tiny-count: option for normalization by genomic hits, improvements in stats collection precision #301

Merged

taimontgomery merged 35 commits intomasterfrom

Apr 17, 2023

Commits on Apr 6, 2023

Preliminary refactor and addition of normalization options to accommodate normalization by genomic hits
AlexTate
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Adding command line option to tiny-count, CWL, and the Run Config for disabling normalization by genomic hits. I renamed "normalize hits" to "normalize by feature hits" to disambiguate and make con…
AlexTate
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Updating the MergedStat abstract base class to include a finalize() abstract method. The goal is to separate the finalization steps from write_output_logfile() leaving minimal calls to whichever wr…
AlexTate
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Refactoring FeatureCounts to use the new ABC methods
AlexTate
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Refactoring RuleCounts to use the new ABC methods. Also cleaning up the code used for reading Features Sheet rules. It will be useful for statistics.py to have a rudimentary copy of the rules table…
AlexTate
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Refactoring NtLenMatrices to use the new ABC methods.
AlexTate
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Refactoring AlignmentStats to use the new ABC methods.
AlexTate
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Refactoring SummaryStats to use the new ABC methods. Also changing method order so that get_mapped_seqs/reads is listed near the other stats calculations.
AlexTate
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Commits on Apr 8, 2023

Commits on Apr 9, 2023

Increasing rounding precision. 2 decimal places was far too strict for intermediate operations. Also increasing the equality tolerance by a small amount to help with erroneous warnings for large co…
AlexTate
committed

Commits on Apr 16, 2023

Commits on Apr 17, 2023

Small correction for mapped len dist tables. Rounding should be performed before conversion to int since .astype('int64') is functionally equivalent to .apply(np.floor). Also raising the default eq…
AlexTate
committed