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Change BAM and BAI length/count fields to uint32_t (PRs #460, #476)
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These fields are by definition unsigned, but add notes on their usual
ranges -- which mostly do not extend beyond the int32_t maximum and
mostly are much smaller.

Co-authored-by: John Marshall <[email protected]>
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@brainstorm @jmarshall
brainstorm and jmarshall committed Apr 30, 2020
1 parent 82e60fc commit 31d6e44
Showing 1 changed file with 30 additions and 16 deletions.
46 changes: 30 additions & 16 deletions SAMv1.tex
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Original file line number Diff line number Diff line change
Expand Up @@ -36,6 +36,8 @@
\newcommand*{\cclass}[1]{{\rm\sf :#1:}}
\newcommand*{\caret}{\textsuperscript{$\wedge$}}

\newcommand*{\memlimited}{\textcolor{gray}{\footnotesize\it limited}}

\begin{document}

\input{SAMv1.ver}
Expand Down Expand Up @@ -1027,23 +1029,24 @@ \subsection{The BAM format}
\cline{1-6}
\multicolumn{3}{|c|}{\bf Field} & \multicolumn{1}{c|}{\bf Description} & \multicolumn{1}{c|}{\bf Type} & \multicolumn{1}{c|}{\bf Value} \\\cline{1-6}
\multicolumn{3}{|l|}{\sf magic} & BAM magic string & {\tt char[4]} & {\tt BAM\char92 1}\\\cline{1-6}
\multicolumn{3}{|l|}{\sf l\_text} & Length of the header text, including any {\tt NUL} padding & {\tt int32\_t} & \\\cline{1-6}
\multicolumn{3}{|l|}{\sf l\_text} & Length of the header text, including any {\tt NUL} padding & {\tt uint32\_t} & $< 2^{31}$ \\\cline{1-6}
\multicolumn{3}{|l|}{\sf text} & Plain header text in SAM; not necessarily {\tt NUL}-terminated & {\tt char[{\sf l\_text}]} & \\\cline{1-6}
\multicolumn{3}{|l|}{\sf n\_ref} & \# reference sequences & {\tt int32\_t} & \\\cline{1-6}
% Pedantically this should be <= but we restrict |refs| by one so n_ref fits in a signed 32-bit int.
\multicolumn{3}{|l|}{\sf n\_ref} & \# reference sequences & {\tt uint32\_t} & $< 2^{31}$ \\\cline{1-6}
\multicolumn{6}{|c|}{\textcolor{gray}{\it List of reference information (n=n\_ref)}} \\\cline{2-6}
& \multicolumn{2}{l|}{\sf l\_name} & Length of the reference name plus 1 (including {\tt NUL}) & {\tt int32\_t} & \\\cline{2-6}
& \multicolumn{2}{l|}{\sf l\_name} & Length of the reference name plus 1 (including {\tt NUL}) & {\tt uint32\_t} & \memlimited \\\cline{2-6}
& \multicolumn{2}{l|}{\sf name} & Reference sequence name; {\tt NUL}-terminated & {\tt char[{\sf l\_name}]} & \\\cline{2-6}
& \multicolumn{2}{l|}{\sf l\_ref} & Length of the reference sequence & {\tt int32\_t} & \\\cline{1-6}
& \multicolumn{2}{l|}{\sf l\_ref} & Length of the reference sequence & {\tt uint32\_t} & $< 2^{31}$ \\\cline{1-6}
\multicolumn{6}{|c|}{\textcolor{gray}{\it List of alignments (until the end of the file)}} \\\cline{2-6}
& \multicolumn{2}{l|}{\sf block\_size} & Total length of the alignment record, excluding this field & {\tt int32\_t} & \\\cline{2-6}
& \multicolumn{2}{l|}{\sf block\_size} & Total length of the alignment record, excluding this field & {\tt uint32\_t} & \memlimited \\\cline{2-6}
& \multicolumn{2}{l|}{\sf refID} & Reference sequence ID, $-1\leq{\sf refID}<{\sf n\_ref}$; -1 for a read without a mapping position & {\tt int32\_t} & [-1] \\\cline{2-6}
