From cca15e80c9ba49444a010ea03f1dcf54864c7789 Mon Sep 17 00:00:00 2001 From: James Bonfield Date: Tue, 2 May 2023 15:21:19 +0100 Subject: [PATCH] Document the ambiguity of 1-base long seq with QUAL * This is an extreme edge case likely to never occur, but nevertheless tool implementors still need to know how to handle it. Given it *may* be QUAL 9 or it *may* be QUAL "unknown", we treat it as always unknown. Fixes #715 --- SAMv1.tex | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/SAMv1.tex b/SAMv1.tex index 97b8e74c3..f2c1f99ad 100644 --- a/SAMv1.tex +++ b/SAMv1.tex @@ -636,9 +636,13 @@ \subsection{The alignment section: mandatory fields}\label{sec:alnrecord} \item {\sf QUAL}: ASCII of base QUALity plus 33 (same as the quality string in the Sanger FASTQ format). A base quality is the phred-scaled base error probability which equals $-10\log_{10}\Pr\{\mbox{base is - wrong}\}$. 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}. + wrong}\}$. + This field can be a `*' when quality is not stored.\footnote{Note an + ambiguity exists for the unlikely case of a non-`*' sequence of length 1 + with base quality 9 (ASCII `*'). Given the ambiguity, the quality + should always deemed to be unavailable in this scenario.} + If not a `*', {\sf SEQ} must not be a `*' and the length of the quality + string ought to equal the length of {\sf SEQ}. \end{enumerate} \subsection{The alignment section: optional fields}\label{sec:alnaux}