htsjdk.samtools.filter

Class IntervalKeepPairFilter

java.lang.Object

htsjdk.samtools.filter.IntervalKeepPairFilter

All Implemented Interfaces:

SamRecordFilter

public class IntervalKeepPairFilter
extends java.lang.Object
implements SamRecordFilter

Filter out SAMRecords where neither record of a pair overlaps a given set of intervals. If one record of a pair overlaps the interval list, than both are kept. It is required that the SAMRecords are passed in coordinate order, have non-null SAMFileHeaders, and that Mate Cigar (MC) is present.

Constructor Summary

Constructors

Constructor and Description
IntervalKeepPairFilter(java.util.List<Interval> intervals) Prepare to filter out SAMRecords that do not overlap the given list of intervals

Method Summary

Modifier and Type	Method and Description
boolean	filterOut(SAMRecord record) Determines whether a SAMRecord matches this filter.
boolean	filterOut(SAMRecord first, SAMRecord second) Determines whether a pair of SAMRecord matches this filter

Methods inherited from class java.lang.Object

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

Constructor Detail

IntervalKeepPairFilter

public IntervalKeepPairFilter(java.util.List<Interval> intervals)

Prepare to filter out SAMRecords that do not overlap the given list of intervals

Parameters:

intervals -

Method Detail

filterOut

public boolean filterOut(SAMRecord record)

Determines whether a SAMRecord matches this filter. Takes record, finds the location of its mate using the MC tag. Checks if either record overlaps the current interval using overlap detector. If yes, return false -> don't filter it out. If a read is secondary or supplementary, filter read out. Use IntervalFilter if you want to keep these reads, but NOTE: the resulting bam may not be valid.

Specified by:

filterOut in interface SamRecordFilter

Parameters:

record - the SAMRecord to evaluate

Returns:

true if the SAMRecord matches the filter, otherwise false

filterOut

public boolean filterOut(SAMRecord first,
                         SAMRecord second)

Determines whether a pair of SAMRecord matches this filter

Specified by:

filterOut in interface SamRecordFilter

Parameters:

first - the first SAMRecord to evaluate

second - the second SAMRecord to evaluate

Returns:

true if both SAMRecords do not overlap the interval list