& \multicolumn{2}{l|}{\sf pos} & 0-based leftmost coordinate ($=\underline{\sf POS}-1$)& {\tt int32\_t} & [-1]\\\cline{2-6}
& \multicolumn{2}{l|}{\sf l\_read\_name} & Length of {\sf read\_name} below ($={\sf length}(\underline{\sf QNAME})+1$) & {\tt uint8\_t} & \\\cline{2-6}
& \multicolumn{2}{l|}{\sf mapq} & Mapping quality (=\underline{\sf MAPQ}) & {\tt uint8\_t} & \\\cline{2-6}
& \multicolumn{2}{l|}{\sf bin} & BAI index bin, see Section~\ref{sec:bin-field} & {\tt uint16\_t} & \\\cline{2-6}
& \multicolumn{2}{l|}{\sf n\_cigar\_op} & Number of operations in \underline{\sf CIGAR}, see Section~\ref{sec:ncigar} & {\tt uint16\_t} & \\\cline{2-6}
& \multicolumn{2}{l|}{\sf flag} & Bitwise flags (= \underline{\sf FLAG})\footnotemark\ & {\tt uint16\_t} & \\\cline{2-6}
& \multicolumn{2}{l|}{\sf l\_seq} & Length of \underline{\sf SEQ} & {\tt int32\_t} & \\\cline{2-6}
& \multicolumn{2}{l|}{\sf l\_seq} & Length of \underline{\sf SEQ} & {\tt uint32\_t} & \memlimited \\\cline{2-6}
& \multicolumn{2}{l|}{\sf next\_refID} & Ref-ID of the next segment ($-1\le{\sf next\_refID}<{\sf n\_ref}$) & {\tt int32\_t} & [-1] \\\cline{2-6}
& \multicolumn{2}{l|}{\sf next\_pos} & 0-based leftmost pos of the next segment ($=\underline{\sf PNEXT}-1$) & {\tt int32\_t} & [-1] \\\cline{2-6}
& \multicolumn{2}{l|}{\sf tlen} & Template length ($=\underline{\sf TLEN}$) & {\tt int32\_t} & [0] \\\cline{2-6}
Expand All @@ -1064,6 +1067,13 @@ \subsection{The BAM format}
\stepcounter{footnote}
\footnotetext{For backward compatibility, an absent {\sf QNAME} (represented as `{\tt *}' in SAM) is stored as a C string {\tt "*\char92 0"}.}
\noindent
Most length and count fields described as {\tt uint32\_t} have additional constraints on their range:
$\mbox{\sf l\_text} < 2^{31}$ due to implementation limits;
$\mbox{\sf n\_ref} < 2^{31}$ because {\sf refID} and {\sf next\_refID} are signed;
$\mbox{\sf l\_ref} < 2^{31}$ because {\sf tlen} is signed;
those marked ``\textit{limited}'' are limited by available memory and the practical size of the data represented well before they are limited by, e.g., Java's signed 32-bit integer maximum array size.
\subsubsection{BIN field calculation}\label{sec:bin-field}
{\sf BIN} is calculated using the {\sf reg2bin()} function in
Section~\ref{sec:code}.
Expand Down Expand Up @@ -1147,9 +1157,10 @@ \subsubsection{Auxiliary data encoding}\label{sec:aux-type-codes}
\newcommand*{\arraytagfield}[3]{\tagfield{B}{\bytebox{1}{\tt #1}\bytebox{4}{\em count}\byteboxvector{#2}{#3}}}
\begin{samepage}
The representation of a `{\tt B}' array field starts with a sub-type character
similar to the numeric field types above and an {\tt int32\_t} \emph{count}
giving the number of elements in the array.
similar to the numeric field types above and a \emph{count} ({\tt uint32\_t}, but
limited by memory and {\sf block\_size}) giving the number of elements in the array.
The array elements follow, encoded as binary integers or IEEE floats sized
according to the sub-type:
\begin{center}\small\byteboxsetup\begin{tabular}{l}
Expand All @@ -1161,6 +1172,7 @@ \subsubsection{Auxiliary data encoding}\label{sec:aux-type-codes}
\arraytagfield{I}{4}{uint32\_t} \\
\arraytagfield{f}{4}{float}
\end{tabular}\end{center}
\end{samepage}
\pagebreak
Expand Down Expand Up @@ -1271,27 +1283,29 @@ \subsubsection{A conceptual example}
\subsection{The BAI index format for BAM files}
