[0.0.9]

Fixed

• Wrong variable name causing no chromosomes to be retained in chromosome info table.

[0.0.8]

Added

• Added assertion for correct chromosome start position when using --cinfo-path.
• Options for stricter chromosome matching (discards patches).

Fixed

• Enforced integer bed coordinates when using --bin-bed.
• Using specified chromosome number and heterosome names when binning.

[0.0.7]

Changed

• If duplicated regions are found in input bed file, a warning is triggered and the minimum score is used.

Fixed

• Bug in binning when --site-domain universe option is used.
• Now supporting correct naming of bins where size is not a multiple of 10.

[0.0.6]

Added

• --chrom-tag option, to define the number of chromosomes and heterosome names.

Changed

• Using --chrom-tag to select chromosomes from retrieved/read chromosome information.

Fixed

• Now retrieving correct chromosome size information from UCSC, if not provided.
• All bins are now retained in the output, even if no sites/reads are present or the estimated centrality is NaN.

[0.0.5]

Added

• --bin-bed option to focus calculation on regions of interest (e.g., FISH probes).
• Now checking for mask bed consistency.
• --version option for easier version tracking.
• --debug-info option for easier debugging.

Changed

• Now masking before binning (on dcasted input bed data), but after the normalization factors are calculated.

[0.0.4]

Added

• Additional merged rds output.

Fixed

• Solved score masking crashes due to missing argument passing.

[0.0.3]

Changed

• Now using exid from input metadata and running one experiment at a time.
• The default --bin-tags parameter now include 1e6:1e5,1e5:1e4.

[0.0.2]

Added

• Assert for fpath column in input metadata file.
• Assert for at least 2 bed files in input.
• The input metadata table is now automatically copied to the output folder.
• Help page description.
• Full detail help apge with --more-help.

Changed

• The default --bin-tags parameter now include only 1e6:1e5,1e5.
• It is now possible to skip input bed outlier removal by using --bed-outlier-tag "".
• It is now possible to skip score rescaling by using --score-outlier-tag "".

Fixed

• Centrality estimation is now using the proper ratio of condition pairs.
• Using specified score outlier tag for rescaling purposes, previously using bed outlier tag due to a bug.

[0.0.1] First release