Skip to content

Commit

Permalink
Describe case-insensitivity in a footnote, as this is not really norm…
Browse files Browse the repository at this point in the history
…ative.
  • Loading branch information
jmarshall committed Nov 5, 2024
1 parent 43419d3 commit 3cfc7b4
Showing 1 changed file with 4 additions and 3 deletions.
7 changes: 4 additions & 3 deletions SAMv1.tex
Original file line number Diff line number Diff line change
Expand Up @@ -329,9 +329,10 @@ \subsection{The header section}
& {\tt PG} & Programs used for processing the read group.\\\cline{2-3}
& {\tt PI} & Predicted median insert size, rounded to the nearest integer.\\\cline{2-3}
& {\tt PL} & Platform/technology used to produce the reads. \emph{Valid values}:
{\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 SINGULAR}, {\tt SOLID}, and {\tt ULTIMA}.
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.
The values should be written as described in uppercase, however due to the existance of public data with lowercase values tools should also accept lowercase when decoding.\\\cline{2-3}
{\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 SINGULAR}, {\tt SOLID}, and {\tt ULTIMA}.%
\footnote{The {\tt PL} value should be written in uppercase exactly as shown in this list of valid values.
Tools should also accept lowercase when reading the {\tt @RG PL} field, due to the existence of public data files with lowercase {\tt PL} values.}
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}
& {\tt PM} & Platform model. Free-form text providing further details of the platform/technology used.\\\cline{2-3}
& {\tt PU} & Platform unit (e.g., flowcell-barcode.lane for Illumina or slide for SOLiD). Unique identifier.\\\cline{2-3}
& {\tt SM} & Sample. Use pool name where a pool is being sequenced.\\\cline{1-3}
Expand Down

0 comments on commit 3cfc7b4

Please sign in to comment.