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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 and this project adheres to Semantic Versioning.

Unreleased

...

  • ...

[2.3.6] - 2019-06-13

Added

  • Support for custom temporary directory when parallelizing.

Fixed

  • Bug affecting all probability-based metrics that calculated the number of recognition sites sensed in a library instead of the total number of reads in that library.

[2.3.5] - 2019-03-25

Fixed

  • gpseqc_estimate
    • Fixed -l option.

[2.3.4] - 2018-09-05

Fixed

  • gpseqc_estimate
    • Settings confirmation page.
    • Removed NaN when calculating IQR and quartiles. Discarding NaN when asking for outliers with IQR method and lim specified.
    • Colliding temporary files issue using tempfile.TemporaryDirectory().

[2.3.3] - 2018-08-16

Added

  • gpseqc_estimate
    • Additional help page with -H.
    • Added "rescaled" scores output, with scores rescaled based as 2**((score-min(score)/max(score-min(score)))). Only non-outlier scores are considered in the calculation of min/max. Hence, non-outlier scores are in the [1;2] interval, lower outliers in the [0;1) interval, and upper outliers in the (2;Inf] interval.
    • Added parameters to define outliers for rescaling: --score-outliers, --score-outlier-alpha and --score-outlier-lim.

Changed

  • gpseqc_estimate
    • Use only chromosomes present in the input bed files when running chromosome-wide with -G option.
    • Split script help page in -h for attributes and standard help, and -H for more descriptive and readable text.
    • Renamed bed outlier parameters to avoid confusion with new score outliers:
      • --outliers to --bed-outliers
      • --outlier-alpha to --bed-outlier-alpha
      • --outlier-lim to --bed-outlier-lim
    • Renamed second parameter of gpseqc.stats.score_outliers to method (previously stype).

[2.3.2] - 2018-08-16

Fixed

  • gpseqc_estimate
    • Fixed masking with -M, now removing all bins overlapping of even 1 bp with the masked regions.

[2.3.1] - 2018-07-09

Added

  • Option to mask gpseqc_estimate output (-M).

[2.3.0] - 2018-06-26

Added

  • gpseqc_estimate
    • New variability-based estimates, where conditions are combined in the same way as the probability-based ones. The names are the same, with a prefix s.
    • Estimates list and ermetic description in main help page.

[2.2.0] - 2018-06-07

Added

  • gpseqc_estimate
    • Outlier export (only in debug mode).
    • Added alpha/lim outlier options.
    • Forced flushing of temporary files.
    • Fixed sorting issues.
    • Bed file masking at the beginning of the pipeline.

Changed

  • gpseqc_estimate
    • Remove all outliers as default behavior.

[2.1.0] - 2018-06-04

Added

  • Outlier filter to gpseqc_estimate.

[2.0.7] - 2018-05-26

Fixed

  • Axis drop bug in gpseqc_compare.
  • Matplotlib back-end to work when DISPLAY is unavailable.
  • -1 bug when intersecting in gpseqc_estimate.

[2.0.6] - 2018-05-22

Fixed

  • Assert error triggered by Kendall tau weighted when all elements in the ranking have the same weight.

Added

  • Option to allow for custom centrality estimates when comparing rank tables with gpseqc_compare (-C/--custom-estimates).
  • Chromosome size option to gpseqc_estimate when using chromosome wide bins. Using genome size file as in bedtools.

[2.0.5] - 2018-05-21

Fixed

  • Sorting bug in gpseqc_compare.
  • EMD calculation when np.nan values are present, in gpseqc_compare.

[2.0.4] - 2018-05-16

Added

  • gpseqc_compare for ranking comparison.

[2.0.3] - 2018-05-09

Added

  • CMETRICS constant to gpseqc_estimate with lambda functions to calculate centrality metrics.
  • RankTable class to comparison.py.
  • Added timestamp, command line and version tag to gpseqc_estimate settings file for easier bug reporting and debugging.

