Skip to content

Issues: fulcrumgenomics/prymer

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

28 Open 15 Closed
28 Open 15 Closed
Author
Filter by author
Loading
Label
Filter by label
Loading
Use alt + click/return to exclude labels
or ⇧ + click/return for logical OR
Projects
Filter by project
Loading
Milestones
Filter by milestone
Loading
Assignee
Filter by who’s assigned
Sort
Sort by
Newest Oldest Most commented Least commented Recently updated Least recently updated Best match
Most reactions
👍 👎 😄 🎉 😕 ❤️ 🚀 👀

Issues list

Decouple VariantLookup and variant-masking from Primer3
#82 opened Nov 11, 2024 by msto
@tfenne
Decouple OffTargetDetector from the prymer data structures
#81 opened Nov 11, 2024 by msto
@tfenne
Add a gc or gc_content attribute or property to Oligo
#80 opened Nov 8, 2024 by msto
@tfenne
Consider exposing the attributes of an Oligo's span as Oligo properties
#78 opened Nov 7, 2024 by msto
@tfenne
Add a post-init check to PrimerPair to verify that the pair's amplicon and sequence have the same length
#77 opened Nov 6, 2024 by msto
@tfenne
1
Consider OffTargetDetector._to_amplicons specifying alignment strand for primer pairs
#76 opened Oct 28, 2024 by ameynert
1
Local mkdocs issues
#72 opened Oct 15, 2024 by msto
@nh13
1
Primer3Input should use task-specific information to assemble Primer3InputTag values
#67 opened Oct 7, 2024 by emmcauley
Use psyam.AlignedSegment.toString() when reporting errors
#66 opened Oct 4, 2024 by ameynert
Update how primer3.py masks bases for variants
#63 opened Oct 4, 2024 by tfenne
refine the __iter__ method on PrimerPair to accomodate optional inclusion of a probe priority: higher/high
#58 opened Oct 2, 2024 by emmcauley
@emmcauley
1
remove PrimerLike as a base class discussion
#57 opened Oct 2, 2024 by emmcauley
1
doctest usage examples should be more realistic priority: medium
#56 opened Oct 2, 2024 by emmcauley
Primer.bases should not be None priority: higher/high
#55 opened Oct 2, 2024 by emmcauley
@emmcauley
Move module docs to class level for Primer, PrimerPair and any other single-class modules priority: low
#54 opened Oct 2, 2024 by tfenne
Primer3 should accept a variant lookup Path priority: medium
#53 opened Sep 30, 2024 by msto
1
@tfenne
3
PrimerPair should be a Metric, same as Primer
#42 opened Sep 23, 2024 by ameynert
There should be a way to view the logs that bwa emits priority: medium
#41 opened Sep 23, 2024 by clintval
1
Consider returning pybedlite.overlap_detector.Interval instead of BedLikeCoords from Span
#40 opened Sep 23, 2024 by ameynert
Error messages are not always propagated through primer3_error
#15 opened Sep 18, 2024 by msto
@tfenne
2
feat: add standalone calculation functions for thermodynamics
#14 opened Sep 17, 2024 by ameynert
docs: add additional context to BwaAlnInteractive about reverse-complementing queries
#13 opened Sep 17, 2024 by emmcauley
feat: add check_primers Primer3Task priority: higher/high
#12 opened Sep 16, 2024 by emmcauley
@emmcauley
feat: add pick_hyb_probe_only Primer3Task priority: higher/high
#11 opened Sep 16, 2024 by emmcauley
1
@emmcauley
Should OffTargetDetector.mappings_of() return a dict[Primer, BwaResult] instead of dict[str, BwaResult]?
#10 opened Aug 22, 2024 by emmcauley
2
ProTip! What’s not been updated in a month: updated:<2024-10-13.