tiny-count: adding classifier support to sequence-based counting#287
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taimontgomery merged 5 commits intomasterfrom Mar 6, 2023
Merged
tiny-count: adding classifier support to sequence-based counting#287taimontgomery merged 5 commits intomasterfrom
taimontgomery merged 5 commits intomasterfrom
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…that there's a class for SAM_reader, ReferenceFeatures, and CaseInsensitiveAttrs. Also moving the function for running all test suites up to the top of the file for convenience
…dly out of control because I wrote the new test suite before making the previous commit
… format of get_matches() is consistent with that of ReferenceFeatures.get_matches(), though that doesn't factor into the current design. The procedure in add_reference_seq() closely resembles the established procedure used by ReferenceFeatures in _add_subinterval_matches()
…idation is complete
…nce-based counting
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Reviewed documentation. Tested on ram1 data. |
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Counts for individual reference sequences are subset by
Classify as...values in sequence-based counting mode. Unit tests have been added for the ReferenceSeqs class.In unit_tests_hts_parsing.py, I split up the gigantic test suite by target class. This is a good thing but it makes the diff wildly out of control on this PR because I didn't commit the reorganization before adding the ReferenceSeqsTests class.
Additionally, both GFFValidator and SamSqValidator classes now report when validation has finished
Closes #277