org.opencb.biodata.tools.variant.metadata.VariantMetadataUtils Maven / Gradle / Ivy

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/*
 * 
 *
 */

package org.opencb.biodata.tools.variant.metadata;

import org.apache.commons.lang3.StringUtils;
import org.opencb.biodata.formats.variant.io.VariantReader;
import org.opencb.biodata.models.metadata.Sample;
import org.opencb.biodata.models.variant.VariantFileMetadata;
import org.opencb.biodata.models.variant.metadata.VariantStudyMetadata;
import org.opencb.biodata.tools.variant.VariantVcfHtsjdkReader;
import org.opencb.commons.utils.FileUtils;

import java.io.IOException;
import java.io.InputStream;
import java.nio.file.Path;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Objects;

/**
 * Created on 08/07/16.
 *
 * @author Jacobo Coll <[email protected]>
 */
public class VariantMetadataUtils {

    /**
     * @deprecated We are not storing the header in plain text anymore
     */
    @Deprecated
    public static final String VARIANT_FILE_HEADER = "variantFileHeader";

    /**
     * Reads the VariantFileMetadata from a Vcf file given a file Path
     *
     * @param path    Path to the Vcf file
     * @param fileMetadata  Optional fileMetadata to fill up
     * @return        The read variant fileMetadata
     * @throws IOException if an I/O error occurs
     */
    public static VariantFileMetadata readVariantFileMetadata(Path path, VariantFileMetadata fileMetadata) throws IOException {
        Objects.requireNonNull(path);
        try (InputStream is = FileUtils.newInputStream(path)) {
            return readVariantFileMetadata(is, fileMetadata);
        }
    }

    /**
     * Reads the VariantFileMetadata from a Vcf file given a input stream
     *
     * @param is    Vcf input stream
     * @param fileMetadata  Optional fileMetadata to fill up
     * @return        The read variant fileMetadata
     * @throws IOException if an I/O error occurs
     */
    public static VariantFileMetadata readVariantFileMetadata(InputStream is, VariantFileMetadata fileMetadata) throws IOException {
        Objects.requireNonNull(is);
        return readVariantFileMetadata(new VariantVcfHtsjdkReader(is, fileMetadata.toVariantStudyMetadata("")), fileMetadata);
    }

    /**
     * Reads the VariantSource from a Variant file given an initialized VariantReader
     *
     * @param reader    Initialized variant reader
     * @param metadata    Optional metadata to fill up
     * @return          The read variant metadata
     * @throws IOException if an I/O error occurs
     */
    public static VariantFileMetadata readVariantFileMetadata(VariantReader reader, VariantFileMetadata metadata) throws IOException {
        Objects.requireNonNull(reader);
        if (metadata == null) {
            metadata = new VariantFileMetadata("", "");
        }

        try {
            reader.open();
            reader.pre();
            if (reader.getVariantFileMetadata() != metadata) {
                metadata.setHeader(reader.getVariantFileMetadata().getHeader());
                metadata.setSampleIds(reader.getVariantFileMetadata().getSampleIds());
                metadata.setStats(reader.getVariantFileMetadata().getStats());
                if (reader.getVariantFileMetadata().getAttributes() != null) {
                    if (metadata.getAttributes() == null) {
                        metadata.setAttributes(reader.getVariantFileMetadata().getAttributes());
                    } else {
                        metadata.getAttributes().putAll(reader.getVariantFileMetadata().getAttributes());
                    }
                }
            }

            reader.post();
        } finally {
            reader.close();
        }
        return metadata;
    }

    /**
     * Get sample names form a variant study metadata.
     *
     * @param variantStudyMetadata  Variant study metadata target
     * @return                      List of sample names
     */
    public static List getSampleNames(VariantStudyMetadata variantStudyMetadata) {
        if (variantStudyMetadata == null) {
            return null;
        }

        List sampleNames = new ArrayList<>();
        if (variantStudyMetadata.getIndividuals() != null) {
            for (org.opencb.biodata.models.metadata.Individual individual : variantStudyMetadata.getIndividuals()) {
                for (Sample sample : individual.getSamples()) {
                    if (!StringUtils.isEmpty(sample.getId())) {
                        sampleNames.add(sample.getId());
                    }
                }
            }
        }
        return sampleNames;
    }
}