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Fix missing columns in kestrel_result.tsv and implement detailed screening summary #78

Merged
merged 10 commits into from
Jan 13, 2025
Merged

Fix missing columns in kestrel_result.tsv and implement detailed screening summary #78

merged 10 commits into from
Jan 13, 2025

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berntpopp
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Enhance the logic for populating the Motifs, Frame_Score, Motif_left, and Motif_right columns in kestrel_result.tsv to ensure they contain meaningful data. Update the motif_correction_and_annotation function to retain these columns during processing. Implement a detailed summary of screening results in the final report, addressing various scenarios based on confidence levels and quality metrics.

Fixes #73
Fixes #72
Fixes #76

@berntpopp
refactor: Enhance scoring functions with type hints and improve logic…
222e3e5 
… for frameshift identification
@berntpopp
fix: Uncomment summary_text in generate_summary_report for inclusion …
29cb689 
…in context
@berntpopp
refactor: Improve VCF reading and filtering functions with error hand…
8b2ac43 
…ling and logging
@berntpopp
fix: Update confidence assignment logic to include high precision sta…
2f3a74b 
…r condition and improve error handling
@berntpopp
test: Add unit tests for scoring functions including frame-score calc…
498c9f9 
…ulations and frameshift extraction
@berntpopp
test: Add unit tests for ALT filtering in variant_parsing.py
28754f6
@berntpopp
fix: Update confidence values in test data
3646e4a
@berntpopp
refactor: Enhance motif processing and variant filtering logic with e…
4df6efc 
…arly exits and improved comments
@berntpopp
refactor: Update kestrel filter logic to output the complete df always
957d2b4 
fixes problems previously introduced with logging
introduces High_star class which was previously missing
Update report generation to handle new class

Closes: #73
Closes: #74
Bump version to 2.0.0-alpha.55
@berntpopp
feat: Implement detailed summary of screening results in the final re…
4cfc2e8 
…port

Closes #76
@berntpopp berntpopp requested a review from hassansaei January 13, 2025 14:19
@hassansaei hassansaei merged commit 5da3399 into main Jan 13, 2025
1 check passed
@berntpopp berntpopp deleted the refactor_kestrel_logic branch January 15, 2025 11:17
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@hassansaei hassansaei hassansaei approved these changes

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