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Copy the tag type text from SAM spec to SAMtags (PR #804) #804

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Copy the tag type text from SAM spec to SAMtags (PR #804) #804

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42 changes: 33 additions & 9 deletions SAMtags.tex
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Expand Up @@ -42,17 +42,41 @@

\section{Standard tags}

All optional fields follow the {\tt TAG:TYPE:VALUE} format
where {\tt TAG} is a two-character string that matches {\tt /[A-Za-z][A-Za-z0-9]/}.
In an optional field, {\tt TYPE} is a single case-sensitive letter which
defines the format of {\tt VALUE}:
\begin{center}\small
\begin{tabular}{cll}
\hline
{\bf Type} & {\bf Regexp matching {\tt VALUE}} & {\bf Description} \\
\hline
A & {\tt [!-\char126]} & Printable character \\
i & {\tt [-+]?[0-9]+} & Signed integer\footnotemark\\
f & {\tt [-+]?[0-9]*\char92.?[0-9]+([eE][-+]?[0-9]+)?} & Single-precision floating number \\
Z & {\tt [\,\,\,!-\char126]*} & Printable string, including space\\
H & {\tt ([0-9A-F][0-9A-F])*} & Byte array in the Hex format\footnotemark\\
B & {\tt [cCsSiIf](,[-+]?[0-9]*\char92.?[0-9]+([eE][-+]?[0-9]+)?)*} & Integer or numeric array\\
\hline
\end{tabular}
\addtocounter{footnote}{-1}
\footnotetext{The number of digits in an integer optional field is not
explicitly limited in SAM. However, BAM can represent values in the
range~$[-2^{31},2^{32})$, so in practice this is the realistic range
of values for SAM's `{\tt i}' as well.}
\stepcounter{footnote}
\footnotetext{For example, the six-character Hex string `{\tt 1AE301}' represents the byte array $[{\tt 0x1a},{\tt 0xe3},{\tt 0x1}]$.}
\end{center}
For an integer or numeric array (type `{\tt B}'), the first letter indicates the type of numbers
in the following comma separated array. The letter can be one of `{\tt cCsSiIf}', corresponding to
{\tt int8\_t} (signed 8-bit integer), {\tt uint8\_t} (unsigned 8-bit integer), {\tt int16\_t}, {\tt uint16\_t}, {\tt int32\_t}, {\tt uint32\_t}
and {\tt float}, respectively.\footnotemark\@ During import/export, the element type
may be changed if the new type is also compatible with the array.
\footnotetext{Explicit typing eases format parsing and helps to reduce the file size when SAM is converted to BAM.}

\vspace*{1em}
Predefined standard tags are listed in the following table and described
in greater detail in later subsections.
Optional fields are usually displayed as {\tt TAG:TYPE:VALUE}; the {\it type\/}
may be one of
{\tt A} (character),
{\tt B} (general array),
{\tt f} (real number),
{\tt H} (hexadecimal array),
{\tt i} (integer),
or
{\tt Z} (string).

\begin{center}\small
% This table is sorted alphabetically
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