htsjdk.samtools.filter

Class InsertSizeFilter

java.lang.Object

htsjdk.samtools.filter.InsertSizeFilter

All Implemented Interfaces:

SamRecordFilter

public class InsertSizeFilter
extends java.lang.Object
implements SamRecordFilter

Filter things that fall outside a specified range of insert sizes. This will automatically omit unpaired reads.

Constructor Summary

Constructors

Constructor and Description
InsertSizeFilter(int minInsertSize, int maxInsertSize)

Method Summary

Methods

Modifier and Type	Method and Description
boolean	filterOut(SAMRecord rec) Determines whether a SAMRecord matches this filter
boolean	filterOut(SAMRecord r1, SAMRecord r2) Determines whether a pair of SAMRecords matches this filter

Methods inherited from class java.lang.Object

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

Constructor Detail

InsertSizeFilter

public InsertSizeFilter(int minInsertSize,
                int maxInsertSize)

Method Detail

filterOut

public boolean filterOut(SAMRecord rec)

Description copied from interface: SamRecordFilter

Determines whether a SAMRecord matches this filter

Specified by:

filterOut in interface SamRecordFilter

Parameters:

rec - the SAMRecord to evaluate

Returns:

true if the SAMRecord matches the filter, otherwise false

filterOut

public boolean filterOut(SAMRecord r1,
                SAMRecord r2)

Description copied from interface: SamRecordFilter

Determines whether a pair of SAMRecords matches this filter

Specified by:

filterOut in interface SamRecordFilter

Parameters:

r1 - the first SAMRecord to evaluate

r2 - the second SAMRecord to evaluate

Returns:

true if the pair of records matches filter, otherwise false