* copy changes from bgruening

* this file should not be here since years (#845)

* Develop (#827)

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

* use better conda link (#799)

* Estimated filtering fix (#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 (#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 (#818)

* Cache resulting counts rather than just decreasing the bin size

* sanity check

* Implement #815

* [skip ci] update change log

* Implement #816 (#825)

* Implement #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 #822 (#826)

* fixes linting issues (#837)

* this file should not be here since years

* Add Arabidopsis TAIR10 (A_thaliana_Jun_2009) (#853)

Using output from:
faCount A_thaliana_Jun_2009.fa 
#seq	len	A	C	G	T	N	cpg
Chr1	30427671	9709674	5435374	5421151	9697113	164359	697370
Chr2	19698289	6315641	3542973	3520766	6316348	2561	457572
Chr3	23459830	7484757	4258333	4262704	7448059	5977	559031
Chr4	18585056	5940546	3371349	3356091	5914038	3032	439585
Chr5	26975502	8621974	4832253	4858759	8652238	10278	630299
ChrC	154478	48546	28496	27570	49866	0	4639
ChrM	366924	102464	82661	81609	100190	0	13697
total	119667750	38223602	21551439	21528650	38177852	186207	2802193
hpc $ python
Python 2.7.11 (default, Jul 25 2019, 12:10:26) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-28)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> 119667750-186207
119481543

* Fix python version in Azure tests  (#860)

* Develop (#827)

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

* use better conda link (#799)

* Estimated filtering fix (#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 (#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 (#818)

* Cache resulting counts rather than just decreasing the bin size

* sanity check

* Implement #815

* [skip ci] update change log

* Implement #816 (#825)

* Implement #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 #822 (#826)

* fixes linting issues (#837)

* Delete #test.bg# (#859)

File is removed upon clean.

* Fix python version

* Update azure-pipelines.yml

* fixed typo (#864)

* Develop (#827)

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

* use better conda link (#799)

* Estimated filtering fix (#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 (#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 (#818)

* Cache resulting counts rather than just decreasing the bin size

* sanity check

* Implement #815

* [skip ci] update change log

* Implement #816 (#825)

* Implement #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 #822 (#826)

* fixes linting issues (#837)

* Delete #test.bg# (#859)

File is removed upon clean.

* fixed typo

* Update test images, skip testing if the wrong matplotlib version is used (#865)

* Update test images, skip testing if the wrong matplotlib version is used

* Update test-template.yml

* linting

* can't conda activate on azure

* now the heatmap is correct and the profile is wrong

* lint

* only one test should fail now

* Fix #844

* Should fix one test at least

* fix last tests

* fix #838 (#843)

* fix #838

* fixes

* Update CHANGES.txt

* Close #868 #867 and #851 (#869)

* Fix #868

* Fix #867

* Default ALL the things!

* Fix #866 (#871)

* Release 3.3.1 (#873)

* Develop (#827)

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

* use better conda link (#799)

* Estimated filtering fix (#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 (#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 (#818)

* Cache resulting counts rather than just decreasing the bin size

* sanity check

* Implement #815

* [skip ci] update change log

* Implement #816 (#825)

* Implement #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 #822 (#826)

* fixes linting issues (#837)

* Delete #test.bg# (#859)

File is removed upon clean.

* release 3.3.1

* try github actions

* each action is a file

* OK, that's inflexible

* OK, the action.yml thing is a mess

* syntax

* ok, try this

* uses

* spacing

* ok

* do anchors work?

* boo, so duplicative!

* oops

* maybe this will work for pypi

* ensure dist is empty

* nev

* rename

* bump version number

* Actionable active actions acting actively (#874)

* give actions another try

* wrong docs?

* ok

* hmm

* WTF

* ah, we CAN give a path

* hmm

* actions everywhere

* foo

* artifacts

* fix #889 (#891)

* Fix888 (#892)

* fix x-axis profile tick positions

* set minimum matplotlib version to 3.1.0

* fix hexbin and overlapped_lines too

* fix #887 (#893)

* update change log

* Seaborn colormaps (#894)

* add seaborn colormaps

* bump version and finally change license

* indenting

* update colormaps in galaxy wrapper

* update version in galaxy wrapper

* changelog

* wrong issue number

* pep8

* pep8

* pep8

* pep8

* added clusterUsingSamples to heatmap

* Added a couple of assertions to cehck the range of samples' indices

* Using --xRange and --yRange fails in galaxy due to the single quote. … (#901)

* Develop (#827)

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

* use better conda link (#799)

* Estimated filtering fix (#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 (#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 (#818)

* Cache resulting counts rather than just decreasing the bin size

* sanity check

* Implement #815

* [skip ci] update change log

* Implement #816 (#825)

* Implement #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 #822 (#826)

* fixes linting issues (#837)

* Delete #test.bg# (#859)

File is removed upon clean.

