Rewrote HLA_prefix_remove to skip the GL-string expand-and-reassemble round-trip. The previous implementation expanded each GL string into an ambiguity tibble, ran str_replace on it, and reassembled — which was the dominant cost in any pipeline that called HLA_prefix_remove per cell. Now four direct regex passes on the GL-string character vector. ~100× faster end-to-end, up to ~420× less memory allocated on 100,000-input workloads. Because many other functions in the package (including HLA_columns_to_GLstring) call HLA_prefix_remove internally, every downstream caller picks up the speedup for free.
Rewrote HLA_columns_to_GLstring to compute column-level decisions (locus mapping from column name, serologic-name lookup, "always molecular" flag for DQA1/DPA1/DPB1) once per column instead of once per cell, and replaced the two trailing summarise(str_flatten(...)) passes with vectorised split + paste. End-to-end ~68× faster at 1000 rows (7.4 s -> 109 ms) and ~200× faster at 10,000 rows (~272 s -> ~1.3 s).
Rewrote HLA_mismatch_base to replace the per-pair purrr::map2_chr loop and stringr wrappers with base-R / stringi primitives, hoist invariants out of the per-pair loop, and short-circuit the null-allele regex on alleles that cannot match. ~26× faster at 100 pairs, ~11× faster at 10,000 pairs, and ~1000× less memory allocated on the large workload. Also tuned the residual unify_locus / DRB3/4/5 classification / molecular prefix extraction hot spots exposed by the post-merge re-profile.
Rewrote the four HLA_mismatch_* derivatives (HLA_mismatch_logical, HLA_mismatch_number, HLA_mismatch_alleles, HLA_mismatched_alleles) to replace the shared tibble -> separate_longer_delim -> separate_wider_delim -> summarise post-processing pipeline with direct character-vector ops on an integer mismatch count matrix. 10-50× less memory; 10-15% faster per call (the underlying HLA_mismatch_base call now dominates).
Rewrote HLA_match_number and HLA_match_summary_HCT to share a new internal helper hla_mismatch_count_matrix() that exposes the integer count matrix HLA_mismatch_number already builds, skipping the format-and-reparse round-trip through its string output. 15-20% faster end-to-end, 10-21× less memory per call.
Rewrote GLstring_expand_longer to replace the 7-level tidyr::separate_longer_delim + row_number() chain with a stringi::stri_split_fixed cascade that assembles the output tibble directly from equal-length index vectors. 20-43× faster depending on input size; up to 4× less memory.
Rewrote ambiguity_table_to_GLstring to replace six chained dplyr::summarise(str_flatten(...)) passes with a single sort-and-paste helper. Subsequent levels of the GL hierarchy skip the redundant sort since the composite index key stays sorted under prefix truncation. 2-13× faster depending on size and the remove_duplicates flag.
Rewrote HLA_truncate to replace the GLstring_expand_longer -> 4x separate_wider_delim -> 4x unite -> ambiguity_table_to_GLstring pipeline with a vectorised per-allele truncator that flattens all fields across all alleles into a single long vector for regex processing, then collapses per allele in one pass. ~5× faster end-to-end at 1000 alleles.
Rewrote GLstring_gene_copies_combine to replace the pivot_longer -> mutate(str_extract) -> summarise(str_c) -> pivot_wider -> rename_with round-trip with a one-pass flat-vector build. ~7× faster at 1000 rows.
Rewrote GLstring_genes to replace separate_longer_delim -> rename -> mutate(str_extract) -> pivot_wider with a direct stringi::stri_split_fixed + per-locus column build. 2.6-3.7× faster.
Rewrote GLstring_genes_expanded to replace the pivot_wider(values_fn = list) -> unnest pipeline with per-row split and bind_rows. ~5× faster on 100 single-row calls, ~16× less memory. As a side effect, the function now handles multi-row input gracefully; the previous implementation errored on unnest when different rows had different allele counts per locus. Single-row semantics — including the intentional recycling of length-1 cells flagged as expected behavior in the test file — are preserved.
Added check_molecular_gl_string() internal validation helper for callers that want to enforce molecular-only GL string inputs (used at API boundaries). Opt-in; not wired into existing functions to preserve compatibility with serologic-input callers.
Fixed a latent correctness bug in the "missing loci" check in HLA_mismatch_base introduced during earlier optimization work. The check silently required a locus to be missing from both recipient and donor before erroring, instead of the original semantics of missing from either side. Restored the original behavior.
Added a round-trip property test suite (tests/testthat/test-round_trip.R) asserting that ambiguity_table_to_GLstring(GLstring_expand_longer(x)) == x for a representative pool of GL strings, and that HLA_prefix_add / HLA_prefix_remove form an inverse pair on raw allele input. Added explicit NA-propagation regression tests for ambiguity_table_to_GLstring and GLstring_genes covering bugs caught during the rewrite. Added tests for check_molecular_gl_string.
Added stringi (>= 1.7.0) as a direct Imports dependency. It was previously a transitive dependency via stringr; this release uses it directly for stri_split_fixed, stri_startswith_fixed, stri_endswith_fixed, and stri_extract_first_regex in the rewritten functions.
Removed glue and magrittr from Imports. No function in the package uses them directly after these rewrites (str_glue calls were replaced with paste0/paste; %>% is still available via @importFrom dplyr %>%).
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.
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.
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.HLA_mismatch_alleles as a synonym of HLA_mismatched_alleles. Added minimum versions in DESCRIPTION. Stable release; updated version to 1.0.0.HLA_columns_to_GLstring to fix issues processing DRB3/4/5 alleles.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.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.