Feature/allele calling

[luissian]

Implementation of allele calling
In this PR, when it is searching the specif allele that match the blast sequence using grep, if grep match then this specific allele name will be set as the field of coding. This is to find the EXC allele, but could be set in conditions of ASM or ALM or PLOT, where part of the sequence match in the locus file.

• save all coordinates in case NIPHEM/NIPH
• if no blast result are with 80% query. it is considered from 75% and assigned to PLOT
• check if programs like mash, prokka, etc exist before start execution
  • mash
  • prokka
  • blast
• create SNP file all alleles compared with their Reference allele. including 3 DNA bases for ref and alt, Amino acid for ref and alt and change type of amino acid
• Create multi alignment for each allele with the reference allele
• create summary graphic for all samples and all allele classification
• update code to process all samples
• ensure that the get_inferred_allele method is accessed safely by multiple instances
• Extend blast sequence for searching start and stop codon due to the variability in reference alleles
• Parallel execution to create the multi alignment files

Important Note .-
This PR includes changes in analyze schema feature. This means it is mandatory to re-run the analyze schema to get the right annotation file