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Recommend 1bp SEQ with QUAL="*" as quality-unavailable. #752

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Recommend 1bp SEQ with QUAL="*" as quality-unavailable. #752

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2543789
Trivial: change type of non-breaking space in SAM spec.
jkbonfield Jan 29, 2024
a8550ef
Document SAM ambiguity of 1bp long seq with QUAL "*".
jkbonfield Jan 29, 2024
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6 changes: 5 additions & 1 deletion SAMv1.tex
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Expand Up @@ -75,7 +75,7 @@ \section{The SAM Format Specification}
Alternatively and equivalently, SAM files are encoded in UTF-8 but non-ASCII characters are permitted only within certain field values as explicitly specified in the descriptions of those fields.%
\footnote{Hence in particular SAM files must not begin with a byte order mark~(BOM) and lines of text are delimited by ASCII line terminator characters only.
% Unicode identifies VT and FF as line break characters as well, but no one uses them in SAM.
In addition to the local platform's text file line termination conventions, implementations may wish to support \textsc{lf} and \textsc{cr\>lf} for interoperability with other platforms.}
In addition to the local platform's text file line termination conventions, implementations may wish to support \textsc{lf} and \textsc{cr\,lf} for interoperability with other platforms.}

Where it makes a difference, SAM file contents should be read and written using the POSIX\,/\,C locale.
For example, floating-point values in SAM always use `{\tt .}' for the decimal-point character.
Expand Down Expand Up @@ -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}
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