/*
* 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;
}
}