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3.4.0 #926

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merged 34 commits into from
Mar 5, 2020
Merged

3.4.0 #926

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ecce499
copy changes from bgruening
dpryan79 May 29, 2019
2252b23
this file should not be here since years (#845)
bgruening Jul 15, 2019
831cdc0
Add Arabidopsis TAIR10 (A_thaliana_Jun_2009) (#853)
aloraine Jul 26, 2019
67c16a0
Fix python version in Azure tests (#860)
jan-janssen Aug 12, 2019
effc969
fixed typo (#864)
bounlu Aug 26, 2019
6a1a7e3
Update test images, skip testing if the wrong matplotlib version is u…
dpryan79 Sep 3, 2019
4843731
fix #838 (#843)
dpryan79 Sep 3, 2019
832a22a
Close #868 #867 and #851 (#869)
dpryan79 Sep 3, 2019
2560d13
Fix #866 (#871)
dpryan79 Sep 9, 2019
f0baf64
Release 3.3.1 (#873)
dpryan79 Sep 10, 2019
07a821b
Actionable active actions acting actively (#874)
dpryan79 Sep 18, 2019
37229d7
fix #889 (#891)
dpryan79 Dec 2, 2019
15bf16c
Fix888 (#892)
dpryan79 Dec 2, 2019
d84222a
fix #887 (#893)
dpryan79 Dec 3, 2019
6178b0f
update change log
dpryan79 Dec 3, 2019
e0f53d0
Seaborn colormaps (#894)
dpryan79 Dec 3, 2019
1793dd1
added clusterUsingSamples to heatmap
Dec 20, 2019
95e8e50
Added a couple of assertions to cehck the range of samples' indices
Dec 23, 2019
d68cb1e
Merge pull request #900 from deeptools/clusterUsingSamples
LeilyR Dec 23, 2019
ad00f93
Using --xRange and --yRange fails in galaxy due to the single quote. …
cgirardot Jan 16, 2020
1b3b367
Documentation fixes, closes #886 (#905)
dpryan79 Jan 17, 2020
3115f1b
Fix #902 (#906)
dpryan79 Jan 17, 2020
e8856ce
[WIP] added a silhouette calculation (#876)
lldelisle Jan 21, 2020
ff79682
mention silhouette score
dpryan79 Jan 21, 2020
386a76a
update help location
dpryan79 Jan 22, 2020
4949d80
see if this fixes things (#909)
dpryan79 Jan 22, 2020
82f85c9
merge in master so this can get released
dpryan79 Jan 23, 2020
4ab0ea9
Merge branch 'master' into develop
dpryan79 Jan 23, 2020
9305a24
update Azure OSX client version
dpryan79 Jan 24, 2020
e5eca25
Fix typos in documentation (#916)
SichongP Feb 25, 2020
c7fe893
copy wrapper fixes from Bjoern's PR
dpryan79 Mar 5, 2020
1c40e47
Fix dotted line (#921)
dpryan79 Mar 5, 2020
e7bc375
Implement #924 (#925)
dpryan79 Mar 5, 2020
0965841
Merge branch 'master' into develop
dpryan79 Mar 5, 2020
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Fix typos in documentation (#916)
Fixes two typos in example code.
SichongP authored Feb 25, 2020

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commit e5eca25d2730207fb231ac5b011b94d1c9f2c35d
4 changes: 2 additions & 2 deletions docs/content/example_api_tutorial.rst
Original file line number Diff line number Diff line change
@@ -261,7 +261,7 @@ a tuple with the parameters: chromosome name, start position, end position, and
f_lens_list = []
for fetch_start in range(start, end, 1000000):
# simply get the reads over a region of 10000 bases
fetch_end = min(end, start + 10000)
fetch_end = min(end, fetch_start + 10000)

f_lens_list.append(np.array([abs(read.template_length)
for read in bam.fetch(chrom, fetch_start, fetch_end)
@@ -290,7 +290,7 @@ to the function, the BAM file name. The next two positional arguments are the na

result = mapReduce.mapReduce([bam_file_name],
get_fragment_length,
chrom_sizes,
chroms_sizes,
genomeChunkLength=10000000,
numberOfProcessors=20,
verbose=True)