TODO

[LeilyR]

• bug in writing a cool matrix but giving it the h5 file ending. hicFindTADs cannot recompute from cooler matrix #377, Recalculating TADs using sep-score-prefix fails #537

• plotting modules doente work from inside a Jupiter notebook. hicexplorer3.4.1 plotting modules cannot be used in python notebooks #536

• @joachimwolff hicDetectLoops dataset error #515 , hicDetectLoops normalisation method #433, hicPlotMatrix cannot be --log transformed #359

• hicAdjustMatrix: remove, mask & keepByMasking. hicAdjustMatrix-remove #454, hicAdjustMatrix new mode: keepByMasking #341

• Saving asymmetric matrices with hicMatrix.save(...) does not work when pSymmetric is set to False. Cannot save asymmetric matrices #467

• hicPlotMatrix --bigwig not at correct position. hicPlotMatrix --bigwig not at correct position #462

• hicPltMatrix doesn't work with cool but h5. hicPlotMatrix has shown error when I took input in .cool format. It works when I take input in .h5 format. #449

• plotTad problem (PGT). hicPlotMatrix has shown error when I took input in .cool format. It works when I take input in .h5 format. #449, boundaries_file #500

• Add a function to check the chromosomes availability for read counting hicBuildMatrix sensitive to input fasta sequence when used with fragment-sized bins #452

• chicViewPoint chicViewpoint #447

• hicAdjustMatrix is removing the weights h5 to cool to cooltools compartments calling - KeyError: 'ignore_diags' #437

• Calculating intra/inter-TAD interactions Calculating intra/inter-TAD interactions #404

• hicAggregateContacts option hicAggregateContacts option request #390

• scaffold name issue Read order error (scaffold name issue) #387

• hicAverageRegions feature hicAverageRegions feature request #333

• z-score in hicFindTADs Suggestion - Zscore transformation a la hicFindTADs #316

• create multiple matrices by reading a use-specified tag from bam improvements for hicEx #278

• hicAggregateContacts all chromosomes at once hicAggregateContacts all chromosomes at once #275

• hic differential analysis hic differential analysis #108