Package htsjdk.samtools.filter

Interface SamRecordFilter

All Known Implementing Classes:

AggregateFilter, AlignedFilter, DuplicateReadFilter, FailsVendorReadQualityFilter, HtsgetBAMFileReader.BAMQueryMultipleIntervalsIteratorFilter, InsertSizeFilter, IntervalFilter, IntervalKeepPairFilter, InvertFilter, JavascriptSamRecordFilter, MappingQualityFilter, NotPrimaryAlignmentFilter, OverclippedReadFilter, ReadNameFilter, SecondaryAlignmentFilter, SecondaryOrSupplementaryFilter, SolexaNoiseFilter, TagFilter, WholeReadClippedFilter

public interface SamRecordFilter

API for filtering SAMRecords $Id$

Method Summary

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

Method Details

filterOut

boolean filterOut(SAMRecord record)

Determines whether a SAMRecord matches this filter

Parameters:

record - the SAMRecord to evaluate

Returns:

true if the SAMRecord matches the filter, otherwise false

filterOut

boolean filterOut(SAMRecord first,
 SAMRecord second)

Determines whether a pair of SAMRecords matches this filter

Parameters:

first - the first SAMRecord to evaluate

second - the second SAMRecord to evaluate

Returns:

true if the pair of records matches filter, otherwise false