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Develop#742

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joachimwolff merged 171 commits intomasterdeeptools/HiCExplorer:masterfrom developdeeptools/HiCExplorer:developCopy head branch name to clipboardJul 27, 2021

+36,059-24,833

Commits

Commits on Oct 22, 2020

• First steps for a hdf5 file support for the chic* modules

  joachimwolff

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Commits on Dec 3, 2020

• impovment in hicAggregate

  

  Leily Rabbani

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Commits on Dec 4, 2020

• improvement in structure/saving outputs and clustering. mode intra-chr is still not working

  

  Leily Rabbani

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Commits on Dec 8, 2020

• add --noNorm in hicCompareMatrices

  lldelisle

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Commits on Dec 14, 2020

• fixed --perChr

  

  Leily Rabbani

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Commits on Dec 15, 2020

• wrapped up the changes on perChr

  

  Leily Rabbani

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• Fix #635 (#637)

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  LeilyR

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• lint

  

  Leily Rabbani

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• more lint

  

  Leily Rabbani

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• fixed a bug. plot_diagnostic_heatmaps is not working

  

  Leily Rabbani

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• lint

  

  Leily Rabbani

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• heatmap fix

  

  Leily Rabbani

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Commits on Dec 17, 2020

• added an option to allow for keeping or removing the outliers. Added a second option to allow for adjusting the deviation

  

  Leily Rabbani

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• lint

  

  Leily Rabbani

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Commits on Dec 22, 2020

• added keep_outlier and fixed the failed tests

  

  Leily Rabbani

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• updated the help message for keep_outlier

  

  Leily Rabbani

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Commits on Dec 23, 2020

• Merge pull request #643 from deeptools/aggregate_fix

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Commits on Jan 4, 2021

• Merge branch 'develop' into chicHDF

  joachimwolff

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• continue implementing hdf for chic

  joachimwolff

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Commits on Jan 5, 2021

• target and signficant data write to hdf5

  joachimwolff

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Commits on Jan 7, 2021

• significant hdf5 files

  joachimwolff

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• target file as hdf5 for chicSignificantInteractions

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Commits on Jan 8, 2021

• write correct file for targets in dual mode

  joachimwolff

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• Implementing read and processing of hdf stored data

  joachimwolff

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Commits on Jan 9, 2021

• aggregate hdf5 file

  joachimwolff

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• out commenting old write method

  joachimwolff

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  e2d2a15

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• start to implement hdf support

  joachimwolff

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• Increased version number to 3.7dev

  joachimwolff

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Commits on Jan 10, 2021

• continue work

  joachimwolff

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Commits on Jan 12, 2021

• Fix non unique name of genes and doubled gene names from different matrices

  joachimwolff

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• correct hdf output

  joachimwolff

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• Fix import of hdf from significant

  joachimwolff

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• Add try/except

  joachimwolff

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Commits on Jan 13, 2021

• continue write of differential hdf

  joachimwolff

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• fix write out of differential results to hdf

  joachimwolff

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Commits on Jan 14, 2021

• start to implement hdf support

  joachimwolff

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Commits on Jan 18, 2021

• Extend help text and potential bug fix for #655

  joachimwolff

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Commits on Jan 19, 2021

• continue to implement hdf support for chic modules

  joachimwolff

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Commits on Jan 20, 2021

• read of interaction data for plotting successful

  joachimwolff

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Commits on Jan 21, 2021

• continue development of hdf support

  joachimwolff

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Commits on Jan 22, 2021

• output to tar.gz file

  joachimwolff

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Commits on Jan 25, 2021

• plotting with interaction, significant and differntial works in principal

  joachimwolff

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• differential fix

  joachimwolff

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Commits on Jan 27, 2021

• Adding export function for hdf data, fixing chicSignificant to operate also without loosepvalue and xfoldbackground. make plot options allgenes and single available

  joachimwolff

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Commits on Jan 28, 2021

• Export of data to text files in gzip files continued

  joachimwolff

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• liniting

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Commits on Feb 19, 2021

• add a test

  lldelisle

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Commits on Mar 1, 2021

• Add bigwig support, however, it is crashing to write it to a tar.gz

  joachimwolff

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Commits on Mar 2, 2021

• writing files to tmp than packing this as tar and delete the temp. Background values work too

  joachimwolff

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• Adding option to extract relative-interactions, p-value, x-fold or raw for bigwig file

  joachimwolff

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Commits on Mar 3, 2021

• liniting

  joachimwolff

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• Merge pull request #645 from lldelisle/noNormInOp

