Added ULTIMA and ELEMENT as valid value for RG-PL according to SAM spec.

samtools / htsjdk

A Java API for high-throughput sequencing data (HTS) formats.

http://samtools.github.io/htsjdk/

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Added ULTIMA and ELEMENT as valid value for RG-PL according to SAM spec. #1619

Closed rickymagner closed 1 year ago

rickymagner commented 1 year ago

Description

The SAM Spec allows for two additional values for PL inside Read Groups than currently implemented. I added both (ELEMENT and ULTIMA), in particular so the Ultima pipelines can be updated to use this for their read group values. I also cleaned up the formatting a bit to help readability of the code / comments.