/*
* The MIT License
*
* Copyright (c) 2014 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.vcf.filter;
import htsjdk.samtools.util.CollectionUtil;
import htsjdk.variant.variantcontext.VariantContext;
import htsjdk.variant.vcf.VCFFilterHeaderLine;
import java.util.List;
/**
* Filters out sites that have a QD annotation applied to them and where the QD value is lower than a
* lower limit.
*
* @author Tim Fennell
*/
public class QdFilter implements VariantFilter {
public static final String FILTER_NAME = "LowQD";
private final double minimumQd;
public QdFilter(final double minimumQd) {
this.minimumQd = minimumQd;
}
@Override public String filter(final VariantContext ctx) {
final double qd = ctx.getAttributeAsDouble("QD", -1d); // If QD is missing, return -1
// QD should always be positive so a value < 0 indicates a missing value
if (qd >= 0 && qd < minimumQd) {
return FILTER_NAME;
}
else {
return null;
}
}
@Override
public List<VCFFilterHeaderLine> headerLines() {
return CollectionUtil.makeList(new VCFFilterHeaderLine(FILTER_NAME, "Site exhibits QD value below a hard limit."));
}
}