VariantFilter.java

/*
 * 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.variant.variantcontext.VariantContext;
import htsjdk.variant.vcf.VCFFilterHeaderLine;

import java.util.List;

/**
 * Interface for classes that can generate filters for VariantContexts. The contract is that a
 * VariantContext is provided, and if the variant should be filtered out then the filter string
 * should be returned, otherwise null.
 *
 * @author tfennell
 */
public interface VariantFilter {
    /** Check to see if the VariantContext should have a filter applied to it. If so return the filter string, otherwise return null. */
    public String filter(final VariantContext ctx);

    /** Return VCF header lines that define filters that may be applied by the VariantFilter. */
    public List<VCFFilterHeaderLine> headerLines();
}