org.dishevelled.bio.convert.BedRecordToFeature.java Source code

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Here is the source code for org.dishevelled.bio.convert.BedRecordToFeature.java

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/*
    
dsh-bio-convert  Convert between dishevelled and bdg-formats data models.
Copyright (c) 2013-2019 held jointly by the individual authors.
    
This library is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License as published
by the Free Software Foundation; either version 3 of the License, or (at
your option) any later version.
    
This library is distributed in the hope that it will be useful, but WITHOUT
ANY WARRANTY; with out even the implied warranty of MERCHANTABILITY or
FITNESS FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public
License for more details.
    
You should have received a copy of the GNU Lesser General Public License
along with this library;  if not, write to the Free Software Foundation,
Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA.
    
> http://www.fsf.org/licensing/licenses/lgpl.html
> http://www.opensource.org/licenses/lgpl-license.php
    
*/
package org.dishevelled.bio.convert;

import java.util.HashMap;
import java.util.Map;

import javax.annotation.concurrent.Immutable;

import com.google.common.base.Joiner;

import com.google.common.primitives.Longs;

import org.bdgenomics.convert.AbstractConverter;
import org.bdgenomics.convert.Converter;
import org.bdgenomics.convert.ConversionException;
import org.bdgenomics.convert.ConversionStringency;

import org.bdgenomics.formats.avro.Feature;
import org.bdgenomics.formats.avro.Strand;

import org.dishevelled.bio.feature.BedRecord;

import org.slf4j.Logger;

/**
 * Convert dishevelled BedRecord to bdg-formats Feature.
 *
 * @author  Michael Heuer
 */
@Immutable
final class BedRecordToFeature extends AbstractConverter<BedRecord, Feature> {

    /** Convert String to Strand. */
    private final Converter<String, Strand> strandConverter;

    /**
     * Convert dishevelled BedRecord to bdg-formats Feature.
     *
     * @param strandConverter convert String to Strand, must not be null
     */
    BedRecordToFeature(final Converter<String, Strand> strandConverter) {
        super(BedRecord.class, Feature.class);

        checkNotNull(strandConverter);
        this.strandConverter = strandConverter;
    }

    @Override
    public Feature convert(final BedRecord bedRecord, final ConversionStringency stringency, final Logger logger)
            throws ConversionException {

        if (bedRecord == null) {
            warnOrThrow(bedRecord, "must not be null", null, stringency, logger);
            return null;
        }
        final Feature.Builder fb = Feature.newBuilder().setReferenceName(bedRecord.getChrom())
                .setStart(bedRecord.getStart()).setEnd(bedRecord.getEnd());

        if (bedRecord.getFormat().isAtLeastBED4() && !isMissingValue(bedRecord.getName())) {
            fb.setName(bedRecord.getName());
        }
        if (bedRecord.getFormat().isAtLeastBED5() && !isMissingValue(bedRecord.getScore())) {
            try {
                fb.setScore(Double.valueOf(bedRecord.getScore()));
            } catch (NumberFormatException e) {
                warnOrThrow(bedRecord, "caught NumberFormatException", e, stringency, logger);
            }
        }
        if (bedRecord.getFormat().isAtLeastBED6()) {
            fb.setStrand(strandConverter.convert(bedRecord.getStrand(), stringency, logger));
        }

        if (bedRecord.getFormat().isAtLeastBED12()) {
            Map<String, String> attributes = new HashMap<String, String>();
            attributes.put("thickStart", String.valueOf(bedRecord.getThickStart()));
            attributes.put("thickEnd", String.valueOf(bedRecord.getThickEnd()));
            attributes.put("itemRgb", bedRecord.getItemRgb());
            attributes.put("blockCount", String.valueOf(bedRecord.getBlockCount()));
            attributes.put("blockSizes", Joiner.on(",").join(Longs.asList(bedRecord.getBlockSizes())));
            attributes.put("blockStarts", Joiner.on(",").join(Longs.asList(bedRecord.getBlockStarts())));
            fb.setAttributes(attributes);
        }
        return fb.build();
    }

    static boolean isMissingValue(final String value) {
        return ".".equals(value);
    }
}