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Changelog

Source: NEWS.md

hlabud 2.1.0

Bug fixes

  • Fix incorrect position numbering again, thanks to Vinicius Stelet for bringing this to my attention in issue #4.

In hlabud version 2.0.0, some genes were correctly numbered and some were not:

A     incorrect
B     incorrect
C     ok
DMA   incorrect
DMB   incorrect
DOA   incorrect
DOB   incorrect
DPA1  ok
DPB1  ok
DQA1  ok
DQA2  incorrect
DQB1  ok
DQB2  ok
DRA   incorrect
DRB   ok
DRB1  ok
DRB3  ok
DRB4  ok
DRB5  ok
E     ok
F     incorrect
G     incorrect
HFE   incorrect
MICA  incorrect
MICB  incorrect
TAP1  incorrect
TAP2  ok

We now have additional tests to confirm that the IMGT files are being parsed correctly, and the positions are numbered correctly.

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.