Creates a new seed structure for SA in order to contain statically the cigar structure (the idea is avoid making many small mallocs)
Computes CIGAR code for seeds, and extends seeds first to the left-side, and then ,to the right-side (for an efficient CIGAR generatiion)
Computes a score for each CAL
Resolves some conflicts
Merge branch 'develop-rna' of https://github.com/opencb/hpg-aligner into develop
Resolves some conflicts and frees some memory
Delete some 'printfs' for debuggin
Merge branch 'develop' of https://github.com/opencb/hpg-aligner into develop-rna
Move 'options_free' to 'hpg-aligner.c'