Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Additional functionality #28

Open
wants to merge 12 commits into
base: master
Choose a base branch
from
Open

Additional functionality #28

wants to merge 12 commits into from

Conversation

kevinmhadi
Copy link
Collaborator

@kevinmhadi kevinmhadi commented Mar 23, 2021 •
edited
Loading

update to gr.findoverlaps(by = ...). Much more efficient for big queries to be matched per levels specified in "by" metadata field. Previously, by queries first search for all possible overlaps and then filters on matching by queries. The newer implementation uses constructor function gr_construct_by which enables findOverlaps to search for overlaps only within factor levels rather than post-filtering.

Also added gaps functionality for GRangesLists. gr.setdiff2(by = ...) makes use of both gaps with grangeslists and also the new by implementation. New method gr.spreduce reduces by levels of a metadata field.

Also gr.start, gr.end, gr.flipstrand, are all now modified to work with grangeslists

@imielinski
Copy link
Collaborator

imielinski commented Mar 23, 2021 via email

@codecov
Copy link

codecov bot commented Mar 24, 2021

Codecov Report

Merging #28 (609dffe) into master (f58b915) will decrease coverage by 7.91%.
The diff coverage is 20.52%.

❗ Current head 609dffe differs from pull request most recent head 666f2ed. Consider uploading reports for the commit 666f2ed to get more accurate results
Impacted file tree graph

@@            Coverage Diff             @@
##           master      #28      +/-   ##
==========================================
- Coverage   74.71%   66.79%   -7.92%     
==========================================
  Files           1        1              
  Lines        1574     1801     +227     
==========================================
+ Hits         1176     1203      +27     
- Misses        398      598     +200
Impacted Files Coverage Δ
R/gUtils.R 66.79% <20.52%> (-7.92%) ⬇️

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update f58b915...666f2ed. Read the comment docs.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers
No reviews
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
2 participants
@kevinmhadi @imielinski