Manuscript version

v2.3.6.post1

Fixed bug and released v2.3.6

[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.