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Changelog

v2.2.0

  • Add the capability to export read-level modification predictions. The read_results option in the configuration can be set to true to export modification probability for each position of each read to the output SQLite database.

v2.1.0

Added

  • Soft clustering: The cluster_counts option was added which can be used to switch to a soft assignment strategy in the GMM clustering. With the soft assignment each point is split proportionally between the two clusters depending on the probability of being assigned to them.

Fixed

  • Fixed how the modified cluster is inferred in the GMM test. The change affects the per-sample count columns, but not the p-value and GMM_LOR statistics.
  • Fixed error that was thrown when there are no results (#233).
  • Fixed the GMM plot subcommand.

v2.0.0

This is major release that represents an almost complete redesign and rewrite of the tool. The more noteworthy changes include:

  • Completely new user interface.
  • Support for the RNA004 sequencing chemistry.
  • Major improvements in performance.
  • GPU support.
  • Support for multiple signal-to-reference aligners (resquigglers): Nanopolish/f5c eventalign, Uncalled4, and Remora.
  • Reduced disk space usage.
  • Automatic test selection strategy.
  • We add the ability to use the dwell time of a nearby position as an additional dimension in the GMM test. This can be used to capture changes in the molecule translocation speed produced by interactions between a modification and the motor protein.

v1.0.4

Fixed

  • Fixed logging levels and verbosity of log messages

v1.0.3

Fixed

  • Fixed bug Eventalign_collapse CLI options

v1.0.2

Added

  • Exposed option to enable/disable anova test
  • Running nanocompore via CLI now disables anova by default
  • SampComp now downsamples to 5000 by default

Fixed

  • Subsampling in whitelist is deterministic (fix for #103)
  • Reworked multiprocessing framework for SampComp (fix for zombie threads, not tested with large datasets)

v1.0.1

Fixed

Added

  • Improved logging

v1.0.0rc3-1

Fixed

  • Fixed bug in CLI entrypoint

v1.0.0rc3

Added

  • Reads simulator now uses variability measured from the data
  • Switched to Poetry
  • Improved error reporting in TxComp

Fixed

  • Fixed multithreading errors
  • Fixed error in SampCompDB.plot_position() (#85)
  • Fixed errors with 0 pvalues (#87 and #90)
  • Fixed error when passing a Whitelist object to SampComp (#91)

v1.0.0rc2

Added

  • Continuous testing with Travis CI
  • Automatic deployment of docs to gh-pages

Fixed

  • Fixed "Not enough p-values" error. Issue #68