Java GATKRead.getLength Examples

Example #1

File: ReadGroupCovariate.java Project: heuermh/gatk

  @Override
  public void recordValues(
      final GATKRead read, final SAMFileHeader header, final ReadCovariates values) {
    final SAMReadGroupRecord rg = ReadUtils.getSAMReadGroupRecord(read, header);
    final String readGroupId = getID(rg);
    final int key = keyForReadGroup(readGroupId);

    final int readLength = read.getLength();
    for (int i = 0; i < readLength; i++) {
      values.addCovariate(key, key, key, i);
    }
  }