Fixes in allele calling module

[saramonzon]

• Added evaluation identity as parameter for reference alleles
• Variable and function renaming as refactor for allele_calling module
• changed exact match detection from grep to biopython
• Fix when allele was LNF was classified as locus_name instead of LNF
• Changed allele_details format from list to dictionary for easier reading and use.
• ASM and ALM evaluation is when sample allele seq is greater or lesser than the reference allele length +/- 20% of its length
• Refactor protein fixed when sample allele seq can't be translated:
  • Now is executed after checking for exact match
  • Now checks for both forward and reverse senses, as well as, contig strand.
  • Tries to extend in case of not stop codon, not start codon and not multiple of three.
  • Now it directly uses biopython translate errors.