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A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.

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/*
 * The MIT License
 *
 * Copyright (c) 2015 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 picard.filter;

import htsjdk.samtools.AlignmentBlock;
import htsjdk.samtools.SAMRecord;
import htsjdk.samtools.filter.SamRecordFilter;

/**
 * A SamRecordFilter that counts the number of bases in the reads which it filters out. Abstract and designed
 * to be sub-classed to implement the desired filter.  The filterOut method will count the number of records
 * and bases that would be filtered out using the result of the reallyFilterOut method.
 */
public abstract class CountingFilter implements SamRecordFilter {
    private long filteredRecords = 0;
    private long filteredBases = 0;

    /** Gets the number of records that have been filtered out thus far. */
    public long getFilteredRecords() { return this.filteredRecords; }

    /** Gets the number of bases that have been filtered out thus far. */
    public long getFilteredBases() { return this.filteredBases; }

    @Override
    public final boolean filterOut(final SAMRecord record) {
        final boolean filteredOut = reallyFilterOut(record);
        if (filteredOut) {
            ++filteredRecords;
            for (final AlignmentBlock block : record.getAlignmentBlocks()) {
                this.filteredBases += block.getLength();
            }
        }
        return filteredOut;
    }

    /**
     * Return true if we are to filter this record out, false otherwise.
     */
    abstract public boolean reallyFilterOut(final SAMRecord record);

    @Override
    public boolean filterOut(final SAMRecord first, final SAMRecord second) {
        throw new UnsupportedOperationException();
    }
}