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.

[0.3.8]

Fixed

missing data_range specification in structural_similarity call

[0.3.7]

Removed

Info about chess filter in the cli help.

Changed

chess pairs now produces 0-based ranges.

[0.3.6]

Fixed

All NaN results in chess sim runs on cooler files, fixed through fanc 0.9.9.
Cooler file loading time via fanc, significant speed up in fanc 0.9.8

Changed

Switch to matplotlib 'pdf' backend

[0.3.5]

Added

Raise error if too small (<20 bins) regions are used in chess sim before running comparisons.

[0.3.4]

Fixed

"ValueError: Image must contain only positive values" in chess extract

[0.3.3]

Added

Explicit error for zero valid pairs in the pairs bed input for chess sim

[0.3.2]

Added

Do output directory checks in chess extract and chess crosscorrelate

Removed

chess filter

[0.3.1]

Added

Check whether output directories exist before running any computations.
Allow paths to output files without basenames.

[0.3.0]

Added

--window-size, --sigma-spatial, --size-medianfilter and --closing-square optional parameters for more control in the feature extraction.
Accept data in FANC, Juicer and Cooler formats (.hic, .cool, .mcool)
Raise a warning message if the pairs file contains chromosomes that are not specified in the provided contact data.

Fixed

chess pairs: Fix error on empty lines in chromosome sizes file.
chess pairs: Catch OSError raised by pybedtools when the provided path is not recognized as a UCSC genome id.

[0.2.0]

Added

chess extract: Extract specific regions that are significantly different
chess crosscorrelate: Get structural clusters from the extracted submatrices