Add --umi_tag option to output UMI as a SAM-style tag (e.g. XR:Z:UMI) - #713
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When --umi_tag is specified (e.g. --umi_tag=XR), the UMI is written as a SAM optional tag after the read name (name XR:Z:UMI) instead of being appended to the name with --umi_delim. Legacy behavior is unchanged. Adds validation for the 2-character tag name and unit tests.
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Implements the UMI tag output suggested in #226.
What
Adds a new optional
--umi_tag=<TAG>parameter (e.g.--umi_tag=XR). When specified, the UMI is written as a SAM-style optional tag after the first field of the read name instead of being appended to the name:Notes
XR,RX);--umi_prefixstill applies inside the tag value (XR:Z:UMI_TCGACC_GCGTAA).--umi_delimcontinues to control only the default name-append mode; the_separator between per_read/per_index UMI parts is unchanged.--umi_tagwithout--umiand malformed tag names.UmiProcessor::test();./fastp testpasses.