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Document the ambiguity of 1-base long seq with QUAL * #724

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Document the ambiguity of 1-base long seq with QUAL * #724

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10 changes: 7 additions & 3 deletions SAMv1.tex
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Expand Up @@ -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}
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