/**
   * Creates an empty GATKSAMRecord with the read's header, read group and mate information, but
   * empty (not-null) fields: - Cigar String - Read Bases - Base Qualities
   *
   * <p>Use this method if you want to create a new empty GATKSAMRecord based on another
   * GATKSAMRecord
   *
   * @param read a read to copy the header from
   * @return a read with no bases but safe for the GATK
   */
  public static GATKSAMRecord emptyRead(GATKSAMRecord read) {
    final GATKSAMRecord emptyRead = new GATKSAMRecord(read.getHeader());
    emptyRead.setReferenceIndex(read.getReferenceIndex());
    emptyRead.setAlignmentStart(0);
    emptyRead.setMappingQuality(0);
    // setting read indexing bin last
    emptyRead.setFlags(read.getFlags());
    emptyRead.setMateReferenceIndex(read.getMateReferenceIndex());
    emptyRead.setMateAlignmentStart(read.getMateAlignmentStart());
    emptyRead.setInferredInsertSize(read.getInferredInsertSize());

    emptyRead.setCigarString("");
    emptyRead.setReadBases(new byte[0]);
    emptyRead.setBaseQualities(new byte[0]);

    SAMReadGroupRecord samRG = read.getReadGroup();
    emptyRead.clearAttributes();
    if (samRG != null) {
      GATKSAMReadGroupRecord rg = new GATKSAMReadGroupRecord(samRG);
      emptyRead.setReadGroup(rg);
    }

    GATKBin.setReadIndexingBin(emptyRead, 0);

    return emptyRead;
  }
Example #2
0
  // copied from LocusViewTemplate
  protected GATKSAMRecord buildSAMRecord(
      final String readName, final String contig, final int alignmentStart) {
    GATKSAMRecord record = new GATKSAMRecord(header);

    record.setReadName(readName);
    record.setReferenceIndex(dictionary.getSequenceIndex(contig));
    record.setAlignmentStart(alignmentStart);

    record.setCigarString("1M");
    record.setReadString("A");
    record.setBaseQualityString("A");
    record.setReadGroup(readGroup);

    return record;
  }