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Changelog

Source: NEWS.md

echotabix 1.0.1

Bug fixes

  • Fix sort_coordinates_bash in-place redirect bug: shell > redirect truncated the input file before grep could read it, producing empty sorted output. Now writes to a temp file and moves it back.
  • Fix sort_coordinates_bash “subscript out of bounds” error: validate that chrom_col, start_col, end_col exist in the file header before accessing column indices.
  • Fix construct_query to validate that start/end positions are not NA before calling IRanges, giving a clear error instead of a cryptic IRanges failure.
  • All tests now detect position column dynamically (POS or BP) instead of hardcoding, fixing failures when echodata::BST1 uses either name.
  • Fix test-run_bgzip: use .tsv instead of .tsv.gz to avoid double-compression issues with run_bgzip.
  • Fix test-convert: replace destructive tempdir() cleanup with targeted file removal to avoid deleting files needed by later tests.

echotabix 1.0.0

Bug fixes

  • Fix column detection logic for tabix query results.
  • Fix test-run_bgzip: recreate temp file for sorted test (consumed by prior unsorted run); coerce CHR type after bgzip roundtrip.
  • Fix test-query_vcf and test-vcf_to_dt assertions to match replacement BST1 VCF (100 rows, 10 samples).
  • Wrap conda-dependent tests (test-convert, test-run_gunzip, test-query_tabular) in tryCatch to handle missing conda binary.
  • Add skip_on_ci() to test-liftover (requires chain file download) and remote VCF query tests.
  • Fix Rd formatting and \dontrun{} example guards.
  • Update install instructions to use BiocManager::install().
  • Fix Codecov icicle graph URL (codecov.io instead of app.codecov.io).
  • Add Rplots.pdf and *.tbi to .gitignore.

echotabix 0.99.13

Bug fixes

  • Local R CMD check fixes and compatibility updates.

echotabix 0.99.12

New features

  • Add docker_registry: ghcr.io to rworkflows.yml for GHCR Docker builds.

echotabix 0.99.11

Bug fixes

liftover: Ensure “CHR” gets retained.

echotabix 0.99.10

New features

  • Cleanup tbi with rm_tbi() func controlled by cleanup_tbi arg.
  • Fix issue with .Rbuilignore ignoring rm_tbi.R #5

Bug fixes

  • query_table_conda:
    • Explicitly specify begin,end,seq col numbers using header.
    • Use query file (“-R” arg) instead of string. Works far better for multi-range queries.

echotabix 0.99.9

New features

  • Implement rworkflows.

Bug fixes

  • convert: Pass force_new to run_bgzip.

echotabix 0.99.8

New features

  • Allow users to specify target_index path in all functions where possible.
  • fix_query_style now takes target_index too.
  • query_vcf_conda Make download_index an argument (i.e. -D).
  • filter_table_snps: new function to actually use the overlapping_only arg.

Bug fixes

  • query: When multiple method are given, take the first valid method (for vcf vs. table).
  • query_vcf_variantannotation:
    • Forgot to pass target_index to fix_query_style.

echotabix 0.99.7

New features

  • Automatically select the a valid method depending on Bioc version.

Bug fixes

  • construct_query: Fix bug caused by converting “chr#” to numeric.

echotabix 0.99.6

New features

  • Updated all functions to use the basilisk-based echoR_mini conda env, which is now the default for echoconda.
  • Moved all VCF examples to example_data.
  • convert can now handle VCFs as well as table inputs (though can only export as the same format).
  • query_vcf: Add alternative methods.
    • “variantannotation”: ideal, but package is broken currently due to issues with Rsamtools/Rhtslib.
    • “conda”: Uses echoconda (default until “variantannotation” is fixed”).
    • “seqminer”: Generates table, but not fully parsed.
    • “rtracklayer”: Generates table, but not fully parsed.
  • Add “-D” flag to query_vcf_conda to avoid downloading index file.

Bug fixes

  • Added expect_failure and expect_error to all Rsamtools/VariantAnnotation-based query methods until these packages are fixed.
  • infer_chrom_type can now handle VCFs.

echotabix 0.99.5

New features

  • Condense all query args further into query_granges.
  • Added standardise_colnames arg to construct_query.
  • Added check_convert_methods to validate convert_methods arg in convert().

Bug fixes

  • Passing all tests, just not when running Test Package in Rstudio. Weirdly, using the Run Tests button in each test script also works fine. Possibly related to this Issue?
  • Add echoconda::yaml_to_env call at the beginning of all conda-based functions.
  • Removed subset_common_snps function (already in echoLD).

echotabix 0.99.4

New features

  • Add Getting Started vignette.
  • Condense all query args into query_dat and query_granges.

echotabix 0.99.3

New features

  • Added a NEWS.md file to track changes to the package.
  • Updated GHA.
  • Removed docs/ folder