Use of int8 for variant_contig results in integer overflow with fragmented reference genomes #584 #667
Conversation
This file contains 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
…ented reference genomes sgkit-dev#584
Codecov Report
@@ Coverage Diff @@
## main #667 +/- ##
=========================================
Coverage 100.00% 100.00%
=========================================
Files 36 36
Lines 2879 2886 +7
=========================================
+ Hits 2879 2886 +7
Continue to review full report at Codecov.
|
jeromekelleher
approved these changes
Sep 14, 2021
sgkit/utils.py
Outdated
| for dtype in (np.int8, np.int16, np.int32, np.int64): | ||
| if np.iinfo(dtype).min <= value <= np.iinfo(dtype).max: | ||
| return dtype | ||
| return None |
There was a problem hiding this comment.
This return None case basically can't happen, so why not raise an OverflowError here rather than requiring client code check the return value (C style)?
There was a problem hiding this comment.
Yes, that's much better. I've implemented this in pystatgen/sgkit@f63600f. Should be ready to go in now.
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Outdated suggestions cannot be applied.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.
Fixes #584
I've included a test that uses a VCF with >128 contigs to check that it correctly picks an appropriate dtype. I haven't added a way to override the dtype, as I'm not sure it's really needed. We could add it, but it would clutter the parameter list a bit.