fulcrumgenomics prymer issues

fulcrumgenomics / prymer

Python Primer Design Library

https://prymer.readthedocs.io/en/latest/

MIT License

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issues

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feat: ensure FileBasedVariantLookup is used as a context manager

#71 clintval opened 3 days ago
1
chore: export PickHybProbeOnly task

#70 msto opened 4 days ago
1
fix: Check against `HN` tag instead of `is_unmapped` property

#69 msto opened 5 days ago
0
Handling unmapped results in `BwaAlnInteractive._to_result`

#68 ameynert opened 5 days ago
1
`Primer3Input` should use task-specific information to assemble `Primer3InputTag` values

#67 emmcauley opened 6 days ago
0
Use `psyam.AlignedSegment.toString()` when reporting errors

#66 ameynert opened 1 week ago
0
feat: remove pysam and bwa warmup hack

#65 clintval closed 1 week ago
2
feat: use OffTargetDetector and ExecutableRunner as ContextManagers

#64 clintval closed 1 week ago
1
Update how primer3.py masks bases for variants

#63 tfenne opened 1 week ago
0
feat: Primer3 takes a list of VCFs instead of a VariantLookup object

#62 emmcauley opened 1 week ago
2
fix: change int weights to float weights, update doctest examples

#61 emmcauley closed 1 week ago
0
feat: add thermodynamic-related weights and parameters for `PickHybProbeOnly` task

#60 emmcauley opened 1 week ago
1
fix: `PrimerAndAmpliconWeights` should all be `float`s

#59 emmcauley closed 1 week ago
0
refine the `__iter__` method on `PrimerPair` to accomodate optional inclusion of a probe

#58 emmcauley opened 1 week ago
1
remove `PrimerLike` as a base class

#57 emmcauley opened 1 week ago
1
`doctest` usage examples should be more realistic

#56 emmcauley opened 1 week ago
0
`Primer.bases` should not be `None`

#55 emmcauley opened 1 week ago
0
Move module docs to class level for Primer, PrimerPair and any other single-class modules

#54 tfenne opened 1 week ago
0
`Primer3` should accept a variant lookup `Path`

#53 msto opened 1 week ago
3
feat: add PickHybProbeOnly logic to Primer3Task and Primer3Input

#52 emmcauley closed 2 weeks ago
1
refactor: Primer -> Oligo, PrimerLike -> OligoLike

#51 emmcauley closed 6 days ago
1
feat: `PickHybProbeOnly()` task in `prymer`

#50 emmcauley closed 1 week ago
2
feat: add `Probe` object to wrap probe design results from Primer3

#49 emmcauley closed 2 weeks ago
2
feat: add probe-specific logic to Primer3

#48 emmcauley closed 2 weeks ago
1
chore(release): bump to 2.2.0

#47 msto closed 2 weeks ago
1
doc: Expand the documentation for `OffTargetDetector`

#46 msto closed 2 weeks ago
1
Move the release process documentation into a `CONTRIBUTING.md`

#45 msto opened 2 weeks ago
1
feat: Add support for `min_primer_pair_hits` to `OffTargetDetector`

#44 msto closed 2 weeks ago
2
`OffTargetDetector` should relax the constraint that each primer pair have at least one hit in the reference

#43 msto closed 2 weeks ago
0
`PrimerPair` should be a `Metric`, same as `Primer`

#42 ameynert opened 2 weeks ago
0
There should be a way to view the logs that bwa emits

#41 clintval opened 2 weeks ago
1
Consider returning `pybedlite.overlap_detector.Interval` instead of `BedLikeCoords` from `Span`

#40 ameynert opened 2 weeks ago
0
refactor: Deprecate `build_and_pick_primer_pairs` and `pick_top_primer_pairs`

#39 msto opened 2 weeks ago
1
Remove `build_and_pick_primer_pairs()` and `pick_top_primer_pairs()`

#38 msto opened 2 weeks ago
0
refactor: export OffTargetDetector

#37 msto closed 2 weeks ago
3
refactor: export Primer3Parameters and Primer3Weights

#36 msto closed 2 weeks ago
1
feat: add `ProbeParameters()` to encapsulate settings for `PickHybProbeOnly` Primer3Task

#35 emmcauley closed 2 weeks ago
1
chore(release): bump to 2.1.1

#34 clintval closed 3 weeks ago
1
chore: on publish only upload prymer wheels

#33 clintval closed 3 weeks ago
1
feat: use bwa-aln-interactive and upgrade developer's docs

#32 clintval opened 3 weeks ago
7
chore(release): bump to 2.1.0

#31 clintval closed 3 weeks ago
1
Update README to refer to bioconda package for `bwa-aln-interactive`

#30 ameynert opened 3 weeks ago
0
chore: fix README publish prymer badge URL

#29 clintval closed 3 weeks ago
1
feat: add penalty weights for pick_hyb_probe task

#28 emmcauley closed 2 weeks ago
1
GitHub Action tests are using deprecated Mambaforge

#27 clintval opened 3 weeks ago
0
chore: fix PyPi trusted publishing in GitHub Actions

#26 clintval closed 3 weeks ago
3
fix: Executable path validation tests should not be dependent on the user environment

#25 msto closed 3 weeks ago
2
The `publish` badge on the home page is marked as failing

#24 msto closed 3 weeks ago
1
fix: Pad target region by `max_amplicon_length`

#23 msto closed 3 weeks ago
1
chore: Update lock file

#22 msto closed 3 weeks ago
1