AlignmentDataset.java

/*
 * Copyright 2015 OpenCB
 *
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
 * You may obtain a copy of the License at
 *
 *     http://www.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 */

package org.opencb.hpg.bigdata.core.lib;

import org.opencb.commons.datastore.core.Query;

/**
 * Created by imedina on 04/08/16.
 */
public class AlignmentDataset extends ParentDataset<AlignmentDataset> {

    private AlignmentParseQuery alignmentParseQuery;
    private String sql;

    public AlignmentDataset() {
        alignmentParseQuery = new AlignmentParseQuery();
    }

    @Override
    protected void updateDataset(Query query) {
        if (this.sql == null) {
            this.sql = alignmentParseQuery.parse(query, null, viewName);
            this.ds = this.sqlContext.sql(this.sql);
        }
    }

    // mapping quality filter
    public AlignmentDataset mappingQualityFilter(String value) {
        query.put("mapq", value);
        return this;
    }

    // template length filter
    public AlignmentDataset templateLengthFilter(String value) {
        query.put("tlen", value);
        return this;
    }

    // alignment length filter
    public AlignmentDataset alignmentLengthFilter(String value) {
        query.put("alen", value);
        return this;
    }

    // alignment length filter
    public AlignmentDataset flagFilter(String value) {
        return flagFilter(value, false);
    }

    public AlignmentDataset flagFilter(String value, Boolean exclude) {
        if (exclude) {
            query.put("filtering-flag", value);
        } else {
            query.put("required-flag", value);
        }
        return this;
    }
}