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CHANGELOG.md

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Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog.

1.0 - 2023-11-18

Added

  • The lineage function now accepts --curated, and --uncurated flags to filter lineage annotated counts based on the family curation status.

Changed

  • Breaking change to HDF5 schema (now v1.0). FamDB is now a database capable of being partitioned. A single root partition is required, however many additional leaf partitions may also be present.
  • The commands available to the user have not changed, but instead of passing the name of the .h5 file to famdb.py with -i, the files must be in a separate directory. The name of that directory is passed to famdb.py with -i instead of the file names. More installation and use details are found in README.md.
  • The structure of the files have also changed. More technical details can be found in README-dev.md.

0.4.3 - 2023-01-09

Added

  • Most subcommands will now accept multiple arguments for a species name and treat it as a single space-separated string instead of raising an error. For instance, famdb.py names homo sapiens now works exactly the same as famdb.py names 'homo sapiens'

Changed

  • Major change to HDF5 schema (now v0.5) fixes performance issues with scaling to >>500k families. HDF5 exhibits an increasing insertion time-cost for entries (datasets or links) within a group. In our original schema families were stored in a single group. In v0.5 we now bin families by two character prefix bins for Dfam and Auxiliary families. Currently 0.4.3 is not backwards compatible and cannot read v0.4 formated files.
  • export_dfam.py has been refactored and extended . It subsumes the previous functionality of convert_hmm.py, which has been removed.

Fixed

  • Fixed numerous bugs with HMM-only libraries produced by convert_hmm.py/export_dfam.py

0.4.2 - 2021-03-30

Fixed

  • famdb now correctly recognizes the "Refineable" annotation for RepeatMasker when reading EMBL files (e.g. 'famdb.py append' and 'export_dfam.py')

0.4.1 - 2021-03-08

Added

  • Added options to the families command: --add-reverse-complement, --include-class-in-name, --uncurated
  • If no file is specified, famdb.py will operate on the file Libraries/RepeatMaskerLib.h5 if it exists
  • The --class option for the families command now accepts a subtype, for example DNA/CMC instead of only DNA

Fixed

  • Disable HDF5's file locking when reading files, since it's unnecessary in that context and unreliable on some filesystems
  • Piping famdb.py to utilities that stop reading output early, such as head or less, no longer produces a BrokenPipeError

0.4 - 2020-09-02

  • Initial release
  • Included with RepeatMasker 4.1.1