Madc2vcf updates

[Cristianetaniguti]

• Change function names: madc2vcf -> madc2vcf_targets ; get_OffTargets -> madc2vcf_all
• Add function to check if botloci file marker names match with MADC: check_botloci
  • The function also checks the padding of the position notation and try to match adding left zeros to the shortest
• Update madc2vcf_targets to get the reverse complementary for the REF and ALT bases if marker is in botloci file
• Expose internal alignment quality filter parameter of madc2vcf_all
• Remove dependency of fasta db from madc2vcf_all. New Behavior:
  • If fasta db is present
    • If there is no Ref_0001 or Alt_0002 missing in the MADC - nothing happens
    • If there is Ref_0001 or Alt_0002 missing - try to find them in the fasta db, if exists, add, if not, exclude the tag
  • If fasta dp is not present
    • If there is no Ref_0001 or Alt_0002 missing in the MADC - nothing happens
    • If there is Ref_0001 or Alt_0002 missing - exclude the tag
• bcftools query was used to match VCF REF bases to the reference genome - they are all matching for both functions