[BAM]: Reestructuration and clean of headers for auxiliar library
[BAM]Implement: Added some operations for nucleotide count to auxiliar library
[BAM]Implement: Prototyping indel realignment from haplotypes
[BAM]Implement: New cigar operations, improvement on existing ones, some bug fixing.
[BAM]Fix: Renamed alig_bam_file2 function to alig_bam_file
[BAM]Test: Changed some printfs
[BAM]Implement: Duplicate haplotype checking in alig_bam_list
[BAM]Implement: Leftaligned cigars are now printed to output log
[BAM]Implement: Added code structure to obtain best haplotype and realign in alig_bam_list_realign function
[BAM]Fix: Bug fixed in nucleotide_compare, miss_count argument can now be NULL
[BAM]Implement: Score duel implemented between reference haplotype and alternative in alig_bam_list_realign
[BAM]Implement: New function for cigar replacement in bam1_t
[BAM]Implement: Indel realigment progress
[BAM]Implement: Added compilation options for realignment in SConstruct
[BAM]Implement: Progress in indel realignment
[BAM]Implement: Progress on indel realignment
[BAM]Implement: Implement progress, something is broken
[BAM]Fix: Bugfix in cigar32_from_haplo from aux_cigar.c
[BAM]Implement: Progress, indel realignment prototype is working
[BAM]Fix: Bug fixed in alig_bam_list_realign, wrong total scores