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sanger-pathogens / ariba

Antimicrobial Resistance Identification By Assembly
http://sanger-pathogens.github.io/ariba/
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Megares fixes v3 #334

Closed aastha-batta closed 1 year ago

aastha-batta commented 1 year ago

I have added a few fixes for megares v3.0 Kindly look into it.

aastha-batta commented 1 year ago

Added relevant changes to samtools_variants.py for issue #327 Kindly look into it.

martinghunt commented 1 year ago

One of the megares tests is broken by these changes. Here's the relevant part of the github actions log:

2023-05-24T08:14:36.3352482Z test _zips_from_index_page_string
2023-05-24T08:14:36.3352879Z ----------------------------------------------------------------------
2023-05-24T08:14:36.3353189Z Traceback (most recent call last):
2023-05-24T08:14:36.3353535Z   File "/ariba/ariba/tests/megares_data_finder_test.py", line 26, in test_zips_from_index_page_string
2023-05-24T08:14:36.3353886Z     self.assertEqual(expected, got)
2023-05-24T08:14:36.3354467Z AssertionError: {'1.00': 'megares_v1.00.zip', '1.01': 'megares_v1.01.zip'} != {}
2023-05-24T08:14:36.3354894Z - {'1.00': 'megares_v1.00.zip', '1.01': 'megares_v1.01.zip'}
2023-05-24T08:14:36.3355120Z + {}

For the bcftools/mpileup issue, I just commented on it: https://github.com/sanger-pathogens/ariba/issues/327#issuecomment-1564086795

aastha-batta commented 1 year ago

Hi, the test broke as i added the newest version of megares which is version3 to the code. I will update the test file too in order to ensure efficient testing. Thank you @martinghunt

martinghunt commented 1 year ago

Thank you @aastha-batta . Could you also remove the mpileup changes and keep this PR to just fix megares? I'll sort out mpileup in a separate PR, once I've figured out how to do it.

aastha-batta commented 1 year ago

Ok @martinghunt will do the needful.