Feature/pcgr v2.2.1 #10
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… during annotation must be above 1 and not more than 8 (recommended is 4)"
bolt/common/pcgr.py
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| import re | ||
| import shutil | ||
| import tempfile | ||
| import gzip # added import |
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Nice work! I'm seeing a test failure, any thoughts what might be causing that? Run python3 -m unittest discover tests/ --buffer
.F............
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FAIL: test_clinical_potential_rescue_general (test_smlv_somatic_filter.TestSmlvSomaticFilter)
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Traceback (most recent call last):
File "/home/runner/work/bolt/bolt/tests/test_smlv_somatic_filter.py", line 204, in test_clinical_potential_rescue_general
assert not record.FILTER
AssertionError |
I added |
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The idea of this specific test is to simulate variants that were going to be filtered but are saved by what I've called 'clinical potential' rescue. This means that the output variants should have Since the conditions for the 'clinical potential' rescue has changed in this PR (i.e. removal of COSMIC and ICGC-PCAWG conditionals) the existing test variants that relied on those criteria failed. I've updated the test to align with the new conditions for this rescue |
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Update Bolt to work with pcgr v2.2.1
link with sash PR#17