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33 Open 16 Closed
33 Open 16 Closed
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Issues list

Speed up from O(n^2) iteration over all left/right primer hits in OffTargetDetector._to_amplicons
#94 opened Nov 18, 2024 by ameynert
Add a .contains(v) method to MinOptMax that returns true if min <= v <= max.
#92 opened Nov 15, 2024 by tfenne
1
Establish an API for VariantLookup classes
#88 opened Nov 14, 2024 by msto
@tfenne
Extract the body of the main for loop in build_primer_pairs() into an alternative constructor on PrimerPair
#85 opened Nov 13, 2024 by msto
@tfenne
Provide a default value to max_heterodimer_tm in build_primer_pairs()
#83 opened Nov 13, 2024 by msto
@tfenne
Decouple VariantLookup and variant-masking from Primer3
#82 opened Nov 11, 2024 by msto
@tfenne
1
Decouple OffTargetDetector from the prymer data structures
#81 opened Nov 11, 2024 by msto
@tfenne
1
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
ProTip! Follow long discussions with comments:>50.