Merge pull request deeptools#1049 from deeptools/develop

Develop- for the 3.5.1 release

release 3.5.0 (deeptools#990)

* Fixes for 3.4.2

* disable azure on OSX

* Closes deeptools#945

* computeMatricOperation  dataRange (deeptools#951)

* Added dataRange to computeMatricOperation to return min,max,median and 10th and 90th percentile.

* fixed pep8

* more pep8 fix

* fixed test_sieve of azure tests

* one more fix for test_sieve

* imported pysam to test_readFiltering.py

* updated hash values for test_sieve

* fixed galaxy computeMatrixOperation.xml

* More fixes for galaxy wrapper

* fixed a little typo in bamCompare (deeptools#967)

* save the output matrix of the plotheatmap in a format to be compatible with running plotheatmap on it again (deeptools#968)

* Plot profile color map (deeptools#971)

* Now colors can be set by user for any heatmap in plotProfile. A bug in tick index for plotting heatmap is also fixed.

* added a small description

* pep8 fix

* added sortUsingSamples and clusterUsingSamples to the galaxy wrapper

* [WIP] added auto to plotheatmap deeptools#908 (deeptools#982)

* added auto to plotheatmap

* fixed lint, added warning message, updated the help for zmin, zmax

* galaxy test plotPCA

* lower down the delat for potPCA galaxy test

* fix deeptools#969 (deeptools#970)

* fix deeptools#969

* PEP8

* updated changes.txt

* fixed a little bug in parseCommon.py which caused flake8 failure.

* [WIP] added auto to plotheatmap deeptools#908 (deeptools#982)

* added auto to plotheatmap

* fixed lint, added warning message, updated the help for zmin, zmax

* galaxy test plotPCA

* lower down the delat for potPCA galaxy test

* updated version and changes

* removed alpha from plotPCA test

* removed compare="sim_size"


* fixed plotHeatmap.xml by removing size from the the params and adding anitizer for the 2 new params.

* upated change.txt

* updated the doc html

Co-authored-by: Devon Ryan <[email protected]>

Merge pull request deeptools#943 from deeptools/develop

changed iteritmes() in estimateEscaleFactor to its python3 compatible items()

disable azure on OSX

Merge branch 'master' into develop

Merge branch 'master' into develop

merge in master so this can get released

bump version number

Develop (deeptools#827)

* Merged into the wrong branch without noticing :( (deeptools#814)

* use better conda link (deeptools#799)

* Estimated filtering fix (deeptools#813)

* oops

* fix testing and set a max number of filtered reads

* apparently a bunch of things were getting skipped

* fix wrappers

* update computeMatrix wrapper

* Decrease memory needs (deeptools#817)

* Use an iterator to not blow memory up

* Update a bit more

* The GC bias stuff is all deprecated, I'm not fixing that old code

* Cache resulting counts rather than just decreasing the bin size (deeptools#818)

* Cache resulting counts rather than just decreasing the bin size

* sanity check

* Implement deeptools#815

* [skip ci] update change log

* Implement deeptools#816 (deeptools#825)

* Implement deeptools#816

* expose option

* Add a test using pseudocounts and skipZeroOverZero

* syntax

* Fix tests

* Make --skipZeroOverZero a galaxy macro and add to bigwigCompare

* [ci skip] a bit of formatting

* Fix deeptools#822 (deeptools#826)