* Release 3.3.1 (#872)

* copy changes from bgruening

* this file should not be here since years (#845)

* Develop (#827)

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

* use better conda link (#799)

* Estimated filtering fix (#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 (#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 (#818)

* Cache resulting counts rather than just decreasing the bin size

* sanity check

* Implement #815

* [skip ci] update change log

* Implement #816 (#825)

* Implement #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 #822 (#826)

* fixes linting issues (#837)

* this file should not be here since years

* Add Arabidopsis TAIR10 (A_thaliana_Jun_2009) (#853)

Using output from:
faCount A_thaliana_Jun_2009.fa 
#seq	len	A	C	G	T	N	cpg
Chr1	30427671	9709674	5435374	5421151	9697113	164359	697370
Chr2	19698289	6315641	3542973	3520766	6316348	2561	457572
Chr3	23459830	7484757	4258333	4262704	7448059	5977	559031
Chr4	18585056	5940546	3371349	3356091	5914038	3032	439585
Chr5	26975502	8621974	4832253	4858759	8652238	10278	630299
ChrC	154478	48546	28496	27570	49866	0	4639
ChrM	366924	102464	82661	81609	100190	0	13697
total	119667750	38223602	21551439	21528650	38177852	186207	2802193
hpc $ python
Python 2.7.11 (default, Jul 25 2019, 12:10:26) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-28)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> 119667750-186207
119481543

* Fix python version in Azure tests  (#860)

* Develop (#827)

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

* use better conda link (#799)

* Estimated filtering fix (#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 (#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 (#818)

* Cache resulting counts rather than just decreasing the bin size

* sanity check

* Implement #815

* [skip ci] update change log

* Implement #816 (#825)

* Implement #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 #822 (#826)

* fixes linting issues (#837)

* Delete #test.bg# (#859)

File is removed upon clean.

* Fix python version

* Update azure-pipelines.yml

* fixed typo (#864)

* Develop (#827)

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

* use better conda link (#799)

* Estimated filtering fix (#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 (#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 (#818)

* Cache resulting counts rather than just decreasing the bin size

* sanity check

* Implement #815

* [skip ci] update change log

* Implement #816 (#825)

* Implement #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 #822 (#826)

* fixes linting issues (#837)

* Delete #test.bg# (#859)

File is removed upon clean.

* fixed typo

* Update test images, skip testing if the wrong matplotlib version is used (#865)

* Update test images, skip testing if the wrong matplotlib version is used

* Update test-template.yml

* linting

* can't conda activate on azure

* now the heatmap is correct and the profile is wrong

* lint

* only one test should fail now

* Fix #844

* Should fix one test at least

* fix last tests

* fix #838 (#843)

* fix #838

* fixes

* Update CHANGES.txt

* Close #868 #867 and #851 (#869)

* Fix #868

* Fix #867

* Default ALL the things!

* Fix #866 (#871)

* release 3.3.1

* try github actions

* each action is a file

* OK, that's inflexible

* OK, the action.yml thing is a mess

* syntax

* ok, try this

* uses

* spacing

* ok

* do anchors work?

* boo, so duplicative!

* oops

* maybe this will work for pypi

* ensure dist is empty

* nev

* rename

* bump version number

* Using --xRange and --yRange fails in galaxy due to the single quote. Removed them.

* Try just changing the wrapper

* fix wrapper linting

* plotCorrelation wrapper works properly now

* Add separate linting step to catch some of this in the future

Co-authored-by: Devon Ryan <dpryan79@users.noreply.github.com>
Co-authored-by: Björn Grüning <bjoern@gruenings.eu>
Co-authored-by: Steffen Möller <steffen_moeller@gmx.de>

* Documentation fixes, closes #886 (#905)

* Fix #902 (#906)

* [WIP] added a silhouette calculation (#876)

* Develop (#827)

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

* use better conda link (#799)

* Estimated filtering fix (#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 (#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 (#818)

* Cache resulting counts rather than just decreasing the bin size

* sanity check

* Implement #815

* [skip ci] update change log

* Implement #816 (#825)

* Implement #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 #822 (#826)

* fixes linting issues (#837)

* Delete #test.bg# (#859)

File is removed upon clean.

