fix: rename-contigs to include target bed intersection and add mapping files to resources

[famosab]

• Avoiding errors with contigs not being present in the target file.
• Adding more elaborate rename files as resources.

[famosab]

I am intersecting with the confidence regions and run into

[E::faidx_adjust_position] The sequence "chrEBV" was not found
faidx_fetch_seq failed at chrEBV:68570
Error: line number 30405 of file /dev/fd/63 has 7 fields, but 11 were expected.

Edit: Same error for target regions. But using test regions does not work directly because they are stratified by coverage?

Edit 2: Removing EBV and decoy manually leads to everything working again -> but we want to avoid doing that, something about the way I do it seems wrong to me.

[famosab]

I tried. out confidence and target regions locally and I am not sure which one should be used. I changed the norm to pipe the result of the intersect into bcftools norm otherwise I always ran into the above error.

[famosab]

Also works with the Freiburg data (the VCFs containing chrEBV and _decoy).