8000 Release `v0.1.0` - Fender stratocaster by nleroy917 · Pull Request #48 · databio/gtars · GitHub
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Merged
merged 601 commits into from
Dec 3, 2024
Merged

Release v0.1.0 - Fender stratocaster #48

merged 601 commits into from
Dec 3, 2024

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nleroy917
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@nleroy917 nleroy917 commented Dec 3, 2024 •
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Release v0.1.0

This release will encompass a lot of changes... notably:

  • Rust implementation of uniwig that expands on the C++ version
    • Uniwig now accepts a single sorted .bed file, .narrowPeak file, or .bam file.
    • Outputs now include .wig, .npy, .bedGraph, and .bw
    • Accumulations can now be counted via .narrowPeak scoring
  • Rust implementation of igd ported from the C version (experimental).
  • Region scoring matrix calculation for region clustering
  • Fragment file splitter for pseudobulking

donaldcampbelljr and others added 30 commits October 10, 2024 16:17
@donaldcampbelljr
code cleanup remove unnecessary items
e051423
@donaldcampbelljr
revert count changes
90bec30
@donaldcampbelljr
fix accumulation issues
da90f3d
@donaldcampbelljr
remove rayon for now
518f97d
@donaldcampbelljr
Revert "remove rayon for now"
884e7b6 
This reverts commit 518f97d.
@donaldcampbelljr
add rayon parallel processing with -p flag and using pool.install
a0b2cfe
@donaldcampbelljr
fix npy meta file during parallel processing
04a77b0
@donaldcampbelljr
remove single chromosome wiggle files during combination step
d69d2a0
@donaldcampbelljr
implement FromStr for file type enum
84f3da1
@donaldcampbelljr
clarify file type
7ebcf07
@donaldcampbelljr
Merge branch 'dev' into dev_add_bam_uniwig
bd99ea4
@donaldcampbelljr
Merge pull request #31 from databio/dev_add_bam_uniwig
fbdac0b 
Performance improvements for writing to .wig files
@nleroy917
Merge branch 'dev' into pararead
6615dfd
@nleroy917
Merge pull request #35 from databio/pararead
b834993 
Add pseudobulking code
@nleroy917
fix Cargo.toml
99c204f
@nleroy917
create fragment file globber
7e3fc5b
@donaldcampbelljr
2nd fix issue where wiggle file can extend beyond chrom.sizes end, re…
8244ca6 
…-instate correct start position due to start-smoothing
@donaldcampbelljr
Merge remote-tracking branch 'origin/dev' into dev
2ab6b8f
@nleroy917
create more models/structs
649e98b
@nleroy917
build trees
99abd44
@nleroy917
implement the find-overlaps function for the consensus set
dddd778
@nleroy917
fix tests, set up scoring
cc6b8a3
@nleroy917
create fragment abstraction
7b3b01d
@donaldcampbelljr
add test for _start.wig output
0bbce39
@donaldcampbelljr
cargo fmt
932b30d
@donaldcampbelljr
add _core.wig output test
3de8a4b
@donaldcampbelljr
clean up igd warnings by removing unused variables
9d7aa83
@donaldcampbelljr
clean up remaining uniwig warnings
cbb418f
@nleroy917
finish the loop
cb48827
@nleroy917
safegaurd count matrix scoring
bc73511
@nleroy917
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nleroy917 commented Dec 3, 2024 •
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@donaldcampbelljr one test failing in uniwig and I think its probably something simple like a missing file...

Its fixed

@nleroy917 nleroy917 changed the title Release v0.0.16 - Fender Stratocaster Release v0.0.16 - Fender stratocaster Dec 3, 2024
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codecov bot commented Dec 3, 2024 •
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Codecov Report

Attention: Patch coverage is 67.57221% with 943 lines in your changes missing coverage. Please review.

Project coverage is 64.47%. Comparing base (4162f72) to head (e3cac35).
Report is 606 commits behind head on master.

Files with missing lines Patch % Lines
gtars/src/uniwig/counting.rs 45.38% 521 Missing ⚠️
gtars/src/uniwig/mod.rs 78.43% 187 Missing ⚠️
gtars/src/uniwig/cli.rs 0.00% 53 Missing ⚠️
gtars/src/scoring/cli.rs 0.00% 39 Missing ⚠️
gtars/src/fragsplit/cli.rs 0.00% 27 Missing ⚠️
gtars/src/igd/create.rs 44.44% 25 Missing ⚠️
gtars/src/scoring/fragment_scoring.rs 82.35% 15 Missing ⚠️
gtars/src/fragsplit/split.rs 85.71% 14 Missing ⚠️
gtars/src/fragsplit/map.rs 73.33% 12 Missing ⚠️
gtars/src/uniwig/reading.rs 95.52% 11 Missing ⚠️
... and 8 more
Additional details and impacted files 
@@             Coverage Diff             @@
##           master      #48       +/-   ##
===========================================
+ Coverage   49.05%   64.47%   +15.42%     
===========================================
  Files          18       36       +18     
  Lines        1580     5754     +4174     
===========================================
+ Hits          775     3710     +2935     
- Misses        805     2044     +1239

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

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R-CMD-Check is still failing... but we arnt ready to deploy to CRAN anyways
8891

@nleroy917 nleroy917 changed the title Release v0.0.16 - Fender stratocaster Release v0.1.0 - Fender stratocaster Dec 3, 2024
@nleroy917 nleroy917 merged commit 3c0e799 into master Dec 3, 2024
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3 participants
@nleroy917 @donaldcampbelljr @sanghoonio
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