diff --git a/SAMv1.tex b/SAMv1.tex index c1d76d1a..28467b9a 100644 --- a/SAMv1.tex +++ b/SAMv1.tex @@ -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. @@ -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}