/*
 * 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 picard.analysis.directed;

import picard.cmdline.CommandLineProgramProperties;
import picard.cmdline.Option;
import picard.cmdline.programgroups.Metrics;

import static picard.cmdline.StandardOptionDefinitions.MINIMUM_MAPPING_QUALITY_SHORT_NAME;

/**
 * Calculates a set of HS metrics from a sam or bam file.  See HsMetricsCollector and CollectTargetedMetrics for more details.
 *
 * @author Tim Fennell
 */

@CommandLineProgramProperties(
        usage = "DEPRECATED: Use CollectHsMetrics instead. Calculates a set of Hybrid Selection specific metrics from an aligned SAM" +
                "or BAM file. If a reference sequence is provided, AT/GC dropout metrics will " +
                "be calculated, and the PER_TARGET_COVERAGE option can be used to output GC and " +
                "mean coverage information for every target.",
        usageShort = "DEPRECATED: Use CollectHsMetrics instead.",
        programGroup = Metrics.class
)
@Deprecated
public class CalculateHsMetrics extends CollectHsMetrics {

    @Option(shortName = MINIMUM_MAPPING_QUALITY_SHORT_NAME, doc = "Minimum mapping quality for a read to contribute coverage.", overridable = true)
    public int MINIMUM_MAPPING_QUALITY = 1;

    @Option(shortName = "Q", doc = "Minimum base quality for a base to contribute coverage.", overridable = true)
    public int MINIMUM_BASE_QUALITY = 0;

    @Option(doc = "True if we are to clip overlapping reads, false otherwise.", optional=true)
    public boolean CLIP_OVERLAPPING_READS = false;

}
