Add @SQ-TP molecule topology field (PR samtools#405 part 1)

This is to support annotating reference sequences as circular,
e.g., for bacterial organisms or the human mitochondrial chromosome.
[Summarise @nh13's footnote text so it fits on one line, so `@RG-SM`
is not pushed off to the next page as an orphan. Remove now unneeded
pagebreak hint.] Fixes samtools#403.

SAMv1.tex

@@ -275,7 +275,7 @@ \subsection{The header section}
   & {\tt AN} & Alternative reference sequence names.
 A comma-separated list of alternative names that tools may use when referring
 to this reference sequence.%
-\footnote{For example, given `{\tt @SQ SN:MT AN:chrMT,M,chrM LN:16569}',
+\footnote{For example, given `{\tt @SQ SN:MT AN:chrMT,M,chrM LN:16569 TP:circular}',
 tools can ensure that a user's request for any of `MT', `chrMT', `M',
 or~`chrM' succeeds and refers to the same sequence.}
 These alternative names are not used elsewhere within the SAM file;
@@ -287,6 +287,9 @@ \subsection{The header section}
   & {\tt DS} & Description.  UTF-8 encoding may be used.\\\cline{2-3}
   & {\tt M5} & MD5 checksum of the sequence.  See Section~\ref{sec:ref-md5}\\\cline{2-3}
   & {\tt SP} & Species.\\\cline{2-3}
+  & {\tt TP} & Molecule topology. \emph{Valid values}: {\tt linear} (default) and {\tt circular}.%
+\footnote{The previous footnote's example identifies MT as a circular chromosome.
+The {\tt TP} field is often omitted, which implies linear.}\\\cline{2-3}
   & {\tt UR} & URI of the sequence.  This value may start with one of the standard
   protocols, e.g http: or ftp:.  If it does not start with one of these protocols, it is assumed to be a file-system path.\\\cline{1-3}
   \multicolumn{2}{|l}{\tt @RG} & Read group. Unordered multiple {\tt @RG} lines are allowed.\\\cline{2-3}
@@ -310,7 +313,6 @@ \subsection{The header section}
   platform/technology used.\\\cline{2-3}
   & {\tt PU} & Platform unit (e.g. flowcell-barcode.lane for Illumina or slide for SOLiD). Unique identifier.\\\cline{2-3}
   & {\tt SM} & Sample. Use pool name where a pool is being sequenced.\\\cline{1-3}
-\pagebreak[4]
   \multicolumn{2}{|l}{\tt @PG} & Program. \\\cline{2-3}
   & {\tt ID}* & Program record identifier. Each {\tt @PG} line must have a unique {\tt ID}.
   	The value of {\tt ID} is used in the alignment {\tt PG} tag and {\tt PP} tags of other {\tt @PG} lines.
@@ -1314,6 +1316,7 @@ \section{SAM Version History}\label{sec:history}
 \subsection*{1.6: 28 November 2017 to current}
 
 \begin{itemize}
+\item Add {\tt @SQ TP} circular/linear topology header tag. (May 2019)
 \item\textbf{Restricted the allowable punctuation characters in reference sequence names} (in {\tt @SQ SN}, {\sf RNAME}, etc).
 The sets of characters allowed in {\tt @SQ SN} and {\tt @SQ AN} are now identical, which enlarges the previous {\tt AN} set. (Jan 2019)