Account for different UAS versions #59
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This is ready for review @standage |
standage
approved these changes
Oct 18, 2023
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| "--kintelligence", | ||
| ] | ||
| lusSTR.cli.main(lusSTR.cli.get_parser().parse_args(arglist)) | ||
| all_arglist = ["snps", "all", "-w", str(tmp_path)] | ||
| lusSTR.cli.main(lusSTR.cli.get_parser().parse_args(all_arglist)) |
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It looks like this test isn't checking the output in any way. It's just making sure the code runs without exploding? (I call these "smoke tests" and use them frequently. 😎)
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| forward_strand_allele = check_rev_comp(uas_allele, snpid, metadata) | ||
| if ver == "2.0": | ||
| forward_strand_allele = check_rev_comp(uas_allele, snpid, metadata) | ||
| else: | ||
| forward_strand_allele = uas_allele |
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That makes sense based on your description.
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Ok now this is ready for review 😅 |
Boom! |
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It came to my attention that newer versions of the UAS software (at least v2.5) have a different format for the Sample Report than earlier versions. Further, the newest version no longer reports some SNPs on the reverse strand but all SNPs are reported on the forward strand. This PR will address these changes in order to be able to process any version of the UAS Sample Report.