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@joachimwolff joachimwolff released this 23 Nov 13:24
2.2-beta
2083edd

The beta version of release 2.2 contains:

  • replaced hicExport by hicConvertFormat and hicAdjustMatrix
  • extended functionality for hicConvertFormat:
    • read support for homer, hicpro, cool, h5
    • write support for h5, homer, cool
    • convert hic to cool
    • creation of mcool matrices
  • hicAdjustMatrix:
    • remove, keep or mask specified regions from a file, or chromosomes
  • hicNormalize:
    • normalize matrices to 0 - 1 range or to the read coverage of the lowest given
  • hicBuildMatrix:
    • support for build mcool
  • restructuring the central lass HiCMatrix to object oriented model and moved to its own library: deeptools/HiCMatrix.
    • Extended read / write support for file formats
    • better (faster, less memory) support for cool format
    • remove of old, unused code
    • restrict support to h5 and cool matrices, except hicConvertFormat
  • hicPlotTADs: removed code and calls pyGenomeTracks
  • hicAverageRegions: Sum up in a given range around defined reference points. Useful to detect changes in TAD structures between different samples.
  • hicPlotAverageRegions: Plots such a average region
  • hicTransform: Restructuring the source code, remove of option 'all' because it was generating confusion. Adding option 'exp_obs', exp_obs_norm and exp_obs_lieberman. These three different options use different expectation matrix computations.
  • hicPCA:
    • Adding --norm option to compute the expected matrix in the way HOMER is doing it. Useful for drosophila genomes
    • Adding option to write out the intermediate matrices 'obs_exp' and 'pearson' which are necessary in the computation of the PCA
  • hicPlotMatrix:
    • Add option to clip bigwig values
    • Add option to scale bigwig values
  • Removed hicLog2Ration, functionality is covered by hicCompareMatrices
  • Extending test cases to cover more source code and be hopefully more stable.
  • Many small and big bugfixes
  • Updating minimum requirements to:
    • numpy >= 1.15
    • scipy >= 1.1.
    • matplotlib >= 2.2
    • pysam >= 0.14
    • intervaltree == 2.1.
    • biopython >= 1.72
    • tables >= 3.4
    • pandas >= 0.23
    • pyBigWig >= 0.3
    • six >= 1.11
    • future >= 0.17
    • cooler >= 0.7.11
    • jinja2 >= 2.10
    • unidecode >= 1.0
    • hicmatrix >= 5
    • pygenometracks >= 2.1
    • scikit-learn >= 0.20
    • psutil >= 5.4.8
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