Commit [r3625] Maximize Restore History

Moved the cram index creation out of cram_index program and into the

cram_index.c part of io_lib library.

Bug fixed both the index creation and decode range checking to handle
containers/slices with ref_seq_id of -2, indicating that multiple
references share the same container.

jkbonfield 2014-04-10

changed /io_lib/trunk/io_lib/cram_decode.c
changed /io_lib/trunk/io_lib/cram_index.c
changed /io_lib/trunk/io_lib/cram_index.h
changed /io_lib/trunk/progs/cram_index.c
/io_lib/trunk/io_lib/cram_decode.c Diff Switch to side-by-side view
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/io_lib/trunk/io_lib/cram_index.c Diff Switch to side-by-side view
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/io_lib/trunk/io_lib/cram_index.h Diff Switch to side-by-side view
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/io_lib/trunk/progs/cram_index.c Diff Switch to side-by-side view
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