Fixed bwtio.c functions for I/O. Changed type of sa_intv from int to bwtint_t.
Use err_fread_noeof() instead of fread().
Fixed invocation to bwa_refine_gapped_core(). Fixed usage of n_gapo and n_mm.
Fix invocation of bwa_refine_gapped_core() again.
Fixed scope of local variable 'q'.
Avoid uninitialized variable warning.
Removed stdaln.ol from $(OBJS_LIB).
Removed cs2nt.ol from $(OBJS_LIB)
Explicit type cast to uint32_t* for bwt->bwt field.
Merge pull request #4 from okulev/port-bwa-0.7

Fixed all compiled errors except those in bwape.c. Fixed struct field alignment problems in bwtio.c.