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Fix cleavage profile #73

Merged
merged 39 commits into from
May 15, 2024
Merged

Fix cleavage profile #73

merged 39 commits into from
May 15, 2024

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jamesli124
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  • Fixed intersect policy for cleavage_profile
  • Clean up some comments
  • Fixed logging from coverage function
  • Added numerous util functions
  • Added left and right options to cleavage_profile and CLI
    cleavage-profile.
  • Added tests for cleavage profiling.

jamesli124 and others added 30 commits April 30, 2024 14:08
@jamesli124
Merge pull request #60 from epifluidlab/develop
8578dd0 
Develop
@jamesli124
Merge pull request #64 from epifluidlab/develop
cbdaf09 
Develop
@jamesli124
Merge pull request #65 from epifluidlab/develop
aecfc37 
Develop
@jamesli124
change cleavage profile intersect_policy to any
e49833e
@jamesli124
fix typo in docstring
718657d
@ravibandaru-lab
Update README.md
7933c9c
@ravibandaru-lab
Update README.md
1aaa02d
@ravibandaru-lab
Update README.md
5c19b57
@ravibandaru-lab
Update README.md
7c27b46
@ravibandaru-lab
Update README.md
ada7658
@ravibandaru-lab
Update README.md
9ba5e40
@ravibandaru-lab
Update README.md
e1ae467
@ravibandaru-lab
Delete src/finaletoolkit/methylation directory
e7ed11e
@ravibandaru-lab
Delete src/finaletoolkit/qc directory
aa970a7
@ravibandaru-lab
Delete src/finaletoolkit/too directory
f936b57
@jamesli124
Merge pull request #66 from epifluidlab/readme_change
7cea2b1 
Readme change
@jamesli124
Merge pull request #67 from epifluidlab/remove-redundant-files
d65e910 
Remove redundant files
@jamesli124
Merge pull request #68 from epifluidlab/main
9aceebd 
update branch
@jamesli124
mask for zeros when calculating proportions to avoid errors
facc6b4
@jamesli124
remove _get_contigs and add _parse_chrom_sizes
ff727c4
@jamesli124
fix coverage verbose log
5044c82
@jamesli124
add numerous util functions related to merging overlapping bins
1c092f9
@jamesli124
Changed _cli_cleavage_profile
000c2be 
    - simplify internal calculations with helper functions
    - add option for chrom_sizes file to allow compatability with frag.gz files.
@ravibandaru-lab
update documentation
be3037b
@jamesli124
Merge pull request #69 from epifluidlab/documentation-update
ef477b7 
update documentation
@jamesli124
Create .nojekyll
4faca95
@jamesli124
Create static.yml
4379aa6
@jamesli124
Merge pull request #70 from epifluidlab/documentation-update
914d1fd 
Create .nojekyll
@jamesli124
Merge pull request #71 from epifluidlab/github-pages-integration
9a07747 
GitHub pages integration
@jamesli124
Merge pull request #72 from epifluidlab/main
1751523 
update branch
@jamesli124 jamesli124 merged commit cb10781 into develop May 15, 2024
@jamesli124 jamesli124 deleted the fix-cleavage-profile branch May 15, 2024 07:28
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@jamesli124 @ravibandaru-lab