\begin{table}[ht]
{\small
\centering\small
\begin{tabular}{|l|l|l|l|l|l|r|}
\cline{1-7}
\multicolumn{4}{|c|}{\bf Field} & \multicolumn{1}{c|}{\bf Description} & \multicolumn{1}{c|}{\bf Type} & \multicolumn{1}{c|}{\bf Value} \\\cline{1-7}
\multicolumn{4}{|l|}{\sf magic} & Magic string & {\tt char[4]} & {\tt BAI\char92 1}\\\cline{1-7}
\multicolumn{4}{|l|}{\sf n\_ref} & \# reference sequences & {\tt int32\_t} & \\\cline{1-7}
\multicolumn{4}{|l|}{\sf n\_ref} & \# reference sequences & {\tt uint32\_t} & $< 2^{31}$ \\\cline{1-7}
\multicolumn{7}{|c|}{\textcolor{gray}{\it List of indices (n=n\_ref)}} \\\cline{2-7}
& \multicolumn{3}{l|}{\sf n\_bin} & \# distinct bins (for the binning index) & {\tt int32\_t} & \\\cline{2-7}
& \multicolumn{3}{l|}{\sf n\_bin} & \# distinct bins (for the binning index) & {\tt uint32\_t} & $\le 37451$ \\\cline{2-7}
& \multicolumn{6}{c|}{\textcolor{gray}{\it List of distinct bins (n=n\_bin)}} \\\cline{3-7}
& & \multicolumn{2}{l|}{\sf bin} & Distinct bin & {\tt uint32\_t} & \\\cline{3-7}
& & \multicolumn{2}{l|}{\sf n\_chunk} & \# chunks & {\tt int32\_t} & \\\cline{3-7}
& & \multicolumn{2}{l|}{\sf bin} & Distinct bin & {\tt uint32\_t} & $\le 37450$ \\\cline{3-7}
& & \multicolumn{2}{l|}{\sf n\_chunk} & \# chunks & {\tt uint32\_t} & \memlimited\footnotemark \\\cline{3-7}
& & \multicolumn{5}{c|}{\textcolor{gray}{\it List of chunks (n=n\_chunk)}} \\\cline{4-7}
& & & {\sf chunk\_beg} & (Virtual) file offset of the start of the chunk & {\tt uint64\_t} & \\\cline{4-7}
& & & {\sf chunk\_end} & (Virtual) file offset of the end of the chunk & {\tt uint64\_t} & \\\cline{2-7}
& \multicolumn{3}{l|}{\sf n\_intv} & \# 16kbp intervals (for the linear index) & {\tt int32\_t} & \\\cline{2-7}
& \multicolumn{3}{l|}{\sf n\_intv} & \# 16kbp intervals (for the linear index) & {\tt uint32\_t} & $\le 2^{17}$ \\\cline{2-7}
& \multicolumn{6}{c|}{\textcolor{gray}{\it List of intervals (n=n\_intv)}} \\\cline{3-7}
& & \multicolumn{2}{l|}{\sf ioffset} & (Virtual) file offset of the first alignment in the interval & {\tt uint64\_t} & \\\cline{1-7}
\multicolumn{4}{|l|}{{\sf n\_no\_coor} (optional)} & Number of unplaced unmapped reads ({\sf RNAME} *) & {\tt uint64\_t} & \\\cline{1-7}
\end{tabular}}
\end{tabular}
\end{table}
\footnotetext{The number of chunks in a single bin is effectively limited by available memory and in any case is typically a maximum of some thousands.}
The index file may optionally contain additional metadata providing a summary
of the number of mapped and unmapped read-segments per reference sequence,
and of any unplaced unmapped read-segments.\footnote{By \emph{placed unmapped
Expand All @@ -1313,7 +1327,7 @@ \subsection{The BAI index format for BAM files}
\begin{tabular}{|l|l|l|r|}
\hline
{\sf bin} & Magic bin number & {\tt uint32\_t} & 37450 \\\hline
{\sf n\_chunk} & \# chunks & {\tt int32\_t} & 2 \\\hline
{\sf n\_chunk} & \# chunks & {\tt uint32\_t} & 2 \\\hline
{\sf unmapped\_beg} & (Virtual) file offset of the start of placed unmapped reads & {\tt uint64\_t} & \\\hline
{\sf unmapped\_end} & (Virtual) file offset of the end of placed unmapped reads & {\tt uint64\_t} & \\\hline
{\sf n\_mapped} & Number of mapped read-segments for this reference & {\tt uint64\_t} & \\\hline
Expand Down

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