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yfarjounjmarshall
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Add ULTIMA (Ultima Genomics) as a legal value for the PL tag (PR #662)
Closes #648.
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SAMv1.tex

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@@ -317,7 +317,7 @@ \subsection{The header section}
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& {\tt PG} & Programs used for processing the read group.\\\cline{2-3}
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& {\tt PI} & Predicted median insert size.\\\cline{2-3}
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& {\tt PL} & Platform/technology used to produce the reads. \emph{Valid values}:
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{\tt CAPILLARY}, {\tt DNBSEQ} (MGI/BGI), {\tt ELEMENT}, {\tt HELICOS}, {\tt ILLUMINA}, {\tt IONTORRENT}, {\tt LS454}, {\tt ONT} (Oxford Nanopore), {\tt PACBIO} (Pacific Biosciences), and {\tt SOLID}.
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{\tt CAPILLARY}, {\tt DNBSEQ} (MGI/BGI), {\tt ELEMENT}, {\tt HELICOS}, {\tt ILLUMINA}, {\tt IONTORRENT}, {\tt LS454}, {\tt ONT} (Oxford Nanopore), {\tt PACBIO} (Pacific Biosciences), {\tt SOLID}, and {\tt ULTIMA}.
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This field should be omitted when the technology is not in this list (though the {\tt PM} field may still be present in this case) or is unknown.\\\cline{2-3}
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& {\tt PM} & Platform model. Free-form text providing further details of the platform/technology used.\\\cline{2-3}
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& {\tt PU} & Platform unit (e.g., flowcell-barcode.lane for Illumina or slide for SOLiD). Unique identifier.\\\cline{2-3}
@@ -1442,7 +1442,7 @@ \section{SAM Version History}\label{sec:history}
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\subsection*{1.6: 28 November 2017 to current}
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\begin{itemize}
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\item Add {\tt ELEMENT} to the list of {\tt @RG PL} header tag values. (Aug 2022)
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\item Add {\tt ELEMENT} and {\tt ULTIMA} to the list of {\tt @RG PL} header tag values. (Aug 2022)
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\item Clarify that header field tags must be distinct within each line, and that the ordering of both header fields and alignment optional fields is not significant. (Jun 2021)
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\item Clarify the meaning of TLEN when secondary alignments are present. (May 2021)
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\item Bin calculation changed for alignment records whose CIGAR strings consume no reference bases: like unmapped records, they are considered to have length one (rather than zero). (Jan 2021)

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