Retain the old Makefile from bowtie, as a reference.
sbndm.h: fix some 'char as array index' warnings
mapsplice_search.h: fix 'possibly uninitialised' warning
sbndm.h: fix crash when chromosome data uses ambiguous V, W or Y symbols.

The two_gram arrays were previously declared to work for A,C,G,T only.
The maximum index was thus (('T'<<8) | 'T') == 21588.
TAIR10 chromosomes contain Y, for example, which results in indices too
big for the array.

Zero out the arrays in the constructors to ensure such indiced have a
sensible value.
Makefile: disable some warnings which I won't touch
read_block.h: fix potential build failure with seqan-1.4.1
gtf2genetab: replace the cpp code with a python script

A. thaliana gene annotations use a slightly different format.
I could have modified the cpp code, but the python is simpler and
actually runs much faster.