Implement actions for simple loci library creation

[dbolotin]

User story 1 (from IMGT-like reference):

1. I have a set of fasta files with reference sequences of V, D, J or C genes.

2. Each file is padded with . symbols or something similar to align anchor points. So each anchor point has the same position in all sequences. (exactly like IMGT gaps)

3. There is file or command-line argument with positions of all anchor points. Something like this:

   V=108:117:125:148:157: etc...
   

4. I can create new loci library from this information or append it to already existing one:

   mixcr addReferenceGenes --taxonId 9615 --speciesCommonName dog,canis --locus TRB --geneType V --anchorPoints 108:117:125:148:157 --geneNamePattern '...' input.fasta myLL.ll
   

   this will create myLL.ll file or add locus information to it if it already exists.

   • Loci library file can't store two records with the same combination of taxonId, locus and geneName.

User story 2 (library from genomic data, MiXCR way of LL creation):

1. I have a big fasta file with genomic sequence of chromosome or particular locus.

2. There is another file with tab-delimited list of reference genes. Example segments.txt:

   GeneName	Locus	GeneType	AnchorPoints
   TRBV12-3	TRB	V	123341:123356:123387:123456
   ...	...	...	...

3. I can create new loci library from this information or append it to already existing one:

   mixcr addReferenceLocus --taxonId 9615 --speciesCommonName dog,canis input.fasta segments.txt myLL.ll