[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