Code

pRegion for all#172

Code

Merged

bgruening merged 37 commits intodeeptools:developdeeptools/pyGenomeTracks:developfrom lldelisle:pRegionForAlllldelisle/pyGenomeTracks:pRegionForAllCopy head branch name to clipboardJul 5, 2020

+531-228

Commits

Commits on Jan 9, 2020

• use pRegion for HiC tracks to speed up

  lldelisle

  committed
  404c264

• added a test with a bed with multiple chr

  lldelisle

  committed
  28d5653

• added pybedtools

  lldelisle

  committed
  7e38dfa

• added pRegion everywhere there is an intervaltree

  lldelisle

  committed
  9d7a3a4

Commits on Jan 10, 2020

• remove try/catch but use UCSC format

  lldelisle

  committed
  1cea057

• remove the chr added to the region

  lldelisle

  committed
  34cb06a

Commits on Jan 20, 2020

• use one cool in the test of hic rasterize

  lldelisle

  committed
  3c0a900

• deal with cases where the matrix is empty on the region

  lldelisle

  committed
  3b051fa

Commits on Jan 21, 2020

• change error to warning and trycatch the vmax as percentile

  lldelisle

  committed
  de5b0fd

• linting

  lldelisle

  committed
  329b153

• new test

  lldelisle

  committed
  20c929f

Commits on Jun 3, 2020

• Merge branch 'develop' of https://github.com/deeptools/pyGenomeTracks into pRegionForAll

  lldelisle

  committed
  0a3a3da

• remove ununsed matplotlib

  lldelisle

  committed
  bd88273

• put back HUGE_NUMBER

  lldelisle

  committed
  815c8ea

• update comment

  lldelisle

  committed
  afa1fe2

• forgot a , in merge

  lldelisle

  committed
  1ec106d

• update gtfTrack

  lldelisle

  committed
  ca58b09

• fix issues when plotting matrix on the chr end

  lldelisle

  committed
  8aa4c21

• update output of hic_small_test

  lldelisle

  committed
  836e54d

• add test for bed vs region

  lldelisle

  committed
  16c76b1

• remove y_axis when no data

  lldelisle

  committed
  9e9c062

• adapt pChrnameList to exceptions

  lldelisle

  committed
  3c39a02

• update and add new tests

  lldelisle

  committed
  40bc04b

• remove debug prints

  lldelisle

  committed
  f68a2b7

• require hicmatrix>=13

  lldelisle

  committed
  4f559b7

• update doc

  lldelisle

  committed
  4144cc7

• linting

  lldelisle

  committed
  0823bef

• remove redundant test

  lldelisle

  committed
  2318fa8

• mv self.img=None on top

  lldelisle

  committed
  a140022

• remove useless comments

  lldelisle

  committed
  fbf9eb5

Commits on Jun 4, 2020

• linting

  lldelisle

  committed
  5357f7d

• change pRegion to plot_regions and intersect with all plot_regions except in HiC.

  lldelisle

  committed
  c9a32f7

• update tests/doc to use imbricated bed

  lldelisle

  committed
  96fbd6b

• linting

  lldelisle

  committed
  254c911

• make prettier the coding

  lldelisle

  committed
  e46f72f

• Merge branch 'develop' of https://github.com/deeptools/pyGenomeTracks into pRegionForAll

  lldelisle

  committed
  a68dbbe

Commits on Jul 5, 2020

• Merge branch 'develop' of https://github.com/deeptools/pyGenomeTracks into pRegionForAll

  lldelisle

  committed
  63e103d