* Release 3.3.1 (#872)

* copy changes from bgruening

* this file should not be here since years (#845)

* Develop (#827)

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

* use better conda link (#799)

* Estimated filtering fix (#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 (#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 (#818)

* Cache resulting counts rather than just decreasing the bin size

* sanity check

* Implement #815

* [skip ci] update change log

* Implement #816 (#825)

* Implement #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 #822 (#826)

* fixes linting issues (#837)

* this file should not be here since years

* Add Arabidopsis TAIR10 (A_thaliana_Jun_2009) (#853)

Using output from:
faCount A_thaliana_Jun_2009.fa 
#seq	len	A	C	G	T	N	cpg
Chr1	30427671	9709674	5435374	5421151	9697113	164359	697370
Chr2	19698289	6315641	3542973	3520766	6316348	2561	457572
Chr3	23459830	7484757	4258333	4262704	7448059	5977	559031
Chr4	18585056	5940546	3371349	3356091	5914038	3032	439585
Chr5	26975502	8621974	4832253	4858759	8652238	10278	630299
ChrC	154478	48546	28496	27570	49866	0	4639
ChrM	366924	102464	82661	81609	100190	0	13697
total	119667750	38223602	21551439	21528650	38177852	186207	2802193
hpc $ python
Python 2.7.11 (default, Jul 25 2019, 12:10:26) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-28)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> 119667750-186207
119481543

* Fix python version in Azure tests  (#860)

* Develop (#827)

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

* use better conda link (#799)

* Estimated filtering fix (#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 (#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 (#818)

* Cache resulting counts rather than just decreasing the bin size

* sanity check

* Implement #815

* [skip ci] update change log

* Implement #816 (#825)

* Implement #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 #822 (#826)

* fixes linting issues (#837)

* Delete #test.bg# (#859)

File is removed upon clean.

* Fix python version

* Update azure-pipelines.yml

* fixed typo (#864)

* Develop (#827)

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

* use better conda link (#799)

* Estimated filtering fix (#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 (#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 (#818)

* Cache resulting counts rather than just decreasing the bin size

* sanity check

* Implement #815

* [skip ci] update change log

* Implement #816 (#825)

* Implement #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 #822 (#826)

* fixes linting issues (#837)

* Delete #test.bg# (#859)

File is removed upon clean.

* fixed typo

* Update test images, skip testing if the wrong matplotlib version is used (#865)

* Update test images, skip testing if the wrong matplotlib version is used

* Update test-template.yml

* linting

* can't conda activate on azure

* now the heatmap is correct and the profile is wrong

* lint

* only one test should fail now

* Fix #844

* Should fix one test at least

* fix last tests

* fix #838 (#843)

* fix #838

* fixes

* Update CHANGES.txt

* Close #868 #867 and #851 (#869)

* Fix #868

* Fix #867

* Default ALL the things!

* Fix #866 (#871)

* release 3.3.1

* try github actions

* each action is a file

* OK, that's inflexible

* OK, the action.yml thing is a mess

* syntax

* ok, try this

* uses

* spacing

* ok

* do anchors work?

* boo, so duplicative!

* oops

* maybe this will work for pypi

* ensure dist is empty

* nev

* rename

* bump version number

* added a silhouette calculation

* remove sklearn, implement with scipy and numpy

* Update requirements.txt

* Update setup.py

* Update heatmapper.py

* update galaxy wrapper

* Fix run time issues

* refactor, the order matters here.

* removing debugging stuff

* Update heatmapper.py

* Update plotHeatmap.py

Co-authored-by: Devon Ryan <dpryan79@users.noreply.github.com>
Co-authored-by: Björn Grüning <bjoern@gruenings.eu>
Co-authored-by: Steffen Möller <steffen_moeller@gmx.de>

* mention silhouette score

* update help location

* see if this fixes things (#909)

* update Azure OSX client version

* Fix typos in documentation (#916)

Fixes two typos in example code.

