tiny-count: new scope of hierarchy value#229
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taimontgomery merged 9 commits intomasterfrom Sep 20, 2022
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…age 3 selection by sorting Stage 2 matches by their hierarchy value. Once a feature-rule pair passes Stage 3 selection, it sets min_rank to which all subsequent matches are compared. The Stage 3 loop exits as soon as a feature-rule pair is found to differ from min_rank. Strand representation in tiny-count has been converted to boolean values: True for '+' and False for '-'. This can later be extended to include None for '.', but this currently isn't needed. The strand selector has been similarly updated. Strand matches are now determined by a chain of boolean XOR operations which are substantially more efficient.
# Conflicts: # tests/unit_tests_hts_parsing.py # tiny/rna/counter/hts_parsing.py # tiny/rna/counter/statistics.py
… been disambiguated to "larger" and "smaller"
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Passed counts tests with ram1 dataset. |
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Rather than eliminating candidates in Stage 2 by hierarchy value, we now use the value to sort Stage 2 matches so that they are evaluated by ascending order of hierarchy in Stage 3. These changes have resulted in a 4% average decrease in unassigned reads in our internal testing dataset.
This PR also contains a new approach for the Strand selector. Strand relationships are now evaluated as chained XOR operations rather than the prior approach of combined string and boolean equality checks.
Unit tests and documentation have been updated.
Closes #223