Skip to content

Commit

Permalink
Bump version to VN:1.6 due to >65535 CIGAR strings
Browse files Browse the repository at this point in the history
The new CG tag field BAM representation for long CIGAR strings
(PR samtools#227, merged as dab57f4)
will be unnoticed by older code. Such code will see the placeholder
CIGAR string, so it needs to be possible to signal the presence of
CG tags via the @HD-VN version number header field.
  • Loading branch information
jmarshall committed May 2, 2018
1 parent 5b84bd3 commit 3f5a63e
Showing 1 changed file with 10 additions and 5 deletions.
15 changes: 10 additions & 5 deletions SAMv1.tex
Original file line number Diff line number Diff line change
Expand Up @@ -59,7 +59,7 @@ \section{The SAM Format Specification}
information such as mapping position, and variable number of optional
fields for flexible or aligner specific information.

This specification is for version 1.5 of the SAM and BAM formats. Each SAM and
This specification is for version 1.6 of the SAM and BAM formats. Each SAM and
BAM file may optionally specify the version being used via the
{\tt @HD VN} tag. For full version history see Appendix~\ref{sec:history}.

Expand Down Expand Up @@ -95,7 +95,7 @@ \subsection{An example}\label{sec:example}
properly aligned\slash multiple segments.}
\begin{framed}\small
\begin{verbatim}
@HD VN:1.5 SO:coordinate
@HD VN:1.6 SO:coordinate
@SQ SN:ref LN:45
r001 99 ref 7 30 8M2I4M1D3M = 37 39 TTAGATAAAGGATACTG *
r002 0 ref 9 30 3S6M1P1I4M * 0 0 AAAAGATAAGGATA *
Expand Down Expand Up @@ -707,7 +707,7 @@ \subsection{Padded SAM}\label{sec:padded-sam}

\begin{framed}\small
\begin{verbatim}
@HD VN:1.5 SO:coordinate
@HD VN:1.6 SO:coordinate
@SQ SN:ref LN:47
ref 516 ref 1 0 14M2D31M * 0 0 AGCATGTTAGATAAGATAGCTGTGCTAGTAGGCAGTCAGCGCCAT *
r001 99 ref 7 30 14M1D3M = 39 41 TTAGATAAAGGATACTG *
Expand Down Expand Up @@ -1218,12 +1218,17 @@ \section{SAM Version History}\label{sec:history}
specification with its own version numbering.\footnote{
\href{http://samtools.github.io/hts-specs/SAMtags.pdf}{http://samtools.github.io/hts-specs/SAMtags.pdf}}

\subsection*{1.5: 23 May 2013 to current}
\subsection*{1.6: 28 November 2017 to current}

\begin{itemize}
\item Add {\tt @RG BC} header tag. (Apr 2018)
\item Permit UTF-8 in a few header tags. (Mar 2018)
\item Add support for $>65535$ cigar operations. (Jul 2017)
\item\textbf{Add support for CIGAR strings with more than 65535 operations.} (Nov 2017)
\end{itemize}

\subsection*{1.5: 23 May 2013 to November 2017}

\begin{itemize}
\item Add {\tt @SQ AH} header tag. (Mar 2017)
\item Auxiliary tags migrated to SAMtags document. (Sep 2016)
\item Z and H auxiliary tags are permitted to be zero length. (Jun 2016)
Expand Down

0 comments on commit 3f5a63e

Please sign in to comment.