* copy wrapper fixes from Bjoern's PR

* Fix dotted line (#921)

* Fix the dashed line in plotHeatmap with reference-point TES and sorting by region_length

* fix test

* Implement #924 (#925)

* Basic implementation of --linesAtTickMarks and galaxy wrapper

* bump version to 3.4.0

* typo

* stupid eigenvalues

* Fix #928 (#929)

* Don't force shared memory.

Co-authored-by: Björn Grüning <bjoern.gruening@gmail.com>
Co-authored-by: Ann Loraine <aloraine@uncc.edu>
Co-authored-by: Jan Janssen <jan-janssen@users.noreply.github.com>
Co-authored-by: bounlu <bounlu@gmail.com>
Co-authored-by: Leily Rabbani <rabbani@pc390.ie-freiburg.mpg.de>
Co-authored-by: LeilyR <leila.rabbani@gmail.com>
Co-authored-by: cgirardot <girardot@embl.de>
Co-authored-by: Björn Grüning <bjoern@gruenings.eu>
Co-authored-by: Steffen Möller <steffen_moeller@gmx.de>
Co-authored-by: Lucille Delisle <lucille.delisle@epfl.ch>
Co-authored-by: Sichong <scpeng@ucdavis.edu>

* copy changes from bgruening

* this file should not be here since years (#845)

* Develop (#827)

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

* use better conda link (#799)

* Estimated filtering fix (#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 (#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 (#818)

* Cache resulting counts rather than just decreasing the bin size

* sanity check

* Implement #815

* [skip ci] update change log

* Implement #816 (#825)

* Implement #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 #822 (#826)

* fixes linting issues (#837)

* this file should not be here since years

* Add Arabidopsis TAIR10 (A_thaliana_Jun_2009) (#853)

Using output from:
faCount A_thaliana_Jun_2009.fa 
#seq	len	A	C	G	T	N	cpg
Chr1	30427671	9709674	5435374	5421151	9697113	164359	697370
Chr2	19698289	6315641	3542973	3520766	6316348	2561	457572
Chr3	23459830	7484757	4258333	4262704	7448059	5977	559031
Chr4	18585056	5940546	3371349	3356091	5914038	3032	439585
Chr5	26975502	8621974	4832253	4858759	8652238	10278	630299
ChrC	154478	48546	28496	27570	49866	0	4639
ChrM	366924	102464	82661	81609	100190	0	13697
total	119667750	38223602	21551439	21528650	38177852	186207	2802193
hpc $ python
Python 2.7.11 (default, Jul 25 2019, 12:10:26) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-28)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> 119667750-186207
119481543

* Fix python version in Azure tests  (#860)

* Develop (#827)

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

* use better conda link (#799)

* Estimated filtering fix (#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 (#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 (#818)

* Cache resulting counts rather than just decreasing the bin size

* sanity check

* Implement #815

* [skip ci] update change log

* Implement #816 (#825)

* Implement #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 #822 (#826)

* fixes linting issues (#837)

* Delete #test.bg# (#859)

File is removed upon clean.

* Fix python version

* Update azure-pipelines.yml

* fixed typo (#864)

* Develop (#827)

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

* use better conda link (#799)

* Estimated filtering fix (#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 (#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 (#818)

* Cache resulting counts rather than just decreasing the bin size

* sanity check

* Implement #815

* [skip ci] update change log

* Implement #816 (#825)

* Implement #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 #822 (#826)

* fixes linting issues (#837)

* Delete #test.bg# (#859)

File is removed upon clean.

* fixed typo

* Update test images, skip testing if the wrong matplotlib version is used (#865)

* Update test images, skip testing if the wrong matplotlib version is used

* Update test-template.yml

* linting

* can't conda activate on azure

* now the heatmap is correct and the profile is wrong

* lint

* only one test should fail now

* Fix #844

* Should fix one test at least

* fix last tests

* fix #838 (#843)

* fix #838

* fixes

* Update CHANGES.txt

* Close #868 #867 and #851 (#869)

* Fix #868

* Fix #867

* Default ALL the things!

* Fix #866 (#871)

* Release 3.3.1 (#873)

* Develop (#827)

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

* use better conda link (#799)

* Estimated filtering fix (#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 (#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 (#818)

* Cache resulting counts rather than just decreasing the bin size

* sanity check

* Implement #815

* [skip ci] update change log

* Implement #816 (#825)

* Implement #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 #822 (#826)

* fixes linting issues (#837)

* Delete #test.bg# (#859)

File is removed upon clean.

