コード例 #1
0
  /**
   * Generates tab delimited string containing details about the passed SAMReadGroupRecord
   *
   * @param readGroupRecord record
   * @return tab delimited string containing details about the SAMReadGroupRecord
   */
  private String getReadGroupDetails(final SAMReadGroupRecord readGroupRecord) {
    final List<String> elements = new ArrayList<>(5);

    final String tmp[] =
        readGroupRecord
            .getPlatformUnit()
            .split("\\."); // Expect to look like: D047KACXX110901.1.ACCAACTG
    String runBarcode = "?";
    String lane = "?";
    String molBarcode = "?";
    if ((tmp.length == 3) || (tmp.length == 2)) {
      runBarcode = tmp[0];
      lane = tmp[1];
      molBarcode =
          (tmp.length == 3)
              ? tmp[2]
              : ""; // In older BAMS there may be no molecular barcode sequence
    } else {
      log.error("Unexpected format " + readGroupRecord.getPlatformUnit() + " for PU attribute");
    }
    elements.add(runBarcode);
    elements.add(lane);
    elements.add(molBarcode);
    elements.add(readGroupRecord.getLibrary());
    elements.add(readGroupRecord.getSample());
    return String.join("\t", elements);
  }
コード例 #2
0
ファイル: ReadGroupCovariate.java プロジェクト: heuermh/gatk
 /** Get the ID of the readgroup. */
 public static String getID(final SAMReadGroupRecord rg) {
   final String pu = rg.getPlatformUnit();
   return pu == null ? rg.getId() : pu;
 }
コード例 #3
0
ファイル: ReadUtils.java プロジェクト: AriesLL/gatk
 /**
  * Returns the platform unit associated with the provided read's read group.
  *
  * @param read read whose platform unit to retrieve
  * @param header SAM header containing read groups
  * @return the platform unit for the provided read's read group as a String, or null if the read
  *     has no read group.
  */
 public static String getPlatformUnit(final GATKRead read, final SAMFileHeader header) {
   final SAMReadGroupRecord readGroup = getSAMReadGroupRecord(read, header);
   return readGroup != null ? readGroup.getPlatformUnit() : null;
 }