolean

size

public int size()

Return filter pool size

Returns:

int