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pha4ge
/
primaschema
Infrastructure for tiled amplicon PCR primer scheme definitions
MIT License
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Validate schemes pass through common tooling without problems
#57
bede
opened
1 month ago
1
Automatically generate single chrom tiled subsets for multi chrom schemes
#56
bede
opened
1 month ago
1
Use JSON not YAML for schemes manifest in primer-schemes repo root
#55
bede
closed
1 month ago
1
Add region mask to model (follow up to #52)
#54
bede
closed
1 month ago
0
Validate organism/taxon
#53
bede
opened
1 month ago
0
Add region mask [WIP]
#52
pvanheus
closed
1 month ago
1
Merge v1a (1.0.0a0) into main
#51
bede
closed
1 month ago
0
validate derived_from field
#50
bede
opened
1 month ago
1
Use lowercase for scheme name aliases in info.yml
#49
bede
opened
1 month ago
2
Support for primer.bed preamble/comments
#48
bede
opened
1 month ago
0
Automate creation of `definition_url`
#47
bede
opened
1 month ago
0
Decision, guidance on versioning schemes e.g. `v1` vs `v1.0.0`
#46
bede
closed
1 month ago
1
Allow primer-schemes repository override using environment variable
#45
bede
closed
1 month ago
1
Rename organism to taxon
#44
bede
opened
1 month ago
1
Test coverage for all subcommands
#43
bede
opened
1 month ago
0
Bundle schemas with primaschema using package_data
#42
bede
opened
1 month ago
0
Agree new manifest format
#41
bede
opened
1 month ago
0
CI: Update index.yml manifest on push
#40
bede
opened
2 months ago
1
Create PR templates for new schemes
#39
bede
opened
2 months ago
0
V1 documentation
#38
bede
opened
2 months ago
1
Detect duplicate primer names
#37
bede
closed
2 months ago
1
Validate samtools ampliconclip and ampliconstats compatibility
#36
bede
closed
2 months ago
2
Validate BED contents using Pydantic
#35
bede
closed
2 months ago
1
Validate scheme tiling
#34
bede
closed
2 months ago
1
Optionally plot during build
#33
bede
closed
1 month ago
1
Include primaschema plot output in scheme directory
#32
bede
closed
1 month ago
2
Automatically fetch and cache PHA4GE primer-schemes repo into platform-appropriate path
#31
bede
closed
1 month ago
1
YAML often parsed directly without schema, meaning chaotic type inference and loss of optional fields with defaults
#30
bede
closed
1 month ago
1
Simplify build-manifest
#29
pvanheus
closed
2 months ago
2
Convert manifest schema to linkml
#28
bede
closed
1 month ago
0
Source manifest header yaml from file
#27
bede
closed
2 months ago
2
Seperate version field and new manifest format
#26
bede
closed
2 months ago
0
Normalise, validate to ACGT (not U) and throw exception for ambiguous nucleotides
#25
bede
opened
3 months ago
1
Validate that chroms and coords in primer.bed exist in reference.fasta (primaschema validate)
#24
bede
closed
2 months ago
1
Subcommand to plot bed records
#23
bede
closed
2 months ago
2
Fix validation regression
#22
bede
closed
2 months ago
2
Add subcommand to print intervals spanned by primers
#21
pvanheus
closed
4 months ago
1
Redundant LinkML model generation during recursive scheme validation
#20
bede
closed
1 month ago
2
Model validation requires network connectivity
#19
bede
closed
1 month ago
2
List and get subcommands
#18
bede
opened
11 months ago
2
Allow querying schemes by name alias(es)
#17
bede
opened
11 months ago
0
Add diff mode to compute difference only using primer positions
#15
pvanheus
closed
5 months ago
1
Make recursive-build --nested output match primer-schemes dir structure
#14
bede
closed
2 months ago
1
Silence annoying INFO messages from LinkML during validation
#13
bede
closed
2 months ago
1
Validate primer naming?
#12
bede
closed
2 months ago
1
Check URLs during validation
#11
bede
opened
1 year ago
3
Move JSON schemas into primer-schemes repo
#10
bede
closed
4 months ago
1
Autogen manifest from scheme assets
#9
bede
closed
1 year ago
1
Schema update: Remove latest_version, add deprecated
#8
pvanheus
closed
1 year ago
1
Rigorous BED validation
#7
bede
closed
1 year ago
0
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