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A Java API for high-throughput sequencing data (HTS) formats
There is a newer version: 4.1.3
/*
 * The MIT License
 *
 * Copyright (c) 2009 The Broad Institute
 *
 * 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.
 */
package htsjdk.samtools;


import htsjdk.samtools.util.Iso8601Date;
import htsjdk.samtools.util.SamConstants;

import java.util.Arrays;
import java.util.Collections;
import java.util.Date;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;

/**
 * Header information about a read group.
 */
public class SAMReadGroupRecord extends AbstractSAMHeaderRecord
{
    private String mReadGroupId = null;
    public static final String READ_GROUP_ID_TAG = "ID";
    public static final String SEQUENCING_CENTER_TAG = "CN";
    public static final String DESCRIPTION_TAG = "DS";
    public static final String DATE_RUN_PRODUCED_TAG = "DT";
    public static final String FLOW_ORDER_TAG = "FO";
    public static final String KEY_SEQUENCE_TAG = "KS";
    public static final String LIBRARY_TAG = "LB";
    public static final String PROGRAM_GROUP_TAG = "PG";
    public static final String PREDICTED_MEDIAN_INSERT_SIZE_TAG = "PI";
    public static final String PLATFORM_TAG = "PL";
    public static final String PLATFORM_MODEL_TAG = "PM";
    public static final String PLATFORM_UNIT_TAG = "PU";
    public static final String READ_GROUP_SAMPLE_TAG = "SM";
    public static final String BARCODE_TAG = "BC";


    /* Platform values for the @RG-PL tag */
    public enum PlatformValue {
        /** @deprecated Use {@linkplain PlatformValue#DNBSEQ} instead. */
        @Deprecated BGI,

        /** Capillary */
        CAPILLARY,
        
        /** MGI/BGI */
        DNBSEQ,

        /** Element Biosciences */
        ELEMENT,

        /** Helicos Biosciences */
        HELICOS,

        /** Illumina */
        ILLUMINA,

        /** Iontorrent */
        IONTORRENT,

        /** 454 Life Sciences */
        LS454,

        /** Oxford Nanopore */
        ONT,

        /** @deprecated OTHER is not an official value.  It is recommended to omit PL if it is not in this list or is unknown. */
        @Deprecated OTHER,

        /** Pacific Biotechnology */
        PACBIO,
        
        /** Singular Genomics */
        SINGULAR,

        /** Life Technologies */
        SOLID,

        /** Ultima Genomics */
        ULTIMA
    }

    public static final Set STANDARD_TAGS =
            new HashSet<>(Arrays.asList(READ_GROUP_ID_TAG, SEQUENCING_CENTER_TAG, DESCRIPTION_TAG,
                    DATE_RUN_PRODUCED_TAG, FLOW_ORDER_TAG, KEY_SEQUENCE_TAG, LIBRARY_TAG,
                    PROGRAM_GROUP_TAG, PREDICTED_MEDIAN_INSERT_SIZE_TAG, PLATFORM_TAG, PLATFORM_MODEL_TAG,
                    PLATFORM_UNIT_TAG, READ_GROUP_SAMPLE_TAG, BARCODE_TAG));

    public SAMReadGroupRecord(final String id) { mReadGroupId = id; }

    public SAMReadGroupRecord(final String id, final SAMReadGroupRecord srcProgramRecord) {
        mReadGroupId = id;
        for (final Map.Entry entry : srcProgramRecord.getAttributes()) {
            setAttribute(entry.getKey(), entry.getValue());
        }
    }

    @Override
    public String getId() { return getReadGroupId();  }
    public String getReadGroupId() { return mReadGroupId; }

    public String getSample() { return getAttribute(READ_GROUP_SAMPLE_TAG); }
    public void setSample(final String value) { setAttribute(READ_GROUP_SAMPLE_TAG, value); }

    public String getLibrary() { return getAttribute(LIBRARY_TAG); }
    public void setLibrary(final String value) { setAttribute(LIBRARY_TAG, value); }

    public String getPlatformUnit() { return getAttribute(PLATFORM_UNIT_TAG); }
    public void setPlatformUnit(final String pu) { setAttribute(PLATFORM_UNIT_TAG, pu); }

    public String getPlatform() { return getAttribute(PLATFORM_TAG); }
    public void setPlatform(final String platform) { setAttribute(PLATFORM_TAG, platform); }

