Enable FASTA reference inputs + fail-fast contig validation.

[edawson]

Howdy,

My apologies that this got so long, but I hope it's helpful.

This PR adds a ReferenceWrapper class that enables FASTA reference genome inputs and provides a common API for both 2-bit and FASTA inputs. This class then replaces any calls to py2bit in the code. A check on the contigs present in the BAM/CRAM/SAM/Frag(.gz) and the contigs in the reference genome is made immediately after argument parsing, preventing a particular error I was getting often where there was a mismatch that often did not report the error sufficiently for me to debug.

New Features:

• FASTA reference support, in addition to 2-bit
• Single interface for FASTA / 2-bit files
• More aggressive contig checking upfront to surface mismatched refs/inputs sooner

Other changes:

• Freezes dependencies for security purposes. This somewhat assumes code is then run in a venv, a conda env or a Docker container as per modern Python practices.
• Refactors the gen_kmers and reverse_complement functions from end motifs / breakpoint motifs to utils, where they exist only once in the package.

Testing:

• I did not modify the tests.
• All tests pass using pytest tests/

I have a followup PR that refactors the input_file as well, which is another huge chunk of code (as I had to refactor some significant portions of the utils module to break a dependency cycles). Happy to help answer questions and thank y'all for FinaleToolkit!

Best,
Eric

[edawson]

Howdy @Kudostoy0u - it would be great to add a test to make sure the FASTA file wrapper is working as expected. I can likely do so if needed, but I assume y'all have one for the 2-bit version and it seems ideal to simply drop the FASTA in its place and make sure it works as expected.

[Kudostoy0u]

Hi @edawson! Good point, I'll add a small FASTA fixture and a regression test with it to see if the new FASTA reference support produces same results as existing .2bit test coverage.

Your PRs touch a large amount of code (thanks for your contributions!), so I’m also going to add another maintainer as a reviewer for a second pass.

[Kudostoy0u]

Tested locally, the test suite and CI are passing, the new FASTA reference path is now covered by a regression test.

Python 3.9 dropped since it's EOL and wasn't working well with frozen dependency versions.