NEWS.md

In RajLabMSSM/echotabix: echoverse module: automated creation and querying of tabix files

echotabix 0.99.10

New features

• Cleanup tbi with rm_tbi() func controlled by cleanup_tbi arg.

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

RajLabMSSM/echotabix documentation built on Nov. 21, 2023, 8:02 a.m.