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3.2.0 release #77

Merged
merged 13 commits into from
Aug 31, 2023
Merged

3.2.0 release #77

merged 13 commits into from
Aug 31, 2023

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js2264
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@js2264 js2264 commented Aug 29, 2023

CHANGES:

  • --mat_fmt=cool by default

NEW FEATURE(S):

  • by default, an un-binned .cool file is generated
  • if the end user provides a --binning=INT in pipeline, a balanced .mcool file binned at multiple resolutions will be automatically generated
  • specify --zoomify=False to only generate a single-resolution binned .cool
  • balancing arguments can be specified with --balancing_args "..."
  • --exclude=STR in pipeline to remove chromosomes from the final matrix

BUG FIXES:

  • check that provided fastq/bam files have the same length before starting

@cmdoret
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cmdoret commented Aug 29, 2023

This looks great! Before merging, the CI reports a bug in cutsite_read. Would it make sense to fix it before making a new release? (@ABignaud is that an obvious fix?)

___________________ [doctest] hicstuff.cutsite.cutsite_read ____________________
186     --------
187     list of str
188         List of string of the sequences. The split is made at the start of the
189         ligation sites.
190     list of str
191         List of string of the qualities.
192 
193     Examples:
194     ---------
195     >>> cutsite_read(re.compile(r'GA.TA.TC'), "AAGAGTATTC", "FFF--FAFAF")
Expected:
    (['AA', 'GAGTATTC'], ['FF', 'F--FAFAF'])
Got:
    (['AAGAGT', 'ATTC'], ['FFF--F', 'AFAF'])

@js2264
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js2264 commented Aug 29, 2023

Thx for feedback Cyril. Yeah I noticed that. I believe it comes from this change: 16c2a8d#diff-635d9ca98526ebd7bc5b454b727c17ba8f458906eadda7a3b45dc0dc61a9f537L210-R215

I can look into it but @ABignaud if you have an obvious fix please let me know :)

@codecov
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codecov bot commented Aug 29, 2023

Codecov Report

Merging #77 (c5e71eb) into master (ffdc01e) will decrease coverage by 1.98%.
Report is 23 commits behind head on master.
The diff coverage is 54.73%.

@@            Coverage Diff             @@
##           master      #77      +/-   ##
==========================================
- Coverage   67.27%   65.29%   -1.98%     
==========================================
  Files          14       14              
  Lines        3193     3276      +83     
==========================================
- Hits         2148     2139       -9     
- Misses       1045     1137      +92     
Files Changed Coverage Δ
hicstuff/pipeline.py 61.88% <41.53%> (-15.99%) ⬇️
hicstuff/commands.py 69.89% <75.00%> (+0.07%) ⬆️
hicstuff/io.py 72.74% <76.92%> (+0.26%) ⬆️
hicstuff/cutsite.py 90.90% <100.00%> (-0.93%) ⬇️
hicstuff/digest.py 94.41% <100.00%> (ø)
hicstuff/distance_law.py 98.25% <100.00%> (ø)
hicstuff/version.py 100.00% <100.00%> (ø)

... and 1 file with indirect coverage changes

@js2264
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js2264 commented Aug 29, 2023

Got the green tick. Are we happy to merge @cmdoret @ABignaud?

@cmdoret cmdoret self-requested a review August 29, 2023 14:02
@cmdoret cmdoret requested a review from ABignaud August 29, 2023 14:03
@js2264 js2264 merged commit b6b5d25 into master Aug 31, 2023
1 check passed
@js2264 js2264 deleted the 3.2.0 branch August 31, 2023 23:26
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3 participants