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feat: Add option to output resulting plot in an html file by fxwiegand · Pull Request #14 · alignoth/alignoth · GitHub

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feat: Add option to output resulting plot in an html file - #14

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Aug 24, 2022
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feat: Add option to output resulting plot in an html file#14
johanneskoester merged 5 commits into
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fxwiegand commented Aug 16, 2022 •
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This PR introduces a new option --html that allows users to output the plot inserted into an otherwise plain html file like so:

cargo run -- -b ~/Downloads/HG00096.chrom11.ILLUMINA.bwa.GBR.low_coverage.20120522.bam -r ~/Downloads/hs37d5.fa -g 11:160400-161000 --html > plot.html

This PR also adds a link to an example of a generated plot so this also closes #2.

fxwiegand added the feature New feature or request label Aug 16, 2022
fxwiegand self-assigned this Aug 16, 2022
johanneskoester requested changes Aug 16, 2022
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Comment thread resources/plot.html.tera Outdated
johanneskoester requested changes Aug 17, 2022
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Choose a reason Spam Abuse Off Topic Outdated Duplicate Resolved Low Quality

We also need to point to the licenses of the three packages (BSD I think). Better not include those packages in the binary, but rather download them before the rendering. And then, in the HTML there should be links to the three packages github pages (where people can find the license). We can place these links into the vega embed menu: vega/vega-embed#156

codecov-commenter commented Aug 24, 2022

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Codecov Report

Merging #14 (96c253f) into main (a29febc) will decrease coverage by 4.21%.
The diff coverage is 0.00%.

❗ Current head 96c253f differs from pull request most recent head 041b886. Consider uploading reports for the commit 041b886 to get more accurate results

@@            Coverage Diff             @@
##             main      #14      +/-   ##
==========================================
- Coverage   82.96%   78.75%   -4.22%     
==========================================
  Files           3        3              
  Lines         411      433      +22     
==========================================
  Hits          341      341              
- Misses         70       92      +22
Impacted Files Coverage Δ
src/cli.rs 93.18% <ø> (ø)
src/main.rs 27.82% <0.00%> (-6.59%) ⬇️

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johanneskoester merged commit e36ebc4 into main Aug 24, 2022
johanneskoester deleted the html branch August 24, 2022 09:05
github-actions Bot mentioned this pull request Aug 24, 2022
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