v1.0 updates

[nakib103]

Major Features & Enhancements

• Support for structural Variants:
  • Support for variable-length extra fields in bed files for additional SV fields.
  • Script for merging dbVar call and region files
  • Script to process HPRC files to generate haplotype VCF
  • Script to generate of segdup track files for HPRC
• Add MAGIC-16 as Source in Metadata: Updated configuration to include new data sources.

Pipeline & Performance Improvements

• Optimised Memory Allocation: Several steps, especially the VEP step, have been optimised for better memory usage.
• Update to data checks: added skip xfail to skip time-consuming and expected failure tests as well as generation of variant lists to test once in test runtime along with other improvements

Bug Fixes & Maintenance

• Symlink issue: Fixed issues with symlink when multiple source is unset.
• Allele mismatch in Summary Stats: Use allele number to avoid mistake in mismatching in allele names.
• More Restrictive Regex for HPRC gnomAD: Only allow the 89 haplotypes we have data for.
• VEP config generation: Fix cache version and only allow gencode primary for GRCh38.
• Source name extraction: Fix minor bug in extracting source name from the input config.

Other Notable Changes

• Post-Handover Test Script Updates: Added script to check handover was successful (file staging is ok).
• Index Generation Improvements: Added -f flag and fixed symlink issues in track files.