fix: use is not None for region boundary checks in _subset_genome_sequence_region#1082
Open
Carbon14-48 wants to merge 1 commit intomalariagen:masterfrom
Open
Conversation
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
1 participant
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Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be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.
What
Fixed region boundary checks in
_subset_genome_sequence_region()inplasmodium.py,and fixed a typo in the docstring ("Sebset" → "Subset").
Why
The current code uses
if region.start:andif region.end:to check whetherregion boundaries are set. In Python,
0is falsy, so when a user queries aregion starting at position 0, the slicing is silently skipped and the full
contig is returned instead.
This is the same class of bug as described in #940 for the Anopheles side
(
snp_data.py/hap_data.py), but this instance in the Plasmodium codewas not covered there.
Fix
Replaced
if region.start:withif region.start is not None:(and samefor
region.end) to correctly distinguish between "no boundary specified"(None) and "boundary is zero" (0).