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• Implemnting the support for multiple restriction sites. #659

  joachimwolff

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• Extending test case hicFindRestSite

  joachimwolff

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• Adding test data for hicFindRestSite

  joachimwolff

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• Implementing for hicBuildMatrix the restriction cut file limitations to the region which is defined. #646

  joachimwolff

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Commits on Mar 12, 2021

• add hicTADClassifier

  AlbertLidel

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• update requirements

  AlbertLidel

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• fix roc output and update docs

  AlbertLidel

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Commits on Mar 15, 2021

• Renamed hicTrainClassifier to hicTrainTADClassifier, added bin files; adding these to setup.py

  joachimwolff

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• Merge branch 'develop' into albert_TAD

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Commits on Mar 18, 2021

• add missing files

  AlbertLidel

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• rebuild gitignore

  AlbertLidel

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• move lib files

  AlbertLidel

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• fix linting

  AlbertLidel

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• fix docs

  AlbertLidel

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• fix linting 2

  AlbertLidel

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• fix linting 3

  AlbertLidel

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  2b03afa

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• Merge pull request #692 from AlbertLidel/albert_TAD

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  joachimwolff

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• Bringing alberts tad classification into shape

  joachimwolff

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• Merge branch 'albert_TAD' of github.com:deeptools/HiCExplorer into albert_TAD

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Commits on Mar 22, 2021

• Bug fixing and performance improvements by loading only one chromosome instead of all, limiting the distances to compute obs_exp matrices

  joachimwolff

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• Predicting per chromosome implemented.

  joachimwolff

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• Fixing chr-prefix issue

  joachimwolff

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Commits on Mar 23, 2021

• hicFindTADs: change computation with cool files per chromosome and not full matrix

  joachimwolff

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Commits on Mar 24, 2021

• Support for cool files and chromosomes, fixing bugs, adding features. The idea seems to work now

  joachimwolff

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• bug fixing hicFindTADs

  joachimwolff

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Commits on Mar 31, 2021

• adjust docstring of compute_distance_mean

  lldelisle

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• allowToPlotDistVsCounts on specific regions

  lldelisle

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• use it in main

  lldelisle

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  19bae63

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• fix typo

  lldelisle

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• check there is at least one region

  lldelisle

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• add r for the tad_line

  lldelisle

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• use triple quote

  lldelisle

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• fix doctest

  lldelisle

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• remove doctest waiting for hicmatrix release

  lldelisle

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• forgot blank line

  lldelisle

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Commits on Apr 8, 2021

• commiting old changes

  joachimwolff

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Commits on Apr 17, 2021

• hic to cool file only, increase version number, debug info activated

  joachimwolff

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Commits on Apr 24, 2021

• chicSiginficant bug fix

  joachimwolff

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• add function to export only one gene

  joachimwolff

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• Add support for single bed file, bug fixes for support to export per gene name

  joachimwolff

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Commits on Apr 26, 2021

• Implementing no tar.gz for chicExportDate in case a single gene is written out

  joachimwolff

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Commits on May 5, 2021

• Fixing wrong handling of the aggregation

  joachimwolff

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• implementing more metadata usage

  joachimwolff

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Commits on May 6, 2021

• bug fixes and linting

  joachimwolff

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• Remove debug messages

  joachimwolff

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Commits on May 11, 2021

• Fixing a bug to remove multiple chromosomes at once

  joachimwolff

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Commits on Jun 1, 2021

• add new columns to output text of hicPlotDistVsCounts

  lldelisle

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• fix/add tests for hicPlotDistvsCounts

  lldelisle

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• remove Bio.Alphabet

  lldelisle

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Commits on Jun 7, 2021

• fix matplotlib name in pip dependencies

  lldelisle

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Commits on Jun 22, 2021

• Adding test data for hicValidateLocations

  joachimwolff

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• Validate locations for 2D data stored in cool files. Adding test case

  joachimwolff

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• Add test data for 2D text hicConvertFormat

  joachimwolff

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• Add 2d text import and hicpro export; add test cases

  joachimwolff

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• Merge branch 'develop' into chicHDF

  joachimwolff

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• Output Ranksum statistics

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Commits on Jun 23, 2021

• fix a bug that prevented stats to be printed

  dawe

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• Removing old test data of chicViewpoint

  joachimwolff

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• Bug fixing chicViewpoint: closes a bug causing a crash if the number of threads is greater the number of processed elements

  joachimwolff

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Commits on Jun 24, 2021

• Exchanging test data for chic-* modules

  joachimwolff

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• Replace test cases for chic-* modules, linting and minor bug fixes. Make readBead function to accept also space seperated files

  joachimwolff

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Commits on Jun 28, 2021

• Add new test data and test cases for chicExportData

  joachimwolff

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• liniting

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  03c25b2

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• liniting and bug fixes: some typos in the test cases, updating test data and a bug fix in hicBuildMatrix for a case where the region is not defined

  joachimwolff

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• Fixing doc test

  joachimwolff

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• Fixing doc test

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• Update test case number

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Commits on Jun 29, 2021

• Adding test data

  joachimwolff

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• Updating tutorial to new hdf5 based file format

  joachimwolff

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• Merge pull request #729 from deeptools/chicHDF

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Commits on Jun 30, 2021

• documentation

  joachimwolff

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• Merge branch 'chicHDF' into develop

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• Merge branch 'develop' into plotDistVsCounts

  joachimwolff

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• Merge pull request #696 from lldelisle/plotDistVsCounts

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• Merge pull request #718 from lldelisle/biopython

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• Merge pull request #728 from dawe/master

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• Updating test cases

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Commits on Jul 1, 2021

• Fixing a bug in hicDifferentialTAD computation, the first boundary of the second, third etc, chromosome was ignored and the parallel computation was missing elements at the end

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Commits on Jul 7, 2021

• Exchanging test data for hicDifferentialTest

  joachimwolff

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• Fixing bugs in hicDifferentialTADs; issues #725 and maybe #685

  joachimwolff

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• Adding test data for hicAdjustData

  joachimwolff

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• Implementing a feature to remove the inter or intra chromosomal regions in a matrix. Close #704

  joachimwolff

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Commits on Jul 8, 2021

• Implementing new way to control the protein loop overlap for hicHyperoptDetectLoops and improve docs of hicValidateLocations. Feature request #723

  joachimwolff

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• Implementing new way to control the protein loop overlap for hicHyperoptDetectLoopsHiCCUPS; Feature request #723

  joachimwolff

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• Merge pull request #731 from deeptools/interintraremoval

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• Merge branch 'develop' into multiRestrictionSequence

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• First implementation of inter and intra tad computations, feature request #404

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Commits on Jul 9, 2021

• Adding test data for hicInterIntraTAD, fixing density calculation, adding option to plot ratio. Adding test case for hicInterIntraTAD. #404

  joachimwolff

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• adding docs for hicInterIntraTAD

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• Fixing merge

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Commits on Jul 10, 2021

• Bug fix for hicPCA with new test data and test case. Fix #719 #716 #710 #655

  joachimwolff

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• Merge pull request #732 from deeptools/multiRestrictionSequence

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• Merge pull request #733 from deeptools/interintratadratio

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Commits on Jul 12, 2021

• Merge pull request #735 from deeptools/pca_fixes

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• Implementing a feature to return random principal components. User request #669

  joachimwolff

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• Adding a feature to plot tads with hicPlotMatrix

  joachimwolff

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• Implementing a feature request for hicPlotMatrix for loops that are wider than one bin. Issue #640

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• Merge pull request #736 from deeptools/pca_newfeature

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• Typo

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Commits on Jul 13, 2021

• Merge pull request #737 from deeptools/hicPlotMatrix_newfeatures

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• Implementing plotNumbers feature which was outcommented for reasons. Implemented feature improvement request #585

  joachimwolff

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• Adding pdf fonttype 42 for better Adobe Illustrator support. #585

  joachimwolff

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Commits on Jul 14, 2021

• Fixing a bug in hicCorrect for KR and cool files. #724

  joachimwolff

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Commits on Jul 15, 2021

• Implementing the copy of the genome assembly information. #657

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Commits on Jul 19, 2021

• Fixing #720. Multiple different restriction sequences with the same dangling ends led to a crash.

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• Fixing issue #618. masking of bins should be in the if-condition for --ignoringMaskedBins not in front of it. This way the matrix size is kept.

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• merge develop branch to albert tad branch

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Commits on Jul 21, 2021

• Fixing bugs in tad prediction, get the test cases running

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Commits on Jul 26, 2021

• Adding default classifier, adding test case and linting

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• Changing --removeSelfLigation to --keepSelfLigation to make the removal the default case

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• Restoring current master branch version

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• Updating and bug fixing test cases. Linting.

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• Linting

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• fixing test cases

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• Adding test data

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• Azure pipeline reconfigure

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• Merge pull request #741 from deeptools/albert_TAD

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Commits on Jul 27, 2021

• Adding the changes to News.rst, adding version number to chic hdf files, liniting

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• Fixing the docs

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