Repository navigation
docs: find a gene's exons with bedspec and tidy the README's files and names - #2
Merged
Merged
Conversation
clintval
force-pushed
the
docs/bedspec-intervals
branch
from
October 27, 2026 01:17
94269ce to
f340e2d
Compare
clintval
force-pushed
the
docs/bedspec-intervals
branch
from
October 27, 2026 01:39
f340e2d to
56e130d
Compare
clintval
marked this pull request as ready for review
October 27, 2026 01:41
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Adds a README section, before Development and Testing, that finds the exons of a gene among per-target coverage rows with bedspec 4.3.0 and its new
bedspec.ext.captainslog.The example is the one in bedspec's README, and it runs under sybil like every other example, since bedspec
~=4.3joins the test group.Also in the README:
tests/data, through a fixture inconftest.py, so paths read as a user's own files, likepicard/hs.hs_metrics..txt. The Picard fixtures are renamed to match, andscripts/fixtures/make.shgives the outputs of the Picard tools that take only a prefix the.txtextension too, so regenerated fixtures keep these names.withthat opens two files.isize_metrics,isize_histogram, andinsert_size_histogram, in place ofisize(used for two different things) andhist.bedspec joins typeline in the packages exempt from the one-week
exclude-newerwindow, since both are released alongside captainslog.uv run poe check-allpasses: 1039 tests and 100% coverage.