This is the `extdata/germline_sets/AIRR/human/202401/ref/` folder
in the **igblastr** package.

This folder contains germline sequences (in FASTA format) obtained from
AIRR-community/OGRDB for Human. The sequences were extracted from the
following datasets:
- `IGH_VDJ` version 8 "Reference Set" (a.k.a. "extended")
- `IGKappa_VJ` version 3 "Reference Set" (a.k.a. "extended")
- `IGLambda_VJ` version 2 "Reference Set" (a.k.a. "extended")

IMPORTANT NOTE: These were the most current versions at the date indicated
by the name of the parent folder of this folder (202401 i.e. Jan 2024).

The folder also contains the corresponding V gene FWR/CDR annotation files
for the IMGT domain system (`*.ndm.imgt` files).

FWIW these datasets can be manually downloaded with:
```
curl https://ogrdb.airr-community.org/download_germline_set/Homo%20sapiens/IGH_VDJ/9/ungapped_ex >Homo_sapiens_IGH_VDJ_rev_8_ungapped_ex.fasta
curl https://ogrdb.airr-community.org/download_germline_set/Homo%20sapiens/IGKappa_VJ/4/ungapped_ex >Homo_sapiens_IGKappa_VJ_rev_3_ungapped_ex.fasta
curl https://ogrdb.airr-community.org/download_germline_set/Homo%20sapiens/IGLambda_VJ/3/ungapped_ex >Homo_sapiens_IGLambda_VJ_rev_2_ungapped_ex.fasta
```

However, the FASTA files in this folder were obtained programmatically
by running the following code in the folder on Nov 17, 2025:
```r
library(igblastr)
download_germline_sequences_from_OGRDB <- igblastr:::download_germline_sequences_from_OGRDB

Hfile_count <- download_germline_sequences_from_OGRDB("Human", set_name="IGH_VDJ", locus="IGH", release_version="8", extended=TRUE)
stopifnot(identical(Hfile_count, 3L))

Kfile_count <- download_germline_sequences_from_OGRDB("Human", set_name="IGKappa_VJ", locus="IGK", release_version="3", extended=TRUE)
stopifnot(identical(Kfile_count, 2L))

Jfile_count <- download_germline_sequences_from_OGRDB("Human", set_name="IGLambda_VJ", locus="IGL", release_version="2", extended=TRUE)
stopifnot(identical(Jfile_count, 2L))
```

Files `*.ndm.imgt` were obtained programmatically by running the
following code in the folder on Jan 10, 2026:
```r
library(igblastr)
germline_sets <- c(IGH_VDJ=8, IGKappa_VJ=3, IGLambda_VJ=2)
igblastr:::download_V_ndm_data_from_OGRDB("Homo sapiens", germline_sets)
for (group in c("IGHV", "IGKV", "IGLV")) {
    V_names1 <- names(fasta.seqlengths(paste0(group, ".fasta")))
    V_names2 <- read_V_ndm_data(paste0(group, ".ndm.imgt"))$allele_name
    stopifnot(length(V_names1) == length(V_names2),
              setequal(V_names1, V_names2))
}
```

