NEWS

---

igblastr 1.2.0

NEW FEATURES

• Add built-in germline db _OGRDB.rhesus_monkey.IGH+IGK+IGL.202602.
• All the built-in germline dbs now include their own internal and auxiliary data. This is reported in the 2 new columns ('intdata' and 'auxdata') displayed by list_germline_dbs().
• Add arguments 'with.intdata.only' and 'with.auxdata.only' to list_germline_dbs().
• The germline dbs installed with install_IMGT_germline_db() now also include their own internal and auxiliary data.
• Add functions reset_germline_dbs() and reset_c_region_dbs(). See corresponding man pages for the details.
• Add arguments 'loci', 'without.intdata', 'without.auxdata', and 'verbose' to install_IMGT_germline_db().
• Add function install_IMGT_c_region_db().
• Add function install_custom_germline_db().
• Add functions download_IMGT_germline_sequences(), parse_imgt_fasta_headers(), download_OGRDB_germline_sequences(), download_OGRDB_germline_json(), extract_intdata_from_ogrdb_json(), and extract_auxdata_from_ogrdb_json().
• Add utilities to update IgBLAST auxiliary and internal data. See '?update_live_igdata' for more information.
• Add utility functions get_intdata_path() and load_intdata().
• Add function compute_V_gene_delineations() to annotate a set of germline V gene allele sequences.
• Add functions compute_auxdata() and compute_germline_db_auxdata() to annotate a set of germline J gene allele sequences.
• Add IO functions read_ndm_data(), write_ndm_data(), read_auxdata(), and write_auxdata().
• Add low-level utility functions allele2gene(), translate_codons(), extract_codons(), remove_gaps(), translate_V_alleles(), V_allele_has_stop_codon(), translate_J_alleles(), J_allele_has_stop_codon(), translate_fwr4(), and V_genes_with_varying_fwrcdr_boundaries().
• Add low-level utility functions read_igblastn_AIRR_output() and read_igblastn_fmt7_output().

SIGNIFICANT USER-VISIBLE CHANGES

• Two important changes to igblastn(), the main function in the package: 1. If the selected germline db includes its own internal data then igblastn() will use it by default instead of the internal data shipped with IgBLAST. See documentation of the 'custom_internal_data' argument in '?igblastn' for more information. 2. If the selected germline db includes its own auxiliary data then igblastn() will use it by default instead of the auxiliary data shipped with IgBLAST. See documentation of the 'auxiliary_data' argument in '?igblastn' for more information.
• The "_AIRR." prefix in the name of the built-in germline dbs has been replaced with "_OGRDB.".
• The 'force' argument present in several functions (e.g. install_igblast(), install_IMGT_germline_db(), etc..) was renamed 'overwrite'.
• Rename functions get_igblast_auxiliary_data() and load_igblast_auxiliary_data() to get_auxdata_path() and load_auxdata(), respectively. The old names can still be used but are deprecated.

igblastr 1.0.0

• First version of the package that is ready for general use.