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add liftover methods #67

Merged
merged 8 commits into from
May 29, 2024
Merged

add liftover methods #67

merged 8 commits into from
May 29, 2024

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jharenza
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@jharenza jharenza commented May 7, 2024

Purpose

This PR adds gene symbol liftover methods

Issue

Closes #62

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Which areas should receive a particularly close look?

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Pull review checklist

Unless otherwise noted above, this PR will be considered ready for review when all four items have been checked.

Spellcheck Step

The dictionary used for spellchecking can be updated.
Edit the file in build/assets/custom-dictionary.txt by adding new entries to the end.
You do not need to change anything else.
However, if you want to update the first line to have an accurate count of words and you want to remove non-unique ones, run the following command from within build/assets on your favorite OS X or Linux machine:

(( len = $(awk '!a[$0]++' < custom-dictionary.txt | wc -l ) - 1 )); tmpfile="$(mktemp)"; echo "personal_ws-1.1 en $len utf-8" > $tmpfile; tail -n +2 custom-dictionary.txt | awk '!a[$0]++' >> $tmpfile; mv $tmpfile custom-dictionary.txt

jharenza and others added 2 commits May 6, 2024 20:37
Co-Authored-By: Dan Miller <dmiller15@users.noreply.github.com>
@jharenza jharenza requested a review from migbro May 7, 2024 00:39
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hi @migbro this pr is ready for review when you get a chance :)

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Click the link below to download the manuscript build as a ZIP file.
This build is associated with commit c10b81a.

Manuscript build

There were 5 spelling errors.
Check the build link above for details.

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Click the link below to download the manuscript build as a ZIP file.
This build is associated with commit fde8d53.

Manuscript build

There were 0 spelling errors.
Check the build link above for details.

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@migbro migbro left a comment

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Need to update link, should probably update the repo to point at the specific file as well

content/06.methods.md Outdated Show resolved Hide resolved
@migbro migbro self-requested a review May 21, 2024 14:59
migbro
migbro previously requested changes May 21, 2024
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Meant to request changes

@jharenza jharenza requested a review from migbro May 24, 2024 19:37
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@migbro link is updated, thanks!

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Click the link below to download the manuscript build as a ZIP file.
This build is associated with commit e19f6b6.

Manuscript build

There were 0 spelling errors.
Check the build link above for details.

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Click the link below to download the manuscript build as a ZIP file.
This build is associated with commit 61d9bc3.

Manuscript build

There were 0 spelling errors.
Check the build link above for details.

@jharenza jharenza requested a review from rjcorb May 29, 2024 16:46
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looks good to me!

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Click the link below to download the manuscript build as a ZIP file.
This build is associated with commit f994390.

Manuscript build

There were 0 spelling errors.
Check the build link above for details.

@jharenza jharenza dismissed migbro’s stale review May 29, 2024 16:55

@migbro skipped town ;) so @rjcorb did the re-review

@jharenza jharenza merged commit 3cfcb7b into main May 29, 2024
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@jharenza jharenza deleted the liftover branch May 29, 2024 16:55
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Updated manuscript: add liftover process
3 participants