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produce_genes: Compute phase for exons
.github/workflows/ci.yml
#31:
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style: Improve readability and error messages
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produce_genes: Compute phase for exons
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style: Improve readability and error messages
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gene_caller: Fix regression (off by one on reverse strand)
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main: Fix regression (overwritten results with multiple contigs)
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logging: Fix exceptions not being caught with custom logger
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Allow gene predictions to overlap on opposite strands
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logging: Fix exceptions not being caught with custom logger
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outputs: Use numbered transcript and CDS IDs
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some old code snuck back in
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replace gene_range_time_limit with single_recurse_max_num_ops
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outputs: Fix gene order in .gff file
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lint: Organize imports
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lint: Fix imports with isort
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gene_caller: Add option for calling on forward, reverse or both strands
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gene_caller: Add option for calling on forward, reverse or both strands
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Don't hardmask repeats by default
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option to hardmask repeats (defaults to 200 bp)
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comments and cleanup
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help: Change help text for --help
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keep original case in sequences
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fix regression
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cleanup
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lint
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