Enhance CLI and analysis features for QTL Cascade and eQTL/pQTL#79

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enriquea merged 30 commits intomainfrom

Mar 28, 2026

Commits on Mar 28, 2026

fix: add QTL Cascade command to CLI for enhanced analysis capabilities
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fix: add eQTL and pQTL table builders to CLI for enhanced data processing
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fix: add eQTL and pQTL table builders to registry for improved data processing
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feat: implement eQTL and pQTL table builders with enhanced import functionality
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feat: add QTL Cascade module for comprehensive variant analysis and reporting
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feat: add coloc module for colocalization analysis using Approximate Bayes Factors
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feat: add constants for QTL cascade analysis including thresholds and tissue mappings
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feat: add gene-level summary aggregation for QTL cascade evidence
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feat: implement stage-based pipeline orchestration for QTL cascade analysis
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feat: add CLI commands for QTL cascade analysis including cascade, coloc, run, and report
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feat: add HTML report generation for QTL cascade analysis
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update docs with qtl pipelines
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feat: add visualization functions for QTL cascade analysis
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blacked
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feat: add logdiff function and improve tissue filtering in coloc analysis
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feat: add warning for multi-tissue data without a tissue filter in coloc analysis
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feat: update PQTL_SOURCES to reflect current implementation status
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feat: update disease-gene table documentation for clarity on gene_id requirements
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feat: clarify coloc results inclusion in outputs for QTL Cascade
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feat: update tissue option help text for clarity on file import restrictions
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feat: reorder pipeline stages and add single-tissue report generation
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fix: correct formatting of confidence interval in plot output
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feat: add handling for empty data in plot output and enhance heatmap documentation
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fix: correct code block formatting in qtlcascade documentation
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feat: enhance dry run output and update coloc threshold for gene colocalization
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feat: sanitize HTML output in report generation to prevent XSS vulnerabilities
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feat: normalize contig names for reference genome compatibility and update documentation for tissue restriction
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feat: add CLI tests for eQTL and pQTL table creation and cascade command functionality
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feat: enhance error logging for gene summary loading and scope plots by tissue
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fix: resolve Codacy static analysis issues - remove unused imports and fix test module mocking

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