From 86da59b65ec41196348f1b25489afca712ebf169 Mon Sep 17 00:00:00 2001 From: James Bonfield Date: Wed, 9 Nov 2022 11:55:01 +0000 Subject: [PATCH] SAM: add a sentence on case-insensitivity of RG PL (PR #684) This is not changing what is valid / permitted, and indeed this hopefully clarifies it further. However the practicality of dealing with wide-spread non-compliant data with lowercase PL values is that tools may wish to be lenient and use case-insensitive matching. Fixes #679 --- SAMv1.tex | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/SAMv1.tex b/SAMv1.tex index 97b8e74c3..22f38bc04 100644 --- a/SAMv1.tex +++ b/SAMv1.tex @@ -318,7 +318,8 @@ \subsection{The header section} & {\tt PI} & Predicted median insert size.\\\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 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.\\\cline{2-3} + 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 we recommend a case-insensitive approach when decoding.\\\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}