From a8550efeaa6ab2c6147ce4f854bb157bae2a5a53 Mon Sep 17 00:00:00 2001 From: James Bonfield Date: Mon, 29 Jan 2024 16:37:35 +0000 Subject: [PATCH] Document SAM ambiguity of 1bp long seq with QUAL "*". "*" is either QUAL 9, or QUAL unavailable. Made a recommendation in a footnote, mainly as an indication that the ambiguity exists. In practice it's vanishingly unlikely to matter. Fixes #715 --- SAMv1.tex | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/SAMv1.tex b/SAMv1.tex index 4dd87570..28467b9a 100644 --- a/SAMv1.tex +++ b/SAMv1.tex @@ -651,6 +651,10 @@ \subsection{The alignment section: mandatory fields}\label{sec:alnrecord} wrong}\}$. This field can be a `*' when quality is not stored. If not a `*', {\sf SEQ} must not be a `*' and the length of the quality string ought to equal the length of {\sf SEQ}. + \footnote{There is a small ambiguity with a sequence exactly one + base-pair long having quality 9. This is ASCII `*' so it could be + interpreted as either QUAL 9 or as quality unavailable. Given + this ambiguity, we recommend interpreting it as unavailable.} \end{enumerate} \subsection{The alignment section: optional fields}\label{sec:alnaux}