basevar v2.6.0

BaseVar v2.6.0 Release Notes

Bug Fixes

1. Fix sparse index lockstep position loss
2. Fix VCF coordinate corruption in binary batchfile reader

The fix adds a backfill step after the reader loop to ensure all samples have consistent ref_id/ref_pos values before calling the variant caller.

3. Fix redundant file open in binary batchfile reader

Performance Improvements

1. Binary batchfile read path optimizations

2. Buffer-serialized binary I/O

3. Eliminate redundant seek_virtual

4. Dead code removal

What's New

New basevar dump subcommand

A new dump subcommand for inspecting intermediate binary batchfile (.bbf) and binary index (.bbi) files. This is useful for debugging, verifying file integrity, or examining per-sample read data at specific genomic positions.

# Inspect .bbi index summary (magic, version, entries, position range, footer integrity)
basevar dump sample.bbf.bbi

# List all index entries
basevar dump sample.bbf.bbi --entries

# Show .bbf header (sample IDs) only
basevar dump sample.bbf --header

# Show all positions in compact summary format
basevar dump sample.bbf

# Show per-sample details at a specific position
basevar dump sample.bbf -r chr11:5246595-5246595 -v

# Dump first 20 positions with full per-sample read data
basevar dump sample.bbf -n 20 -v