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Changelog

Source: NEWS.md

immunogenetr 1.2.0

CRAN release: 2026-04-14

  • Added scope parameter to HLA_match_summary_HCT with options "locus" (default) and "genotype". When scope = "genotype" and direction = "bidirectional", the function calculates GvH and HvG match summaries separately and returns the maximum of the two totals, rather than taking the minimum match at each locus before summing.

  • Simplified HLA_match_summary_HCT internals: replaced the tibble parsing pipeline with str_extract_all() and map_int() for summing per-locus match counts.

immunogenetr 1.1.0

CRAN release: 2026-04-07

  • Internal code quality improvements: fixed typos in internal variable names, corrected test filenames, and cleaned up globalVariables() declarations.

  • Standardized all error messages to use cli_abort() for consistent, informative error reporting across the package. Bumped cli dependency to >= 3.0.0.

  • Added input validation to all exported functions. Functions now check for NULL, wrong types, and invalid parameter values before processing, providing clear error messages instead of cryptic failures. Added internal validation helper functions (check_gl_string, check_data_frame, check_loci, check_logical_flag, check_homozygous_count, check_fields).

  • Added match.arg() validation for match_grade and direction parameters in HLA_match_summary_HCT.

  • Refactored duplicated matching logic across HLA_match_summary_HCT, HLA_match_number, HLA_mismatch_number, and HLA_mismatch_logical. Replaced repeated direction-branching code blocks with parameterized pipelines, significantly reducing code duplication with no changes to behavior.

  • Optimized HLA_mismatch_base: consolidated duplicated GvH/HvG mismatch calculation into a single parameterized code path, eliminated repeated strsplit() calls within the mismatch loop, and extracted duplicated locus-naming logic into a shared helper function.

  • Optimized HLA_mismatch_number and HLA_mismatch_logical to only compute the requested direction(s). Previously both functions always computed GvH and HvG regardless of the requested direction; now HvG, GvH, and SOT requests only compute a single direction, cutting HLA_mismatch_base calls in half. Bidirectional requests still compute both as needed. Also extracted duplicated multi-locus table-building code into internal helper functions.

  • Expanded test coverage for HLA_mismatch_logical, HLA_match_number, and HLA_mismatched_alleles using the mismatch_table_2010 and mismatch_table_2016 consensus reference tables, matching the existing comprehensive table-based tests in HLA_mismatch_number.

  • Optimized HLA_columns_to_GLstring: replaced 16 case-insensitive regex calls for locus detection with a single tolower() plus startsWith() lookups (~7.5x faster), replaced the serologic name case_when with a named vector lookup (~37x faster), and combined multiple str_detect() calls for molecular typing detection into single patterns.

  • Optimized HLA_truncate: replaced four nearly-identical if/else blocks for field selection with a parameterized approach using computed keep_cols/drop_cols vectors, reducing code duplication and improving maintainability.

  • Optimized ambiguity_table_to_GLstring: extracted a collapse_level() helper function to replace six repetitions of the conditional distinct() + summarise() pattern, significantly reducing code duplication.

  • Optimized GLstring_genotype_ambiguity: simplified the gene-separator error detection from a multi-step pipeline to a single vectorized check, and combined two separate str_replace() + na_if() calls into one operation.

  • Expanded test coverage for HLA_column_repair, GLstring_genes, GLstring_regex, and read_HML with comprehensive tests covering format conversions, parameter combinations, edge cases, input validation, and error handling.

  • Fixed read_HML to dynamically discover the XML namespace instead of hardcoding the d1: prefix. The function now uses xml_ns() to detect the namespace from the file, improving compatibility with HML files from different sources.

  • Fixed null allele detection regex in HLA_mismatch_base to support locus names longer than 4 characters (e.g. HLA-DRB345). The lookbehind now allows up to 10 alphanumeric characters after HLA-.

  • Added a “Getting Started” vignette covering all major workflows: tabular-to-GL-string conversion, locus splitting, mismatch/match calculation, allele name utilities, and HML file reading.

  • Added a package-level help page (?immunogenetr) organizing all exported functions and datasets by category.

  • Added inst/CITATION file for the package publication: Coskun & Brown (2026), “Immunogenetr: A comprehensive toolkit for clinical HLA informatics,” Human Immunology, 87(1):111619. doi:10.1016/j.humimm.2025.111619.

immunogenetr 1.0.1

CRAN release: 2025-10-22

  • Added a disclaimer to the package for it being for research use only. Added a disclaimer to the help file for HLA_truncate to warn users about the ability to make non-WHO-compliant allele names with certain settings. Updated HLA_mismatch_base to better handle missing loci at the DRB3/4/5 locus.

immunogenetr 1.0.0

CRAN release: 2025-08-19

  • Added HLA_mismatch_alleles as a synonym of HLA_mismatched_alleles. Added minimum versions in DESCRIPTION. Stable release; updated version to 1.0.0.

immunogenetr 0.3.1

CRAN release: 2025-06-25

  • Updated HLA_columns_to_GLstring to fix issues processing DRB3/4/5 alleles.

immunogenetr 0.3.0

CRAN release: 2025-06-18

  • Updated ambiguity_table_to_GLstring to remove duplicate entries from an ambiguity table as it is being processed to a GL string. Added this functionality to HLA_truncate so that truncated GL strings could optionally remove duplicates. Added GLstring_to_ambiguity_table as an alias for GL_string_expand_longer.

immunogenetr 0.2.0

CRAN release: 2025-06-06

  • Updated HLA_prefix_add and HLA_prefix_remove to work on all alleles in a GL string. Also added the option of keeping locus designations in HLA_prefix_remove.

immunogenetr 0.1.0

CRAN release: 2025-03-24

  • Initial CRAN submission.