Set eof_block when finishing up on a SAM file.

Technically it hasn't read an EOF block, but as this cannot exist in
SAM we cheat and claim it does in order to avoid outputting spurious
warnings about lacking the correct file termination.


git-svn-id: svn://svn.code.sf.net/p/staden/code/io_lib@3555 ba6f2710-ca9f-427c-89d3-5bf716dbc8e1
Updated the version checking to cope with major/minor versions easier.

Added a prototype for CRC32 checking on container and block
structures.  This is enabled only for CRAM v3.0, but this is under
discussion still so it should not be used in production.  The default
output format is still CRAM v2.0.


git-svn-id: svn://svn.code.sf.net/p/staden/code/io_lib@3556 ba6f2710-ca9f-427c-89d3-5bf716dbc8e1
Removal of compiler warnings


git-svn-id: svn://svn.code.sf.net/p/staden/code/io_lib@3557 ba6f2710-ca9f-427c-89d3-5bf716dbc8e1
Added Illumina 8-way quality binning as an output option for
Scramble. (CRAM only at the moment.)


git-svn-id: svn://svn.code.sf.net/p/staden/code/io_lib@3558 ba6f2710-ca9f-427c-89d3-5bf716dbc8e1
Added Illumina binning option to BAM and SAM I/O too, also controlled
via the scram_set_option function in the same manner.


git-svn-id: svn://svn.code.sf.net/p/staden/code/io_lib@3559 ba6f2710-ca9f-427c-89d3-5bf716dbc8e1