flatviewfs

Mount query results as read-only files via FUSE, materializing on demand with DuckDB.

What works now

• Canonical VCF packages produced by vcf/canonical_tsv.py can be reconstructed back into VCF text through a manifest plus the VCF formatter.
• CSV formatter for simple tabular outputs.
• Prepared-statement binding for user parameters to avoid SQL injection of scalars.

Usage sketch

1. Generate canonical packages (Parquet/TSV) from VCFs:

   python vcf/canonical_tsv.py split vcf/tests/test-files/0GOOR_HG002_subset.vcf vcf/generated

2. Point the manifest at the generated package, e.g. examples/vcf-canonical.toml.

3. Mount:

   cargo run -- --manifest examples/vcf-canonical.toml --mountpoint /tmp/flatviewfs --cache-dir /var/tmp/flatviewfs

   Access files like /tmp/flatviewfs/vcf/0GOOR_HG002_subset/HG002_PacBio_Clc_OTS_PASS_Hg38_no_alt.vcf.

Testing

• cargo test -- --nocapture runs:
  • CSV materialization smoke test.
  • VCF materialization smoke test (synthetic mini package).
  • Canonical end-to-end reconstruction test against the generated package for 0GOOR_HG002_subset.

Notes

• DuckDB table functions require literal file paths; manifests substitute package paths as literals while user inputs are parameter-bound.
• INFO/FORMAT reconstruction depends on the canonical TSV schema emitted by canonical_tsv.py; schema changes will require manifest/formatter updates.