* release 3.3.1

* try github actions

* each action is a file

* OK, that's inflexible

* OK, the action.yml thing is a mess

* syntax

* ok, try this

* uses

* spacing

* ok

* do anchors work?

* boo, so duplicative!

* oops

* maybe this will work for pypi

* ensure dist is empty

* nev

* rename

* bump version number

* Actionable active actions acting actively (#874)

* give actions another try

* wrong docs?

* ok

* hmm

* WTF

* ah, we CAN give a path

* hmm

* actions everywhere

* foo

* artifacts

* fix #889 (#891)

* Fix888 (#892)

* fix x-axis profile tick positions

* set minimum matplotlib version to 3.1.0

* fix hexbin and overlapped_lines too

* fix #887 (#893)

* update change log

* Seaborn colormaps (#894)

* add seaborn colormaps

* bump version and finally change license

* indenting

* update colormaps in galaxy wrapper

* update version in galaxy wrapper

* changelog

* wrong issue number

* pep8

* pep8

* pep8

* pep8

* added clusterUsingSamples to heatmap

* Added a couple of assertions to cehck the range of samples' indices

* Using --xRange and --yRange fails in galaxy due to the single quote. … (#901)

* Develop (#827)

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

* use better conda link (#799)

* Estimated filtering fix (#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 (#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 (#818)

* Cache resulting counts rather than just decreasing the bin size

* sanity check

* Implement #815

* [skip ci] update change log

* Implement #816 (#825)

* Implement #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 #822 (#826)

* fixes linting issues (#837)

* Delete #test.bg# (#859)

File is removed upon clean.

* Release 3.3.1 (#872)

* copy changes from bgruening

* this file should not be here since years (#845)

* Develop (#827)

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

* use better conda link (#799)

* Estimated filtering fix (#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 (#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 (#818)

* Cache resulting counts rather than just decreasing the bin size

* sanity check

* Implement #815

* [skip ci] update change log

* Implement #816 (#825)

* Implement #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 #822 (#826)

* fixes linting issues (#837)

* this file should not be here since years

* Add Arabidopsis TAIR10 (A_thaliana_Jun_2009) (#853)

Using output from:
faCount A_thaliana_Jun_2009.fa 
#seq	len	A	C	G	T	N	cpg
Chr1	30427671	9709674	5435374	5421151	9697113	164359	697370
Chr2	19698289	6315641	3542973	3520766	6316348	2561	457572
Chr3	23459830	7484757	4258333	4262704	7448059	5977	559031
Chr4	18585056	5940546	3371349	3356091	5914038	3032	439585
Chr5	26975502	8621974	4832253	4858759	8652238	10278	630299
ChrC	154478	48546	28496	27570	49866	0	4639
ChrM	366924	102464	82661	81609	100190	0	13697
total	119667750	38223602	21551439	21528650	38177852	186207	2802193
hpc $ python
Python 2.7.11 (default, Jul 25 2019, 12:10:26) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-28)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> 119667750-186207
119481543

* Fix python version in Azure tests  (#860)

* Develop (#827)

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

* use better conda link (#799)

* Estimated filtering fix (#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 (#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 (#818)

* Cache resulting counts rather than just decreasing the bin size

* sanity check

* Implement #815

* [skip ci] update change log

* Implement #816 (#825)

* Implement #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 #822 (#826)

* fixes linting issues (#837)

* Delete #test.bg# (#859)

File is removed upon clean.

* Fix python version

* Update azure-pipelines.yml

* fixed typo (#864)

* Develop (#827)

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

* use better conda link (#799)

* Estimated filtering fix (#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 (#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 (#818)

* Cache resulting counts rather than just decreasing the bin size

* sanity check

* Implement #815

* [skip ci] update change log

* Implement #816 (#825)

* Implement #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 #822 (#826)

* fixes linting issues (#837)

* Delete #test.bg# (#859)

File is removed upon clean.

