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/*
* The MIT License (MIT)
* Copyright (c) 2016-2017 Intel Corporation
*
* 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.
*/
import org.genomicsdb.exception.GenomicsDBException;
import org.genomicsdb.importer.GenomicsDBImporter;
import org.genomicsdb.model.CommandLineImportConfig;
import org.json.simple.parser.ParseException;
import java.util.Arrays;
import java.io.IOException;
public final class TestGenomicsDBImporterWithMergedVCFHeader {
public static void main(String[] args) throws IOException, GenomicsDBException, ParseException, InterruptedException {
CommandLineImportConfig config = new CommandLineImportConfig("TestGenomicsDBImporterWithMergedVCFHeader", args);
GenomicsDBImporter importer = new GenomicsDBImporter(config);
if (config.getNumberCoalesceContigs() > 0) {
importer.coalesceContigsIntoNumPartitions(config.getNumberCoalesceContigs());
}
if (config.getConsolidateOnlyThreads() >= 0) {
importer.doConsolidate(config.getConsolidateOnlyThreads());
}
else{
importer.executeImport();
}
}
}
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