feat: remove pysam and bwa warmup hack

clintval commented 1 week ago

It is mentioned pysam.AlignmentFile internally buffers stdin so a hack was devised to "warm it up".

However, fgpyo.sam.reader and pysam.AlignmentFile are not needed and only provide code indirection since we can build the SAM header and all subsequent records using the from_text()/fromstring() methods of each.

codecov[bot] commented 1 week ago

Codecov Report

Attention: Patch coverage is 84.61538% with 2 lines in your changes missing coverage. Please review.

Project coverage is 97.25%. Comparing base (5515d05) to head (80ea938). Report is 1 commits behind head on main.

Files with missing lines	Patch %	Lines
prymer/offtarget/bwa.py	84.61%	0 Missing and 2 partials :warning:

Additional details and impacted files

```diff @@ Coverage Diff @@ ## main #65 +/- ## ========================================== - Coverage 97.38% 97.25% -0.13% ========================================== Files 25 25 Lines 1605 1603 -2 Branches 302 303 +1 ========================================== - Hits 1563 1559 -4 Misses 23 23 - Partials 19 21 +2 ```

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clintval commented 1 week ago

I have one strangely failing test on GitHub CI (but not locally):

FAILED tests/offtarget/test_bwa.py::test_header_is_properly_constructed - AssertionError: assert {'PG', 'SQ'} == {'HD', 'PG', 'SQ'}
  Extra items in the right set:
  'HD'
  Full diff:
  - {'HD', 'PG', 'SQ'}
  ?  ------
  + {'PG', 'SQ'}

Will debug...

EDIT: the issue is we were using the old bwa repo in FG's org.

fulcrumgenomics / prymer

feat: remove pysam and bwa warmup hack #65

Codecov Report