* fixed typo

* Update test images, skip testing if the wrong matplotlib version is used (#865)

* Update test images, skip testing if the wrong matplotlib version is used

* Update test-template.yml

* linting

* can't conda activate on azure

* now the heatmap is correct and the profile is wrong

* lint

* only one test should fail now

* Fix #844

* Should fix one test at least

* fix last tests

* fix #838 (#843)

* fix #838

* fixes

* Update CHANGES.txt

* Close #868 #867 and #851 (#869)

* Fix #868

* Fix #867

* Default ALL the things!

* Fix #866 (#871)

* release 3.3.1

* try github actions

* each action is a file

* OK, that's inflexible

* OK, the action.yml thing is a mess

* syntax

* ok, try this

* uses

* spacing

* ok

* do anchors work?

* boo, so duplicative!

* oops

* maybe this will work for pypi

* ensure dist is empty

* nev

* rename

* bump version number

* Using --xRange and --yRange fails in galaxy due to the single quote. Removed them.

* Try just changing the wrapper

* fix wrapper linting

* plotCorrelation wrapper works properly now

* Add separate linting step to catch some of this in the future

Co-authored-by: Devon Ryan <dpryan79@users.noreply.github.com>
Co-authored-by: Björn Grüning <bjoern@gruenings.eu>
Co-authored-by: Steffen Möller <steffen_moeller@gmx.de>

* Documentation fixes, closes #886 (#905)

* Fix #902 (#906)

* [WIP] added a silhouette calculation (#876)

* Develop (#827)

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

* use better conda link (#799)

* Estimated filtering fix (#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 (#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 (#818)

* Cache resulting counts rather than just decreasing the bin size

* sanity check

* Implement #815

* [skip ci] update change log

* Implement #816 (#825)

* Implement #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 #822 (#826)

* fixes linting issues (#837)

* Delete #test.bg# (#859)

File is removed upon clean.

* Release 3.3.1 (#872)

* copy changes from bgruening

* this file should not be here since years (#845)

* Develop (#827)

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

* use better conda link (#799)

* Estimated filtering fix (#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 (#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 (#818)

* Cache resulting counts rather than just decreasing the bin size

* sanity check

* Implement #815

* [skip ci] update change log

* Implement #816 (#825)

* Implement #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 #822 (#826)

* fixes linting issues (#837)

* this file should not be here since years

* Add Arabidopsis TAIR10 (A_thaliana_Jun_2009) (#853)

Using output from:
faCount A_thaliana_Jun_2009.fa 
#seq	len	A	C	G	T	N	cpg
Chr1	30427671	9709674	5435374	5421151	9697113	164359	697370
Chr2	19698289	6315641	3542973	3520766	6316348	2561	457572
Chr3	23459830	7484757	4258333	4262704	7448059	5977	559031
Chr4	18585056	5940546	3371349	3356091	5914038	3032	439585
Chr5	26975502	8621974	4832253	4858759	8652238	10278	630299
ChrC	154478	48546	28496	27570	49866	0	4639
ChrM	366924	102464	82661	81609	100190	0	13697
total	119667750	38223602	21551439	21528650	38177852	186207	2802193
hpc $ python
Python 2.7.11 (default, Jul 25 2019, 12:10:26) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-28)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> 119667750-186207
119481543

* Fix python version in Azure tests  (#860)

* Develop (#827)

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

* use better conda link (#799)

* Estimated filtering fix (#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 (#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 (#818)

* Cache resulting counts rather than just decreasing the bin size

* sanity check

* Implement #815

* [skip ci] update change log

* Implement #816 (#825)

* Implement #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 #822 (#826)

* fixes linting issues (#837)

* Delete #test.bg# (#859)

File is removed upon clean.

* Fix python version

* Update azure-pipelines.yml

* fixed typo (#864)

* Develop (#827)

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

* use better conda link (#799)

* Estimated filtering fix (#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 (#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 (#818)

* Cache resulting counts rather than just decreasing the bin size

* sanity check

* Implement #815

* [skip ci] update change log

* Implement #816 (#825)

* Implement #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 #822 (#826)

* fixes linting issues (#837)

* Delete #test.bg# (#859)

File is removed upon clean.

* fixed typo

* Update test images, skip testing if the wrong matplotlib version is used (#865)

* Update test images, skip testing if the wrong matplotlib version is used

* Update test-template.yml

* linting

* can't conda activate on azure

* now the heatmap is correct and the profile is wrong

* lint

* only one test should fail now

* Fix #844

* Should fix one test at least

* fix last tests

* fix #838 (#843)

* fix #838

* fixes

* Update CHANGES.txt

* Close #868 #867 and #851 (#869)

* Fix #868

* Fix #867

* Default ALL the things!

