Bug fix to index initialisation when a CRAM file has non-sequential
ref IDs.


git-svn-id: svn://svn.code.sf.net/p/staden/code/io_lib@3570 ba6f2710-ca9f-427c-89d3-5bf716dbc8e1
Fixed duplicated and missing error check pointed out by dcb314.


git-svn-id: svn://svn.code.sf.net/p/staden/code/io_lib@3571 ba6f2710-ca9f-427c-89d3-5bf716dbc8e1