Fixed some bugs: generating cigar with smith-waterman output, add new functions for map with SA in RNA mode
Fixes a memory leak when generating the sam format
Adds dynamic memory support for extending CIGARs from the initial allocated memory (NUM_INITIAL_CIGAR_OPS)
Updates some comments
fixed bug reporting splice junctions (CT-AC bad strand)
Modifies the seed_cal_print function
Comments some messages
Delete exits in some errors cases
Comments some debug messages
skip
Removes cals without any seed
Skips biggest gaps (to avoid SW), and adds some counters
Fixes some CIGAR codes and comments some counters
Completes the paired support and the README file
Removes some tmp files
Comments some messages
Fixes README
Fixes memory leak
Fixes typo bug in README
Changes CIGAR code (using M codes), updates README and comments some printfs