Fixed some bugs: generating cigar with smith-waterman output, add new functions for map with SA in RNA mode
fixed bug reporting splice junctions (CT-AC bad strand)
Delete exits in some errors cases
Fixes the mate position in paired mode
Fixes mappings in the reverse strand, and includes the beta version function to compute the mapping quality
Includes the beta version function to compute the mapping quality for single-end
Rna DBWT final, SA first workflow finish
Merge from develop-rna branch
Error message add to opening SA Index
Add new file 'sa_rna_mapper.c/.h'
Updates buffers.c/h files
Resolves conflicts
Updates worker