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hlabud 2.0.0

Bug fixes

  • Fix incorrect position numbering, accounting for insertions and deletions that are indicated with the "." character. Thanks to Vinicius Stelet for bringing this to my attention in issue #3.

  • Instead of discarding positions with *, we include them and label them as unk, for example pos241_unk indicates an unknown amino acid at position 241. Thanks to Sreekar Mantena for reporting this issue!

  • Fix an off-by-one error. For example, HLA-A had pos361_- in the colnames(a$onehot) but it should have had the reference allele instead of -. This is now fixed. Thanks again to Sreekar Mantena for reporting this issue!

Changes

  • Change position names from pos21_D to D21. When negative, posn21_D to Dn21.

  • Change dosage() to take a one-hot matrix as the first argument.

  • Change dosage() to return full allele names from IMGT when matching to partial allele names like DRB1*03 or DRB1*03:01. And show messages indicating which alleles were matched when verbose=TRUE.

  • Automatically overwrite {hlabud_dir}/alleles.json if it is older than 24 hours.

  • Automatically overwrite {hlabud_dir}/tags.json if it is older than 24 hours.

hlabud 1.0.0

  • Initial release.

  • Added a NEWS.md file to track changes to the package.