Fix the SAM header requirements. Also clarify slice MD5 value zero.

Fixes samtools#201

CRAMv3.tex

@@ -563,10 +563,6 @@ \subsection{\textbf{BAM header block}}
 \begin{itemize}
 \item The SQ:MD5 checksum is required unless the reference sequence has been embedded 
 into the file.
-
-\item At least one RG record is required.
-
-\item The HD:SO sort order is always POS.
 \end{itemize}
 
 \subsection{\textbf{Compression header block}}
@@ -736,6 +732,13 @@ \subsection{\textbf{Slice header block}}
 the same slice similarly to BAM file. Slices with unsorted reads must not contain 
 any other types of reads.
 
+A slice containing data that does not use the external reference in
+any sequence may set the reference MD5 sum to zero.  This can happen
+because it has an embedded reference, the data is unmapped, or the
+sequence has been stored verbatim instead of via reference-differcing.
+This latter scenario is recommended for unsorted or non-coordinate
+sorted data.
+
 The slice header block contains the following fields.
 
 \begin{tabular}{|l|l|>{\raggedright}p{200pt}|}
@@ -763,7 +766,7 @@ \subsection{\textbf{Slice header block}}
 reference sequence bases or -1 for none\tabularnewline
 \hline
 byte[16] & reference md5 & MD5 checksum of the reference bases within the slice 
-boundaries or 16 \textbackslash{}0 bytes for unmapped or unsorted reads\tabularnewline
+boundaries or 16 \textbackslash{}0 bytes when unused\tabularnewline
 \hline
 byte[] & optional tags & a series of tag,type,value tuples encoded as
 per BAM auxiliary fields.\tabularnewline