Fixed EOF to be set to 1 (expected EOF) on first opening a file and
then changed to 0 (error) before decoding each container+slice.
Previously it started as 0.

The effect of this is that when asking for only the header and not
decoding a single read, we no longer incorrectly claim an unexpected
EOF.


git-svn-id: svn://svn.code.sf.net/p/staden/code/io_lib@3652 ba6f2710-ca9f-427c-89d3-5bf716dbc8e1
Bug fix to the demo pileup tool. It had some memory corruption issues
at high depth.

NOTE: It still isn't perfect when dealing with insertions. This isn't
a new bug, but a discovery of an existing bug during the fixing of the
above problem.


git-svn-id: svn://svn.code.sf.net/p/staden/code/io_lib@3653 ba6f2710-ca9f-427c-89d3-5bf716dbc8e1
Updated for v1.13.6


git-svn-id: svn://svn.code.sf.net/p/staden/code/io_lib@3654 ba6f2710-ca9f-427c-89d3-5bf716dbc8e1