calchoo commented 1 year ago

filtering unmapped, duplicate, qcfailed reads from ref/alt calculation as we want these excluded from the calculations

dustinbleile commented 1 year ago

Seems like one of the tests needs fixing?

=================================== FAILURES =================================== __ TestRefAltCalulator.test_calculate_count2 ___

self = <tests.test_tools.test_ref_alt_count.TestRefAltCalulator object at 0x7efd926ba990> calculator = <tools.calculate_ref_alt_counts.RefAltCalculator object at 0x7efd929595d0>


    def test_calculate_count2(self, calculator):
        ev1 = BreakpointPair(
            Breakpoint('reference11', 9999, orient=ORIENT.LEFT),
            Breakpoint('reference11', 10030, orient=ORIENT.RIGHT),
            opposing_strands=False,
            event_type=SVTYPE.DEL,
        )
        bpp = calculator.calculate_ref_counts(ev1)
        print(bpp.data)
        assert bpp.data["TEST_ref_count"] == 0
        assert bpp.data["TEST_alt_count"] == 63
>       assert bpp.data['TEST_ignored_count'] == 197
E       assert 195 == 197```

codecov[bot] commented 1 year ago

Codecov Report

Patch and project coverage have no change.

Comparison is base (678323e) 86.92% compared to head (749c71a) 86.92%.

Additional details and impacted files

```diff @@ Coverage Diff @@ ## develop_v3 #347 +/- ## =========================================== Coverage 86.92% 86.92% =========================================== Files 57 57 Lines 9390 9390 Branches 2355 2355 =========================================== Hits 8162 8162 Misses 752 752 Partials 476 476 ``` | Flag | Coverage Δ | | |---|---|---| | unittests | `86.92% <ø> (ø)` | | Flags with carried forward coverage won't be shown. [Click here](https://docs.codecov.io/docs/carryforward-flags?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=bcgsc#carryforward-flags-in-the-pull-request-comment) to find out more. Help us with your feedback. Take ten seconds to tell us [how you rate us](https://about.codecov.io/nps?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=bcgsc). Have a feature suggestion? [Share it here.](https://app.codecov.io/gh/feedback/?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=bcgsc)

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bcgsc / mavis

filtering unmapped, duplicate, qcfailed reads from ref/alt calculation #347

Codecov Report