Examples with SAMTag htsjdk.samtools.SAMTag used on opensource projects

Example 1 with SAMTag

use of htsjdk.samtools.SAMTag in project gridss by PapenfussLab.

the class ComputeSamTags method validateParameters.

private void validateParameters() {
    if (isReferenceRequired()) {
        IOUtil.assertFileIsReadable(REFERENCE_SEQUENCE);
    }
    IOUtil.assertFileIsReadable(INPUT);
    IOUtil.assertFileIsWritable(OUTPUT);
    for (String t : TAGS) {
        try {
            SAMTag tag = SAMTag.valueOf(t);
            switch(tag) {
                case CC:
                case CP:
                case FI:
                case HI:
                case IH:
                case NM:
                case Q2:
                case R2:
                case MC:
                case MQ:
                case SA:
                case TC:
                    break;
                default:
                    String msg = String.format("%s is not a predefined standard SAM tag able to be computed with no additional information.", t);
                    log.error(msg);
                    throw new RuntimeException(msg);
            }
        } catch (IllegalArgumentException e) {
        // ignore
        }
    }
}