Fixed generation of MD and NM tags in cram_decode_seq() when using a
non-reference encoding. These cannot be stored or regenerated in such
cases.

(Question: should we therefore explicitly store any MD and NM tags
when generating the CRAM if using non-reference encoding? Probably
yes.)



git-svn-id: svn://svn.code.sf.net/p/staden/code/io_lib@3736 ba6f2710-ca9f-427c-89d3-5bf716dbc8e1
Replaced BLOCK_APPENDF with BLOCK_APPEND_UINT and use the append_int
function that already exists in bam.h for faster encoding.

This saves ~3/4trs of the time added by DECODE_MD option.


git-svn-id: svn://svn.code.sf.net/p/staden/code/io_lib@3737 ba6f2710-ca9f-427c-89d3-5bf716dbc8e1
Added SAM_RGAUX as an additional required field type. This is useful
for when we need the RG:Z: auxiliary tag without also needing to
decode all the other aux data.


git-svn-id: svn://svn.code.sf.net/p/staden/code/io_lib@3738 ba6f2710-ca9f-427c-89d3-5bf716dbc8e1