[BAM]Implement: Code cleaning in progress
[BAM]Implement: Code cleaning in progress
[BAM]Fix: Minor fix in aux_cigar.c
[BAM]Implement: Reestructuration and cleaning progress
[BAM]Implement: Removed obsolete functions
[BAM]Implement: Restored time collection support
Merge branch 'align' into develop
[BAM]Implement: Improved code estructure. Better BAM filtering. Implemented function to process haplotypes scores.
[BAM]Implement: Reference cheking in indel realignment functions
[BAM]Implement: Improvements in haplotypes process
[BAM]Implement: Implemented function to get alternative haplotype from scores
[BAM]Fixes: Bugfix in cigar32_from_haplo function
[BAM]Implement: Improvements, functional reestructuration
[BAM]Implement: Improved code. Realigner context now uses 2 array list instead one linked list. Bug fixing. Code cleaning. Realign options added.
[BAM]Implement: Realignment improvements
[BAM]Implement: Added configurable flags to realigner context
[BAM]Fix: Some fixes and tweaks in realignment
[BAM]Implement: Added version defines and --version option to realigner
[BAM]Bugfix: Start position to get score will be minor always than reference position
[BAM]Fix: Leak memory fixes