0.3.0

What's Changed

• Feature/mfsd variant types by @rhshah in #6

[0.3.0] - 2025-12-16

Added

• mFSD Variant Type Support: Now handles all small variant types:
  • SNV (single nucleotide)
  • MNV (multi-nucleotide)
  • Insertion
  • Deletion
  • Complex (substitution + indel)
• 4-Way Fragment Classification: Fragments classified as REF, ALT, NonREF, or N (low quality)
• Comprehensive Statistics: 6 pairwise KS comparisons (ALT-REF, ALT-NonREF, etc.)
• Derived Metrics: VAF_Proxy, Error_Rate, N_Rate, Size_Ratio, Quality_Score
• Quality Flags: ALT_Confidence (HIGH/LOW/NONE), KS_Valid
• Distributions Output: --output-distributions flag generates per-variant size distributions
• Verbose Logging: --verbose flag for debug-level logging with variant type breakdown
• MRD Support: Proper handling of low fragment counts (1-2) common in MRD settings

Changed

• BREAKING: mFSD output format changed from 11 columns to 39 columns
• Nextflow MFSD: Distributions and verbose logging enabled by default
• Fragment Counting: Now counts fragments (R1 only) instead of reads to avoid double-counting

Fixed

• CIGAR Handling: Improved sequence extraction for INDELs and complex variants

[0.2.3] - 2025-12-16

Changed

• Nextflow Pipeline: Added FILTER_MAF module for multi-sample MAF filtering:
  • New maf and single_sample_maf columns in samplesheet
  • Filters MAF by Tumor_Sample_Barcode matching sample ID (regex: .*sample_id.*)
  • single_sample_maf=true bypasses filtering for per-sample MAFs
  • Skips MFSD when filtered MAF has zero variants (with warning)
  • Memory-efficient streaming for large MAF files (100s of MBs)
  • Outputs filtered MAF + mFSD results
• Nextflow Modules: Updated all container versions to 0.2.3

Full Changelog: 0.2.2...0.3.0