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Improve the list of tools in the README.md #991

Merged
merged 2 commits into from
Jul 15, 2024
Merged

Improve the list of tools in the README.md #991

merged 2 commits into from
Jul 15, 2024

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@nh13 nh13 commented May 27, 2024

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@nh13 nh13 requested a review from tfenne May 27, 2024 16:25
@nh13 nh13 temporarily deployed to github-actions May 27, 2024 16:25 — with GitHub Actions Inactive
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codecov bot commented May 27, 2024

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 95.59%. Comparing base (d5b38ca) to head (a2cc61e).
Report is 3 commits behind head on main.

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@@            Coverage Diff             @@
##             main     #991      +/-   ##
==========================================
- Coverage   95.62%   95.59%   -0.03%     
==========================================
  Files         126      126              
  Lines        7364     7408      +44     
  Branches      500      504       +4     
==========================================
+ Hits         7042     7082      +40     
- Misses        322      326       +4     
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I really like the addition of links to make the documentation more discoverable and accessible

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README.md Outdated
Comment on lines 70 to 72
- Tools for working with Unique Molecular Indexes (UMIs, aka Molecular IDs or Molecular Barcodes):
- Annotating/Extract Umis from read-level data: [`FastqToBam`][fgbio-fastqtobam-link], [`AnnotateBamWithUmis`][fgbio-annotatebamwithumis-link], [`ExtractUmisFromBam`][fgbio-extractumisfrombam-link], and [`CopyUmiFromReadName`][fgbio-copyumifromreadname-link].
- Manipulate read-level data containing Umis: [`CorrectUmis`][fgbio-correctumis-link], [`GroupReadsByUmi`][fgbio-groupreadsbyumi-link], [`CallMolecularConsensusReads`][fgbio-callmolecularconsensusreads-link], [`CallDuplexConsensusReads`][fgbio-callduplexconsensusreads-link], and [`FilterConsensusReads`][fgbio-filterconsensusreads-link].
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Suggested change
- Tools for working with Unique Molecular Indexes (UMIs, aka Molecular IDs or Molecular Barcodes):
- Annotating/Extract Umis from read-level data: [`FastqToBam`][fgbio-fastqtobam-link], [`AnnotateBamWithUmis`][fgbio-annotatebamwithumis-link], [`ExtractUmisFromBam`][fgbio-extractumisfrombam-link], and [`CopyUmiFromReadName`][fgbio-copyumifromreadname-link].
- Manipulate read-level data containing Umis: [`CorrectUmis`][fgbio-correctumis-link], [`GroupReadsByUmi`][fgbio-groupreadsbyumi-link], [`CallMolecularConsensusReads`][fgbio-callmolecularconsensusreads-link], [`CallDuplexConsensusReads`][fgbio-callduplexconsensusreads-link], and [`FilterConsensusReads`][fgbio-filterconsensusreads-link].
- Tools for working with Unique Molecular Indexes (UMIs, aka Molecular IDs or Molecular Barcodes):
- Annotating/Extract UMIs from read-level data: [`FastqToBam`][fgbio-fastqtobam-link], [`AnnotateBamWithUmis`][fgbio-annotatebamwithumis-link], [`ExtractUmisFromBam`][fgbio-extractumisfrombam-link], and [`CopyUmiFromReadName`][fgbio-copyumifromreadname-link].
- Manipulate read-level data containing UMIs: [`CorrectUmis`][fgbio-correctumis-link], [`GroupReadsByUmi`][fgbio-groupreadsbyumi-link], [`CallMolecularConsensusReads`][fgbio-callmolecularconsensusreads-link], [`CallDuplexConsensusReads`][fgbio-callduplexconsensusreads-link], and [`FilterConsensusReads`][fgbio-filterconsensusreads-link].

Although UMI gets title cased in the tool names, I think it should be all caps in the docs (since it's an acronym)

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@nh13 nh13 temporarily deployed to github-actions July 15, 2024 21:31 — with GitHub Actions Inactive
@nh13 nh13 temporarily deployed to github-actions July 15, 2024 21:31 — with GitHub Actions Inactive
@nh13 nh13 merged commit 4331e0d into main Jul 15, 2024
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@nh13 nh13 deleted the nh13-list-of-tools branch July 15, 2024 21:58
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3 participants