Changes:
- Changed thread behavior related to file IO in server code, improving server performance.
- Modified the format for the metadata file for the 'select' command. This is a breaking change.
- Rxfr now builds and installs using the autotools approach with a configure script.
Feature changes:
- Sliding windows queries are now supported.
- Better compression means faster responses for remote queries involving bins and sliding windows.
Changes:
- Download policy objects have been replaced by strings in pyxfr.
- More group manipulation features have been added to the select command.
- The redundant bin end value has been removed from the output format for bins queries.
- The JSON input format for queries has been modified.
- All forms of queries (local/remote; regular/covered) can be done with sliding windows.
- Responses for bins and sliding windows queries are compressed using libdeflate.
Feature changes:
- Queries can accept more options to customize output formats.
- Users can customize how methylome are named in query output.
- The select command now supports methylome groups defined by users.
Changes:
- Documentation for the query command has been expanded.
- LogLevel objects have been replaced by strings in the Python and R APIs.
- Bug fixes now avoid redundant downloads during user (re)configuration.
- Bug fixes allow for faster server responses.
- Incorrect error codes reported to users by the server have been fixed.
- Query output writing performance has been improved.
- Fixed bugs in horizontal scrolling within the select command.
- The transferase Dockerfile has been removed as it is unneeded.
- Fixed bug in which the server kept working on a query after seeing a non-existing methylome
- In the query and config commands, log levels are determined by choices of quiet and verbose, instead of log levels.
Feature changes:
- Added more detail about samples in the 'select' command.
- pyxfr is now on pypi and installable with pip.
- MethBase2 metadata is now available in the Python API as a pandas data frame.
- Renamed Python API to pyxfr to avoid confusion in managing which files are part of which package -- and easier to type.
Changes:
- Configuration file formats have changed; the system should update them as they are now versioned.
- In the Python and R packages, all queries must specify the genome. This was changed in part to simplify code and improve performance, and in part to add an additional confirmation of user intent.