NEWS.md

In gschofl/hlatools: A collection of tools to work with IPD-IMGT/HLA data

hlatools 0.1.6

• Update for IPD-IMGT/HLA 3.44.0

hlatools 0.1.7

Fix more broken parsing of MICA and MICB

hlatools 0.1.6

• Update for IPD-IMGT/HLA 3.40.2, 3.42.0 and 3.43.0
• Fix parsing MICA and MICB, which was broken since 3.40.0

hlatools 0.1.5

• Update for IPD-IMGT/HLA 3.40.0 and 3.41.0

hlatools 0.1.3

• Complete alleles are now defined as featuring the expected set of exons and introns instead of the 2 UTR sequences.
• Update for IPD-IMGT/HLA 3.38.0 and 3.39.0
• As of IPD-IMGT/HLA 3.39.0, the locusname for MICA and MICB has become MICA and MICB instead of HLA-MICA and HLA-MICB.

hlatools 0.1.3

• Include parsing MICA and MICB
• Update for IPD-IMGT/HLA 3.37.0

hlatools 0.1.2

• Update for IPD-IMGT/HLA 3.35.0
• Added HLAGene method x$get_extended_reference_set().
• Handle HLA-DRB before IPD-IMGT/HLA release 3.26.0.

hlatools 0.1.1

• Update for IPD-IMGT/HLA 3.33.0
• Update for git2r 0.23.0

hlatools 0.1.0

API changes

• The code table functions nmdp_table(), g_table, and generate_nmdp_lookup() return tibbles instead of data.tables.
• Renamed fetch_IMGTHLA() to clone_IMGTHLA() and update_IMGHTHLA() to pull_IMGTHLA() (the old functions are aliased to the new).

New or modified functions

• Added allele_table() to parse the hla_nom.txt file.
• Added check_IMGTHLA() to check if the local repo is up-to-date.
• Added noutr() to extract sequences except for UTRs.

Minor improvements and bug fixes

• Added a db_path argument to HLAGene() and read_hla_xml() to allow for alternative repository locations.
• Remove package curl as a dependency.

Internal changes

• Distance calculations between alleles are now based on all available exons instead of only exon 2.
• Added HLAGene method x$calculate_exon_distance_matrix().
• The HLAGene method x$get_closest_complete_neighbor() gains an argument partially = TRUE that allows for partial allele matching.

hlatools 0.0.7

• [feature] db_version() returns a numeric_version object instead of a character string (#3).
• [feature] new hlatools_version() method for HLAGene objects (#2).
• [bug] fix locusname() method for HLAGene objects (#1).
• [feature] add exon(), intron(), and utr() to extract feature sequences.
• [feature] Partial matching of allele names when subsetting HLAAllele objects.
• [feature] Added a NEWS.md file to track changes to the package.

gschofl/hlatools documentation built on July 2, 2021, 10:59 a.m.