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qtl2fst

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R package qtl2fst by rqtl — release notes from GitHub.

github.com/rqtl/qtl2fst ↗

The out-of-memory backend for R/qtl2, feature-complete since 2020 and now purely on upkeep

r-packagegeneticsmemory-efficiencyon-disk-storageparallel-computing
◆Current state
qtl2fst backs R/qtl2 genotype probabilities with on-disk fst files so large crosses don't have to fit in RAM. Its defining release was 0.22 in 2020, which added calc_genoprob_fst() and genoprob_to_alleleprob_fst() to fuse calculation and storage in one step. The five releases since are documentation links, directory-creation robustness, a Windows example fix, and — in 0.32 — a change to how cores=0 is interpreted.
◆Where it's heading
The package has settled into the role of a stable satellite of R/qtl2: it tracks the parent package's conventions rather than setting its own. The cores=0 change in 0.32 arrived alongside the identical change in qtl2convert, so the parallel-computing default is being standardized across the maintainer's packages at once. Release intervals have stretched from months to years.
◆Prediction
Further releases will most likely mirror changes originating in R/qtl2 or CRAN checks, in the same follow-the-parent pattern as 0.24 and 0.32.

◆Recent moves

  1. 1mo ago

    cores=0 now leaves one core free instead of taking all

    Redefines cores=0 as detectCores()-1 rather than every available core. The same change landed in qtl2convert the following day, making this a cohort-wide convention change rather than a qtl2fst-specific decision.

    View source ↗
  2. 1y ago

    Windows fix for the replace_path() example

    Repairs a documentation example that errored on Windows. Example-level only, with no change to the on-disk storage behavior itself.

    View source ↗
  3. 2y ago

    Documentation link fix

    A single broken documentation link corrected. Representative of the low-amplitude releases that have followed the package reaching feature completeness.

    View source ↗
  4. 4y ago

    Creates missing directories instead of erroring out

    fst_genoprob() and bind_fst() now create a missing target directory rather than stopping, and validate that inputs are calc_genoprob objects. Small ergonomics work on the rough edges of a file-backed workflow.

    View source ↗
  5. 5y ago

    Test coverage for qtl2 functions against fst-backed probabilities

    Adds tests for calc_het(), calc_entropy(), calc_geno_freq() and compare_genoprob() against fst-backed probabilities, and raises the qtl2 dependency to 0.24 because those paths previously did not work. Closing compatibility gaps with the parent package is the recurring theme of this package's mid-life releases.

    View source ↗
  6. 6y ago

    Documentation and metadata cleanup for CRAN

    Documentation, vignette, title and description revisions made to satisfy CRAN. Packaging work that follows the substantive 0.22 release rather than adding to it.

    View source ↗