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Release 0.4.1 #76

Merged
merged 86 commits into from
Oct 7, 2024
Merged

Release 0.4.1 #76

merged 86 commits into from
Oct 7, 2024

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khoroshevskyi
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Changes:

  • Updated metadata model
  • Added bedmess to pep processing

donaldcampbelljr and others added 30 commits August 12, 2024 14:49
@donaldcampbelljr
initial work towards ref genome prediction and validation
27a6ddd
@donaldcampbelljr
initial commit for pulling and caching 1000 bedfiles
e2c6502
@donaldcampbelljr
add beginnings of excluded_ranges overlap processing
8e90842
@donaldcampbelljr
add subprocess execution and output checking
e88d019
@donaldcampbelljr
working example for excluded ranges processing
2d027b2
@donaldcampbelljr
some polish, use getattr
9d17108
@donaldcampbelljr
add stats analysis script, creating heatmap
c3bd066
@donaldcampbelljr
adjust heatmap, add example output
4b8f94b
@donaldcampbelljr
update to use more bins when producing heatmap
722ec92
@donaldcampbelljr
sort via column mean
abc0d42
@donaldcampbelljr
wrap sample accessing via Geofetch in try except, only pull file list
9d1314e
@donaldcampbelljr
add sorting for heatmap columns, truncate names for readability, atte…
d8401e9 
…mpt adding clustermaps
@khoroshevskyi
updated metadata model
6939f11
@khoroshevskyi
Added CLI R deps
dfd0a87
@khoroshevskyi
updated install packages scirpt
341affe
@donaldcampbelljr
change to number of hits
7462d30
@donaldcampbelljr
add getting chrom sizes for bed file and doing a comparison with refg…
2ee7594 
…enome chrom sizes
@donaldcampbelljr @nsheff
Update bedboss/refgenome_validator/genome_model.py
98836b4 
Co-authored-by: Nathan Sheffield <[email protected]>
@donaldcampbelljr
Merge branch 'dev' into dev_ref_genome_validator
d208973
@donaldcampbelljr
lint
74310e5
@donaldcampbelljr
rework compatibility to take single bed and return a list of dicts fo…
e4ce058 
…r compatibility vector
@donaldcampbelljr
add more logic to compare_chrom_names
633e4d6
@donaldcampbelljr
large bolus of work, including adding igd execution via existing .igd…
107dd63 
… file
@donaldcampbelljr
add using jaccard index for first layer assessment, add using percent…
56298d8 
…age of chroms extending beyond chrom.sizes for second layer asessment
@donaldcampbelljr
run on larger dataset, fix some bugs
4eac770
@donaldcampbelljr
more polish and bug fixes
fe1be32
@donaldcampbelljr
add using pipestat to report results
0dea1cc
@donaldcampbelljr
update reporting, use proper pephub URL
19b24f8
@donaldcampbelljr
small tweaks to process_exclude_ranges.py script
e6e3ca1
@donaldcampbelljr
lint
f266f5d
donaldcampbelljr and others added 15 commits September 17, 2024 15:29
donaldcampbelljr
donaldcampbelljr reviewed Sep 20, 2024
View reviewed changes
docs/changelog.md Outdated
@@ -2,6 +2,12 @@

This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html) and [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) format.

# [0.4.0] - 2024-09-20
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fix version number/ensure accurate

donaldcampbelljr
donaldcampbelljr previously approved these changes Sep 20, 2024
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I made a change to the ref validator readme just now. Everything else looks good to go!

@donaldcampbelljr
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And tests should pass when new version of bbconf is released before this.

@khoroshevskyi khoroshevskyi merged commit 15be3e3 into main Oct 7, 2024
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@khoroshevskyi @donaldcampbelljr