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V2.0.0 dev #4
V2.0.0 dev #4
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…o be build 38 coordinates. Using broad institute liftover online tool
… allows patient sample to be tested using make test_sample
…lcs to fh.py generated ones
…calcs to fh.py generated ones
made a note of how the genomic coordinates used are now for build 38
Removed notes to self. Added note in PRS(object) docstring that notes the paper this class was based on originally used build 37 genomic coordinates for the SNPs, whereas the v2.0.0 version of this script uses build 38 genomic coordinates.
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Reviewed 6 of 6 files at r1, all commit messages.
Reviewable status: all files reviewed, 3 unresolved discussions (waiting on @isabelrem)
-- commits
line 20 at r1:
Suggestion for future work - it is best practice to use the imperative voice in your commit messages
Makefile
line 23 at r1 (raw file):
build: docker build -t $(IMG_VERSIONED) . #docker buildx build --platform linux/amd64 -t $(IMG_VERSIONED) .
Is this required?
README
line 1 at r1 (raw file):
# FH-PRS v2.0.0
Suggestion to not include version numbers in the readme - this is denoted in the release information and tags. It can easily get out of date when written manually in documentation like this
Remove unnecessary comment
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I've cleaned up the things you pointed out (version number in readme, a comment in the make file) and I've also swapped out the 'docker build -t fhprs .' in the readme file to 'make build', since the make file will do the same thing with less input required from the user and therefore less opportunity for mistake.
Thanks!
Reviewable status: 4 of 6 files reviewed, 3 unresolved discussions (waiting on @RachelDuffin)
Previously, RachelDuffin wrote…
Suggestion for future work - it is best practice to use the imperative voice in your commit messages
Thanks for this tip - I'll do my best to remember this in the future. I have also used the imperative voice in the commit messages I've written since.
Makefile
line 23 at r1 (raw file):
Previously, RachelDuffin wrote…
Is this required?
If you're referring to the comment, no it is not - I've now removed this. Good catch!
README
line 1 at r1 (raw file):
Previously, RachelDuffin wrote…
Suggestion to not include version numbers in the readme - this is denoted in the release information and tags. It can easily get out of date when written manually in documentation like this
Thanks for the tip, I've since removed the version number from the readme.
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This Looks great - well done Isabel!
Reviewed 2 of 2 files at r2, all commit messages.
Reviewable status: complete! all files reviewed, all discussions resolved (waiting on @isabelrem)
This change is