Tags

- update bowtie2 parameters to favor mapping over N characters in the reference (default values --np 1 -n-ceil L,0,0.15 to --np 0 -n-ceil L,10,0.2)
- remove the n_reads threshold and error raising in order to have results even if there are no reads containing genomic barcodes information
- bug fix: 
  - properly write "genotypy_results.tsv" when there is more than one locus

- Run genotypy from reads directly, which involves:
  - running bowtie2 and samtools
  - include "locus configuration"
- Report locus-specific result files
- allow multithreading (for the mapping step only)

- parses a BAM/SAM file and reports genomic barcodes within the provided positions in the BAM.
- uses a haplotype-based strategy, where all combination of 'barcodes' seen within the reads are reported.