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Fix minor typos in the CRAM tag type lists (PR #761) #761

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Mar 21, 2024
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Fix minor typos in the CRAM tag type lists (PR #761) #761

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4 changes: 2 additions & 2 deletions CRAMv3.tex
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Original file line number Diff line number Diff line change
Expand Up @@ -863,7 +863,7 @@ \subsubsection*{Tag encodings}
Thus per alignment record we only need to store tag values and not their ids and types.

The TD is written as a byte array consisting of $L_{i}$ values separated with \textbackslash{}0.
Each $L_{i}$ value is written as a concatenation of 3 byte $T_{ij}$ elements: tag id followed by BAM tag type code (one of A, c, C, s, S, i, I, f, F, Z, H or B, as described in the SAM specification).
Each $L_{i}$ value is written as a concatenation of 3 byte $T_{ij}$ elements: tag id followed by BAM tag type code (one of A, c, C, s, S, i, I, f, Z, H or B, as described in the SAM specification).
For example the TD for tag lists X1:i BC:Z SA:Z and X1:i BC:Z may be encoded as X1CBCZSAZ\textbackslash{}0X1CBCZ\textbackslash{}0, with X1C indicating a 1 byte unsigned value for tag X1.

\subsubsection*{Tag values}
Expand Down Expand Up @@ -1546,7 +1546,7 @@ \subsection{Auxiliary tags}
\end{algorithmic}

In the above procedure, $name$ is a two letter tag name and $type$ is one of the permitted types documented in the SAM/BAM specification.
Type is \texttt{c} (signed 8-bit integer), \texttt{C} (unsigned 8-bit integer), \texttt{s} (signed 16-bit integer), \texttt{S} (unsigned 16-bit integer), \texttt{i} (signed 32-bit integer), \texttt{I} (unsigned 32-bit integer), \texttt{f} (32-bit float), \texttt{Z} (nul-terminated string), \texttt{H} (nul-terminated string of hex digits) and \texttt{B} (binary data in array format with the first byte being one of c,C,s,S,i,I,f using the meaning above, a 32-bit integer for the number of array elements, followed by array data encoded using the specified format). All integers are little endian encoded.
Type is \texttt{A} (a single character), \texttt{c} (signed 8-bit integer), \texttt{C} (unsigned 8-bit integer), \texttt{s} (signed 16-bit integer), \texttt{S} (unsigned 16-bit integer), \texttt{i} (signed 32-bit integer), \texttt{I} (unsigned 32-bit integer), \texttt{f} (32-bit float), \texttt{Z} (nul-terminated string), \texttt{H} (nul-terminated string of hex digits) and \texttt{B} (binary data in array format with the first byte being one of c,C,s,S,i,I,f using the meaning above, a 32-bit integer for the number of array elements, followed by array data encoded using the specified format). All integers are little endian encoded.

For example a SAM tag \texttt{MQ:i} has name \texttt{MQ} and type \texttt{i} and will be decoded using one of MQc, MQC, MQs, MQS, MQi and MQI data series depending on size and sign of the integer value.

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