Split sample SNP evidence files into bins for EFM

[rnmitchell]

Previously, an R script was used to split individual sample kintelligence files into 10 bins for use in EFM. Adding this feature into lusSTR.

This PR also fixes a bug when specifying no references for SNP processing.

[rnmitchell]

Not sure why this keeps failing the style check- it's passing on my computer. Otherwise, this is ready for review @standage

[standage]

Not sure why this keeps failing the style check- it's passing on my computer. Otherwise, this is ready for review @standage

With some dependencies, you can get away with setting a minimum version and be compatible with quite a few different software versions. With style checking and autoformatting, the black package has a narrow range of compatibility.

The CI build has black fixed at version 22.6: you'll want to make sure that's what you have in your local environment. If you ever want to upgrade the version, it's probably worth a dedicated PR, and then you'll need to change the CI and your local environment at the same time.

If that's not the issue, then we'll call up some real gumshoes.

[standage]

Looks good to me. If resetting the black version fixes things, I'll be happy to merge this.

[rnmitchell]

I am trying! I had version 23.3... I'm working on downgrading but Conda doesn't make it easy...

[rnmitchell]

Now I'm running into this error with black 22.6:

(lusstr) FDT010LM-613658:lusSTR rebecca.mitchell$ make format
black --line-length=99 *.py lusSTR/scripts/*.py lusSTR/wrappers/*.py lusSTR/tests/test_*.py
Traceback (most recent call last):
  File "/Users/rebecca.mitchell/mambaforge/envs/lusstr/bin/black", line 10, in <module>
    sys.exit(patched_main())
  File "src/black/__init__.py", line 1447, in patched_main
  File "/Users/rebecca.mitchell/mambaforge/envs/lusstr/lib/python3.7/site-packages/click/core.py", line 1130, in __call__
    return self.main(*args, **kwargs)
  File "/Users/rebecca.mitchell/mambaforge/envs/lusstr/lib/python3.7/site-packages/click/core.py", line 1055, in main
    rv = self.invoke(ctx)
  File "/Users/rebecca.mitchell/mambaforge/envs/lusstr/lib/python3.7/site-packages/click/core.py", line 1404, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/Users/rebecca.mitchell/mambaforge/envs/lusstr/lib/python3.7/site-packages/click/core.py", line 760, in invoke
    return __callback(*args, **kwargs)
  File "/Users/rebecca.mitchell/mambaforge/envs/lusstr/lib/python3.7/site-packages/click/decorators.py", line 26, in new_func
    return f(get_current_context(), *args, **kwargs)
  File "src/black/__init__.py", line 470, in main
TypeError: find_project_root() takes 1 positional argument but 2 were given
make: *** [Makefile:17: format] Error 1
(lusstr) FDT010LM-613658:lusSTR rebecca.mitchell$ black --version
black, 22.6.0 (compiled: yes)
Python (CPython) 3.7.12

[standage]

Ruh roh, looks like we have a test failure with Python 3.9. It doesn't show details, just a false file.cmp result.

[rnmitchell]

I'll do some troubleshooting