Add recommended practice for records spanning the origin of circular

reference sequences

SAMv1.tex

@@ -636,7 +636,8 @@ \section{Recommended Practice for the SAM Format}
   \item If {\sf POS} plus the sum of lengths of {\tt M/=/X/D/N}
     operations in {\sf CIGAR} exceeds the length specified in the {\tt
       LN} field of the {\tt @SQ} header line (if exists) with an SN
-    equal to {\sf RNAME}, the alignment should be unmapped.
+    equal to {\sf RNAME}, the alignment should be unmapped, unless the
+    reference sequence is annotated as circular (see below).
   \item Unmapped reads should be stored in the orientation in which they came
     off the sequencing machine and have their {\sf reverse} flag bit~(0x10)
     correspondingly unset.
@@ -658,7 +659,19 @@ \section{Recommended Practice for the SAM Format}
     should be present.
   \item The {\tt NM} tag should be present.
   \end{enumerate}
-\item At present, this specification does not describe how mappings across the ``join'' in a circular reference sequence should be represented.
+\item Alignment to circular reference sequences
+  This applies to circular reference sequences that are annotated with
+  {\tt TP:circular} in the {\tt @SQ} header line.
+  \begin{enumerate}[label=\arabic*]
+  \item (preferred) {\sf POS} should be between 0 and the length specified 
+    in {\tt LN} field of the {\tt @SQ} header line with an {\tt SN} equal to
+    {\sf RNAME}. {\sf POS} plus the sum of lengths of {\tt M/=/X/D/N} 
+    operations in {\sf CIGAR} should exceed the length specified in the {\tt LN}
+    field of the {\tt @SQ} header line (if exists) with an SN equal to 
+    {\sf RNAME}.
+  \item (alternative) The alignment should be split across multiple records,
+    with one flagged as primary and the remaining flagged as supplementary.
+  \end{enumerate}
 \item Annotation dummy reads:
   These have {\sf SEQ} set to {\tt *}, {\sf FLAG} bits 0x100 and 0x200
   set (secondary and filtered), and a {\tt CT} tag.