/*
* The MIT License
*
* Copyright (c) 2009 The Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
package htsjdk.samtools.filter;
import htsjdk.samtools.SAMRecord;
/**
* Filter to either include or exclude aligned reads
*
* $Id$
*/
public class AlignedFilter implements SamRecordFilter {
private boolean includeAligned = false;
public AlignedFilter(final boolean includeAligned) {
this.includeAligned = includeAligned;
}
/**
* Determines whether a SAMRecord matches this filter
*
* @param record the SAMRecord to evaluate
*
* @return true if the SAMRecord matches the filter, otherwise false
*/
public boolean filterOut(final SAMRecord record) {
if (includeAligned) {
if (!record.getReadUnmappedFlag()) {
return false;
}
} else {
// exclude aligned
if (record.getReadUnmappedFlag()) {
return false;
}
}
return true;
}
/**
* Determines whether a pair of SAMRecord matches this filter
*
* @param first the first SAMRecord to evaluate
* @param second the second SAMRecord to evaluate
*
* @return true if the SAMRecords matches the filter, otherwise false
*/
public boolean filterOut(final SAMRecord first, final SAMRecord second) {
if (includeAligned) {
// both first and second must be mapped for it to not be filtered out
if (!first.getReadUnmappedFlag() && !second.getReadUnmappedFlag()) {
return false;
}
} else {
// exclude aligned - if either first or second is unmapped don't filter it out
if (first.getReadUnmappedFlag() || second.getReadUnmappedFlag()) {
return false;
}
}
return true;
}
}