Pipeline: new location and scope for GFF Source Filters and Column Filters#246

Merged

taimontgomery merged 14 commits intomasterfrom

Nov 3, 2022

Commits on Oct 27, 2022

Added new selector classes for GFF columns 2 and 3. FeatureSelector.build_selectors() has been updated to build them, and has been modified to allow for building partial rules tables (or building o…
AlexTate
committed
Added Source and Type Filter to the expected column config in CSVReader. Also added a routine to catch Features Sheets lacking these columns, which produces a helpful error message rather than a ge…
AlexTate
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ReferenceTables now evaluates Source/Type column filters on a per-rule basis. These selectors are now part of Stage 1 selection.
AlexTate
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Parsing of the Features Sheet has been added back to the Configuration class. Only Source/Type filters are retained. The result is a "rules table" with a single rule containing all filters defined …
AlexTate
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load_gff_files() now passes the rules table to GFFValidator so that it can filter features by source/type before evaluating them. Also simplified load_config() a little bit.
AlexTate
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CWL updates for the new Source/Type filter approach
AlexTate
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Updated config files for the new Source/Type filter approach
AlexTate
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Cleaning up command line arguments and unnecessary comments in tiny-count components
AlexTate
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Drafted updates to the documentation (need to merge changes from other issues and proofread)
AlexTate
committed

Commits on Oct 28, 2022