    /**
     * @return the List of barcodes associated with this read group or null
     */
    public List getBarcodes() {
        final String barcodeString = getAttribute(BARCODE_TAG);
        if (barcodeString == null) {
            return null;
        } else if (barcodeString.isEmpty()) {
            return Collections.emptyList();
        } else {
            return Arrays.asList(barcodeString.split(SamConstants.BARCODE_SEQUENCE_DELIMITER));
        }
    }

    /**
     * Set the barcodes associated with this ReadGroup.
     * Note that an input of null results in unsetting the attribute while an empty list is set as a tag with an empty value.
     * @param barcodes a list of barcodes to associate with this read group
     */
    public void setBarcodes(final List barcodes) {
        if (barcodes == null) {
            setAttribute(BARCODE_TAG, null);
        } else {
            if (barcodes.stream().anyMatch(String::isEmpty)) {
                throw new IllegalArgumentException("A barcode must not be an empty String");
            }
           setAttribute(BARCODE_TAG, String.join(SamConstants.BARCODE_SEQUENCE_DELIMITER, barcodes));
        }
    }

    public Date getRunDate() {
        final String dt = getAttribute(DATE_RUN_PRODUCED_TAG);
        if (dt == null) {
            return null;
        } else {
            return new Iso8601Date(dt);
        }
    }

    public String getFlowOrder() { return getAttribute(FLOW_ORDER_TAG); }
    public void setFlowOrder(final String flowOrder) { setAttribute(FLOW_ORDER_TAG, flowOrder); }

    public String getKeySequence() { return getAttribute(KEY_SEQUENCE_TAG); }
    public void setKeySequence(final String keySequence) { setAttribute(KEY_SEQUENCE_TAG, keySequence); }

    /**
     * Converts to Iso8601Date if not already in that form.
     */
    public void setRunDate(Date runDate) {
        if (runDate != null && !(runDate instanceof Iso8601Date)) {
            runDate = new Iso8601Date(runDate);
        }
        setAttribute(DATE_RUN_PRODUCED_TAG, runDate != null ? runDate.toString() : null);
    }

    public String getSequencingCenter() { return getAttribute(SEQUENCING_CENTER_TAG); }
    public void setSequencingCenter(final String center) { setAttribute(SEQUENCING_CENTER_TAG, center); }

    public String getDescription() { return getAttribute(DESCRIPTION_TAG); }
    public void setDescription(final String description) { setAttribute(DESCRIPTION_TAG, description); }

    public Integer getPredictedMedianInsertSize() {
        final String stringRep = getAttribute(PREDICTED_MEDIAN_INSERT_SIZE_TAG);
        if (stringRep == null) {
            return null;
        }
        return Integer.parseInt(stringRep); 
    }
    public void setPredictedMedianInsertSize(final Integer predictedMedianInsertSize) {

        setAttribute(PREDICTED_MEDIAN_INSERT_SIZE_TAG, (predictedMedianInsertSize == null? null: predictedMedianInsertSize.toString())); 
    }

    public String getProgramGroup() { return getAttribute(PROGRAM_GROUP_TAG); }
    public void setProgramGroup(final String programGroup) { setAttribute(PROGRAM_GROUP_TAG, programGroup); }

    public String getPlatformModel() { return getAttribute(PLATFORM_MODEL_TAG); }
    public void setPlatformModel(final String platformModel) { setAttribute(PLATFORM_MODEL_TAG, platformModel); }
    
    /**
     * @return true if this == that except for the read group ID, which is arbitrary
     */
    public boolean equivalent(final SAMReadGroupRecord that) {
        return attributesEqual(that);
    }

    @Override
    public boolean equals(final Object o) {
        if (this == o) return true;
        if (o == null || getClass() != o.getClass()) {
            return false;
        }

        final SAMReadGroupRecord that = (SAMReadGroupRecord) o;

        if (!attributesEqual(that)) {
            return false;
        }
        if (mReadGroupId != null ? !mReadGroupId.equals(that.mReadGroupId) : that.mReadGroupId != null) {
            return false;
        }

        return true;
    }

    @Override
    public int hashCode() {
        return mReadGroupId.hashCode();
    }

    @Override
    Set getStandardTags() {
        return STANDARD_TAGS;
    }

    @Override
    public String getSAMString() {
      return new SAMTextHeaderCodec().getRGLine(this);
    }
}