LocalAlignmentStoragePipelineTest.java

/*
 * Copyright 2015-2016 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.opencga.storage.core.alignment.local;

import org.junit.Test;
import org.opencb.biodata.models.alignment.RegionCoverage;
import org.opencb.commons.datastore.core.Query;
import org.opencb.commons.datastore.core.QueryOptions;
import org.opencb.commons.datastore.core.QueryResult;

import java.net.URI;
import java.nio.file.Paths;

/**
 * Created by imedina on 01/11/16.
 */
public class LocalAlignmentStoragePipelineTest {
    @Test
    public void transform() throws Exception {
////        String inputPath = getClass().getResource("/HG00096.chrom20.small.bam").toString();
//        String inputPath = "/tmp/kk/ebi.bam";
////        String inputPath = "/tmp/kk/HG00096.chrom20.small.bam";
//        String outputPath = "/tmp/kk/";
//        System.out.println("inputPath = " + inputPath);
//        DefaultAlignmentStorageETL storageETL = new DefaultAlignmentStorageETL();
//        storageETL.transform(new URI(inputPath), null, new URI(outputPath));
    }

    @Test
    public void meanCoverage() {
//        DefaultAlignmentDBAdaptor adaptor = new DefaultAlignmentDBAdaptor();
//
//        String inputPath = "/tmp/kk/ebi.bam";
////        String inputPath = "/tmp/kk/HG00096.chrom20.small.bam";
//        String outputPath = "/tmp/kk/";
//        Query query = new Query();
////        query.put("region", "20:1-70000000");
//        query.put("region", "gi|30407139|emb|AL111168.1|:1-70000000");
//        QueryOptions queryOptions = new QueryOptions();
//        queryOptions.put("contained", false);
//
//        try {
//            QueryResult<RegionCoverage> res = adaptor.coverage(Paths.get(inputPath), Paths.get(outputPath),
//                    query, queryOptions);
//            System.out.println(res.getResult().get(0).toJSON());
//        } catch (Exception e) {
//            e.printStackTrace();
//        }
    }
}