Fixed

  • -y option now working in gpseqc_estimate.
  • Typo in gpseqc_estimate.

[2.0.2] - 2018-04-24

Fixed

  • Empty bin issue during step 6 of gpseqc_estimate.
  • Division by zero in centrality.py.

[2.0.1] - 2018-04-24

Added

  • Error triggered when empty bed files are provided to gpseqc_estimate.

[2.0.0] - 2018-04-24

Changed

  • Implemented as Python package gpseqc.
  • Rank comparison still available only as legacy version.
  • Documentation moved to GitHub Pages.

[1.2.2] - 2018-04-16

Fixed

  • Settings file output name now includes suffix.

[1.2.1] - 2018-03-27

Fixed

  • Fixed behavior when -i/-e are not used.

Added

  • Version option.

[1.2.0] - 2018-03-23

Added

  • Output directory parameter to comparison script.
  • Option to include/exclude metrics from calculation.

Fixed

  • Comparison script displays error message when bed file is required but not provided.
  • Now allowing to plot when DISPLAY is disconnected.

Changed

  • Fixed order of settings in confirmation message.
  • Added common functions in separate module.

[1.1.0] - 2018-02-13

Added

  • Implemented rank comparison script.

Fixed

  • Not skipping first bed file in settings confirmation page.
  • Added prefix to output settings file.

[1.0.0] - 2018-01-17 - First release.

[Unreleased] https://github.com/ggirelli/gpseq-centrality-estimate
[2.3.6] https://github.com/ggirelli/gpseq-centrality-estimate/releases/tag/v2.3.6
[2.3.5] https://github.com/ggirelli/gpseq-centrality-estimate/releases/tag/v2.3.5
[2.3.4] https://github.com/ggirelli/gpseq-centrality-estimate/releases/tag/v2.3.4
[2.3.3] https://github.com/ggirelli/gpseq-centrality-estimate/releases/tag/v2.3.3
[2.3.2] https://github.com/ggirelli/gpseq-centrality-estimate/releases/tag/v2.3.2
[2.3.1] https://github.com/ggirelli/gpseq-centrality-estimate/releases/tag/v2.3.1
[2.3.0] https://github.com/ggirelli/gpseq-centrality-estimate/releases/tag/v2.3.0
[2.2.0] https://github.com/ggirelli/gpseq-centrality-estimate/releases/tag/v2.2.0
[2.1.0] https://github.com/ggirelli/gpseq-centrality-estimate/releases/tag/v2.1.0
[2.0.7] https://github.com/ggirelli/gpseq-centrality-estimate/releases/tag/v2.0.7
[2.0.6] https://github.com/ggirelli/gpseq-centrality-estimate/releases/tag/v2.0.6
[2.0.5] https://github.com/ggirelli/gpseq-centrality-estimate/releases/tag/v2.0.5
[2.0.4] https://github.com/ggirelli/gpseq-centrality-estimate/releases/tag/v2.0.4
[2.0.3] https://github.com/ggirelli/gpseq-centrality-estimate/releases/tag/v2.0.3
[2.0.2] https://github.com/ggirelli/gpseq-centrality-estimate/releases/tag/v2.0.2
[2.0.1] https://github.com/ggirelli/gpseq-centrality-estimate/releases/tag/v2.0.1
[2.0.0] https://github.com/ggirelli/gpseq-centrality-estimate/releases/tag/v2.0.0
[1.2.2] https://github.com/ggirelli/gpseq-centrality-estimate/releases/tag/v1.2.2
[1.2.1] https://github.com/ggirelli/gpseq-centrality-estimate/releases/tag/v1.2.1
[1.2.0] https://github.com/ggirelli/gpseq-centrality-estimate/releases/tag/v1.2.0
[1.1.0] https://github.com/ggirelli/gpseq-centrality-estimate/releases/tag/v1.1.0
[1.0.0] https://github.com/ggirelli/gpseq-centrality-estimate/releases/tag/v1.0.0