* Fix #866 (#871)

* release 3.3.1

* try github actions

* each action is a file

* OK, that's inflexible

* OK, the action.yml thing is a mess

* syntax

* ok, try this

* uses

* spacing

* ok

* do anchors work?

* boo, so duplicative!

* oops

* maybe this will work for pypi

* ensure dist is empty

* nev

* rename

* bump version number

* added a silhouette calculation

* remove sklearn, implement with scipy and numpy

* Update requirements.txt

* Update setup.py

* Update heatmapper.py

* update galaxy wrapper

* Fix run time issues

* refactor, the order matters here.

* removing debugging stuff

* Update heatmapper.py

* Update plotHeatmap.py

Co-authored-by: Devon Ryan <dpryan79@users.noreply.github.com>
Co-authored-by: Björn Grüning <bjoern@gruenings.eu>
Co-authored-by: Steffen Möller <steffen_moeller@gmx.de>

* mention silhouette score

* update help location

* see if this fixes things (#909)

* update Azure OSX client version

* Fix typos in documentation (#916)

Fixes two typos in example code.

* copy wrapper fixes from Bjoern's PR

* Fix dotted line (#921)

* Fix the dashed line in plotHeatmap with reference-point TES and sorting by region_length

* fix test

* Implement #924 (#925)

* Basic implementation of --linesAtTickMarks and galaxy wrapper

* bump version to 3.4.0

* typo

* stupid eigenvalues

Co-authored-by: Björn Grüning <bjoern@gruenings.eu>
Co-authored-by: A. Loraine <aloraine@uncc.edu>
Co-authored-by: Jan Janssen <jan-janssen@users.noreply.github.com>
Co-authored-by: Ömer An <bounlu@gmail.com>
Co-authored-by: LeilyR <leila.rabbani@gmail.com>
Co-authored-by: cgirardot <girardot@embl.de>
Co-authored-by: Steffen Möller <steffen_moeller@gmx.de>
Co-authored-by: Lucille Delisle <lucille.delisle@epfl.ch>
Co-authored-by: Sichong <scpeng@ucdavis.edu>

* copy changes from bgruening

* this file should not be here since years (#845)

* Develop (#827)

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

* use better conda link (#799)

* Estimated filtering fix (#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 (#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 (#818)

* Cache resulting counts rather than just decreasing the bin size

* sanity check

* Implement #815

* [skip ci] update change log

* Implement #816 (#825)

* Implement #816

* expose option

* Add a test using pseudocounts and skipZeroOverZero

* syntax

* Fix tests

* Make --skipZeroOverZero a galaxy macro and add to bigwigC...

* copy changes from bgruening

* this file should not be here since years (#845)

* Develop (#827)

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

* use better conda link (#799)

* Estimated filtering fix (#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 (#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 (#818)

* Cache resulting counts rather than just decreasing the bin size

* sanity check

* Implement #815

* [skip ci] update change log

* Implement #816 (#825)

* Implement #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 #822 (#826)

* fixes linting issues (#837)

* this file should not be here since years

* Add Arabidopsis TAIR10 (A_thaliana_Jun_2009) (#853)

Using output from:
faCount A_thaliana_Jun_2009.fa 
#seq	len	A	C	G	T	N	cpg
Chr1	30427671	9709674	5435374	5421151	9697113	164359	697370
Chr2	19698289	6315641	3542973	3520766	6316348	2561	457572
Chr3	23459830	7484757	4258333	4262704	7448059	5977	559031
Chr4	18585056	5940546	3371349	3356091	5914038	3032	439585
Chr5	26975502	8621974	4832253	4858759	8652238	10278	630299
ChrC	154478	48546	28496	27570	49866	0	4639
ChrM	366924	102464	82661	81609	100190	0	13697
total	119667750	38223602	21551439	21528650	38177852	186207	2802193
hpc $ python
Python 2.7.11 (default, Jul 25 2019, 12:10:26) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-28)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> 119667750-186207
119481543

* Fix python version in Azure tests  (#860)

* Develop (#827)

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

* use better conda link (#799)

* Estimated filtering fix (#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 (#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 (#818)

* Cache resulting counts rather than just decreasing the bin size

* sanity check

* Implement #815

* [skip ci] update change log

* Implement #816 (#825)

* Implement #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 #822 (#826)

* fixes linting issues (#837)

* Delete #test.bg# (#859)

File is removed upon clean.

