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vcfR

INFRA · APIS
Velocity0.0

Manipulate and Visualize VCF Data

github.com/knausb/vcfr ↗

A genomics workhorse whose visible release feed stops dead in mid-2020.

genomicsvcfpopulation-geneticsr-packagebioinformaticsstale-feed
◆Current state
vcfR reads, manipulates and visualises VCF files, the standard format for genomic variant calls, and bridges them into R population-genetics classes such as genind, genlight and DNAbin. The three entries available here all come from the first half of 2020 and stop there, so the feed shows the state of the package six years ago rather than today.
◆Where it's heading
Within that window the direction is unmistakably consolidation, not growth. 1.9.0 pushed error handling down into the C++ layer that actually reads the VCF so failures surface earlier and shared files stop tripping a readability pre-check, tightened class checks, and added conversion options. The two releases after it exist only to keep pace with R 4.0.0 and dplyr 1.0.0. Any development after June 2020 is not visible in this feed, so the current trajectory cannot be read from it.
◆Prediction
No prediction can be grounded in these entries — the feed has been silent for six years, which points at a stale or broken source rather than at a package that stopped.

◆Recent moves

  1. 6y ago

    Compatibility release for R 4.0 and dplyr 1.0

    A compatibility release for R 4.0.0 and dplyr 1.0.0 and nothing else — 75 characters of release note. It is also the last entry in the visible feed.

    View source ↗
  2. 6y ago

    Deprecated dplyr verbs handled in the tidy conversion path

    Absorbs dplyr's deprecation of the underscore-suffixed verbs inside vcfR2tidy and drops unused ellipses from proc.chromR(). Upstream churn, no decision of the package's own.

    View source ↗
  3. 6y ago

    VCF read errors move into C++; allele-return options added

    The one substantive release in the window. Error handling moves into the C++ functions behind read.vcfR() so problems are raised while reading rather than after, and the file-readability pre-check is dropped, fixing failures on shared filesystems. Several conversion functions gain a return.alleles option, is.indel() arrives, and the licence is pinned to GPL-3.

    View source ↗