Restructured exact match filter such that it fits with the new API, e.g. added get_oligo_pair_hits function.
Therefore, added a function to the oligo database that returns a mapping from sequence to oligo ids.
Bug fixes:
write_fasta function from database: added a flag to save description or not. the description caused an error in the parsing of the bowtie and blast results.
check if bowtie or blast index exists: remove the check because if we run multiple specificity filters, we save the reference database with the same filename which leads to not creating a new index for a different reference file
Added tests for exact match and cross hybridization with exact match filter.
Restructured exact match filter such that it fits with the new API, e.g. added get_oligo_pair_hits function. Therefore, added a function to the oligo database that returns a mapping from sequence to oligo ids. Bug fixes: