Code

Chic hdf#729

Code

Merged

joachimwolff merged 54 commits intodevelopdeeptools/HiCExplorer:developfrom chicHDFdeeptools/HiCExplorer:chicHDFCopy head branch name to clipboardJun 29, 2021

+3,565-10,429

Commits

Commits on Oct 22, 2020

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

  joachimwolff

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  9e49387

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Commits on Jan 4, 2021

• Merge branch 'develop' into chicHDF

  joachimwolff

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  0e8f470

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• continue implementing hdf for chic

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  7b9923a

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Commits on Jan 5, 2021

• target and signficant data write to hdf5

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Commits on Jan 7, 2021

• significant hdf5 files

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  5dcfda1

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• target file as hdf5 for chicSignificantInteractions

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  6d7c57e

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Commits on Jan 8, 2021

• write correct file for targets in dual mode

  joachimwolff

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  b3cbfa5

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• Implementing read and processing of hdf stored data

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Commits on Jan 9, 2021

• aggregate hdf5 file

  joachimwolff

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  6d552e8

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• out commenting old write method

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  e2d2a15

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• start to implement hdf support

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  4daf094

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• Increased version number to 3.7dev

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  3e36f5e

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Commits on Jan 10, 2021

• continue work

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Commits on Jan 12, 2021

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

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  0ddd124

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• correct hdf output

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  7f4e55d

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• Fix import of hdf from significant

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  f0182aa

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• Add try/except

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Commits on Jan 13, 2021

• continue write of differential hdf

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  506a28e

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• fix write out of differential results to hdf

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  094198e

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Commits on Jan 14, 2021

• start to implement hdf support

  joachimwolff

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  bd27765

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Commits on Jan 19, 2021

• continue to implement hdf support for chic modules

  joachimwolff

  committed
  ae8ca0e

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Commits on Jan 20, 2021

• read of interaction data for plotting successful

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  06898e0

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Commits on Jan 21, 2021

• continue development of hdf support

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Commits on Jan 22, 2021

• output to tar.gz file

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Commits on Jan 25, 2021

• plotting with interaction, significant and differntial works in principal

  joachimwolff

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  5dc62c6

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• differential fix

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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

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Commits on Jan 28, 2021

• Export of data to text files in gzip files continued

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• liniting

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  870568f

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Commits on Mar 1, 2021

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

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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

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  5633f2f

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

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Commits on Mar 3, 2021

• liniting

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  32eb2d7

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Commits on Apr 24, 2021

• chicSiginficant bug fix

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  abfa8c8

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• add function to export only one gene

  joachimwolff

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  a3ac3f0

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

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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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  341a89d

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Commits on May 5, 2021

• Fixing wrong handling of the aggregation

  joachimwolff

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  24e14ce

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• implementing more metadata usage

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Commits on May 6, 2021

• bug fixes and linting

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  a4dcb9b

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• Remove debug messages

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  d7a75b8

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Commits on Jun 22, 2021

• Merge branch 'develop' into chicHDF

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Commits on Jun 23, 2021

• Removing old test data of chicViewpoint

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  2d7c134

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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

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Commits on Jun 24, 2021

• Exchanging test data for chic-* modules

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  9b272d8

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

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Commits on Jun 28, 2021

• Add new test data and test cases for chicExportData

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  e5d46a6

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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

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  f611e3b

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• Fixing doc test

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• Fixing doc test

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  0237414

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• Update test case number

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Commits on Jun 29, 2021

• Adding test data

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  e222394

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• Updating tutorial to new hdf5 based file format

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