* Fix python version

* Update azure-pipelines.yml

* fixed typo (#864)

* Develop (#827)

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

* use better conda link (#799)

* Estimated filtering fix (#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 (#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 (#818)

* Cache resulting counts rather than just decreasing the bin size

* sanity check

* Implement #815

* [skip ci] update change log

* Implement #816 (#825)

* Implement #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 #822 (#826)

* fixes linting issues (#837)

* Delete #test.bg# (#859)

File is removed upon clean.

* fixed typo

* Update test images, skip testing if the wrong matplotlib version is used (#865)

* Update test images, skip testing if the wrong matplotlib version is used

* Update test-template.yml

* linting

* can't conda activate on azure

* now the heatmap is correct and the profile is wrong

* lint

* only one test should fail now

* Fix #844

* Should fix one test at least

* fix last tests

* fix #838 (#843)

* fix #838

* fixes

* Update CHANGES.txt

* Close #868 #867 and #851 (#869)

* Fix #868

* Fix #867

* Default ALL the things!

* Fix #866 (#871)

* release 3.3.1

* try github actions

* each action is a file

* OK, that's inflexible

* OK, the action.yml thing is a mess

* syntax

* ok, try this

* uses

* spacing

* ok

* do anchors work?

* boo, so duplicative!

* oops

* maybe this will work for pypi

* ensure dist is empty

* nev

* rename

* bump version number

File is removed upon clean.

* Add plotCoverage --BED

* Add coverage threshold stuff

* tweak

* OK, this seems to do the trick

* bump version

* take a stab at a galaxy wrapper

* update galaxy wrapper, sort -ct

* Implement #832

* update dti requirement

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

* use better conda link (#799)

* Estimated filtering fix (#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 (#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 (#818)

* Cache resulting counts rather than just decreasing the bin size

* sanity check

* Implement #815

* [skip ci] update change log

* Implement #816 (#825)

* Implement #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 #822 (#826)

* Implement #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

* Cache resulting counts rather than just decreasing the bin size

* sanity check

* 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

* use better conda link (#799)

* Estimated filtering fix (#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

* oops

* fix testing and set a max number of filtered reads

* apparently a bunch of things were getting skipped

* fix wrappers

* update computeMatrix wrapper

Merging temporary files with using a wrong name - rev1.bam instead of a.rev1.bam and similar

* add --sizeFactors

* Still need to make the galaxy wrapper

* Add tests for scalingFactor

* pep8

* wrong function name

* Add --scalingFactors to the galaxy wrapper

* assert equal

* foo

* Fix #801

* update change log

* Fix #797, scrap sharing axes and manually attend to scaling the axes as desired

* pep8

* Implement #785, which is done with --skipNAs

* [ci skip] update change log

* pep8

* OMFG

* Add --skipZeroOverZero to bamCompare

* Update change log

* oops

* azure has its issues

* Allow two different pseudocounts

* Allow different pseudocounts in galaxy

* pep8

* oops

* Add a pseudocount test

* pep8

* forgot to do the splits

* Fix738

* Screw you PEP8

* OMFG

* [ci skip] Fix #782

* [ci skip] Update change log

* exclude OSX for now

* should have linted

* Wow, glad I tested this

* fix wrapper

* use better conda link (#799)

* Set up CI with Azure Pipelines

* Update azure-pipelines.yml

* Update azure-pipelines.yml

* Update azure-pipelines.yml

* Update azure-pipelines.yml

* create an env

* Remove deeptoolsintervals

* PEP8

* blah

* Try adding planemo

* oops

* forgot steps

* disable travis, fix galaxy

* token change to trigger a rebuild

* Guess I'll switch to circleci, since doesn't allow rerunning steps

* Add 'se' and 'std' to possible heatmap summary plot types

* Ignore W504 and use raw string for regex

* Update modulus calculation on plot_line_styles

pyplot_line_styles has a length of 28, the modulus calculation was taking mod 35. This leads to issues when a file list was longer than 28 files. Now it calculates the mod on the length of pyplot_line_styles.

* Update plotFingerprint.py

* dti is a dependency now

* PEP8 mostly