Develop

[joachimwolff]

• Flake8 passes (flake8 . --exclude=.venv,.build,planemo_test_env,build --ignore=E501,F403,E402,F999,F405,E712)
• Local tests pass (py.test hicexplorer --doctest-modules)

• Major update for hicDetectLoops: Results are now closer to HiCCUPS, it is faster and needs less memory.
• hicHyperoptDetectLoops: New tool to compute the best parameter setting if the number of expected loops is given and a protein boundary file (e.g. CTCF on mammals) is provided
• hicHyperoptDetectLoopsHiCCUPS: New tool to compute the best parameter setting for Juicers HiCCUPS. HiCCUPS and all its dependencies are not part of HiCExplorer and must be provided by the user. Number of expected loops and a protein boundary file (e.g. CTCF on mammals) must be provided.
• hicMergeDomains: New tool to compute a merge of TADs computed on different resolutions. Moreover it provides a cleaning of the boundaries with the help of a protein peak file, and the hierarchical dependencies of TADs can be plotted. This tool is the result of the Bachelor thesis from Sarah Domogalla (@SarahMaria27). Thanks for your contribution!
• hicDifferentialTAD: New tool to compute differential TADs between two samples
• Bug fix for hicFindTADs: The format of the intermediate z-score matrices are now depending on the format of the input Hi-C matrix
• Bug fix for chic*-modules: Fixate range is now correct applied.
• Bug fix for hicPlotMatrix:
  • multiple bigwig tracks in the vertical setting are now supported
  • correct plot of bigwig if the given matrix does not start at the beginning of the chromosome
  • new parameters 'increaseFigureWidth' and 'increaseFigureHeight' to add more space to the plot if multiple bigwigs are plotted. Adjust this parameter to correct the plot of the heatmap which may be not quadratic anymore.
  • restriction of the loop regions to the user given range. This effects especially SVGs that will now contain less objects as before.
• New feature for hicBuildMatrix:
  • multiple restriction cut sequences, dangling ends and restriction cut sites files are now supported
  • restriction cut sequences, dangling ends and restriction cut sites files are now mandatory parameters. This is now enforced to guarantee a correct detection of self ligations and self circles
• hicPrepareQCreport: New support for multiple dangling ends
• hicQuickQC: restriction cut sequences, dangling ends and restriction cut sites files are now mandatory parameters
• hicFindRestSite: gz support for fasta file
• hicAggregate: interactions between two bed files by comparing every row in the first bed file with its corresponding row in the second file. (issue hicAggregateContacts option request #390)
• hicAdjustMatrix: fix hicAdjustMatrix new mode: keepByMasking #341, 454
  • fixed --action remove: it actually remove the part from the matrix previously was masking it
  • the case where the end of the chromosome need to be removed.
• New Azure testing for the general test cases, the trivial ones run on travis. Makes it faster, maybe around half an hour to 45 mins instead of multiple hours of CI