Summer 2021 release

• A new TAD prediction method: hicTADClassifier and a method to train own classifiers hicTrainTADClassifier. Thanks @AlbertLidel for the design and implementation.
• New file formats for capture Hi-C modules. chicViewpoint, chicSignificantInteractions, chicAggregateStatistic and chicDifferentialTest use now HDF5 based files. A new export script chicExportData is provided to retrieve text files from these HDF5 files.
• Implementing a few feature requests:
  • hicPlotMatrix: TADs can be visualized with hicPlotMatrix
  • hicAdjustMatrix is able to remove intra- or inter-chromosomal contacts (#664, #704)
  • hicValidateLocations: An option to validate TADs and to use additional data stored in cool matrices
  • hicPCA: Adding a function to select which eigenvector should be used for the output (#669)
  • hicConvertFormat: Adding the function to export hicpro file format and to import 2D-text files.
  • hicFindRestSites: Support of multiple restriction cut sequences (#659)
  • hicPlotMatrix: Option for loop locations spanning more than one bin to define if the start, center or end should be used for plotting (#640)
  • hicInterIntraTAD: A new script to compute the ratio of inter and intra TAD. (#404)
  • hicAggregateContacts: Option to consider the strand orientation (#633)
  • hicAverageRegions: Option to consider the strand orientation (#633)
  • hicCompareMatrices: An option to not normalize the matrices before the computation. (#677, #645) Thanks @lldelisle
  • hicDifferentialTAD: Adding rank sum statistics to the output (#728, #727). Thanks @dawe
  • hicPlotDistVsCounts: Adding a function to plot the counts vs distance in TAD regions. (#696) Thanks @lldelisle
• Bug fixes:
  • hicCorrectMatrix: A bug that lead to wrong correction factors for the KR correction for cool files (#724)
  • hicDifferentialTAD: Solved multicore issue related to skipping data at the start and end of chromosomes (#725, #685)
  • hicHyperoptDetectLoops: Added an option to set if the chr prefix should be added or removed (#723)
  • hicPCA: Solving an issue if the region defined by the gene track is larger the region stored in the interaction matrix (#655, #710, #716, #719)
  • hicPCA: Fixing a bug where the masking of bins was automatically applied which lead to differing matrix dimensions for the e.g. the Pearson correlation matrices (#618)
  • hicBuildMatrix: Solving a bug if multiple restriction cut sites have the same dangling ends (#720)
  • hicBuildMatrix: Solving a bug that the parameter --removeSelfLigations was always set to true. Changed parameter name to --keepSelfLigations to keep the functionality. If the parameter is not set, the self ligations are removed.
  • hicBuildMatrix: If a region is specified, only the restrictionCutSite file information for that region is loaded to save memory (#646)
  • hicConvertFormat: Fixing a bug to copy the genome annotation information in the case of a cool to cool file conversion (#657)
  • hicCorrelate: Correcting the range of colors for the heatmap (#585)
  • hicCompartmentalization: Fixed index bug (#635, #637) Thanks @LeilyR
• Updating hicBuildMatrix to be able to work with biopython versions > 1.77. Thanks @lldelisle (#691)