Skip to content
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

Jump to bottom

Supercontig features en masse #2455

Closed
wants to merge 193 commits into from
Closed

Supercontig features en masse #2455

wants to merge 193 commits into from

Conversation

sammyjava
Copy link
Member

Details

Summary of pull request, including references to relevant tickets (if applicable).

Testing

Besides running unit tests, how can the reviewer test your feature / bug fix? Are there edge cases to be aware of?

Checklist

Before your pull request can be approved, be sure to check all boxes:

  • Passing unit test for new or updated code (if applicable)
  • Passes all tests – according to Travis
  • Documentation (if applicable)
  • Single purpose
  • Detailed commit messages
  • Well commented code
  • Checkstyle

@sammyjava
More project.xml options for GFF3Converter; GOTerm -> OntologyTerm
61882dd
@sammyjava
Added Supercontig to core model.
8126c3c
@sammyjava
Added supercontig and supercontigLocation to SequenceFeature.
1130f76
@sammyjava
Strain.name,accession,description; Organism.description
0cbaa0e
@sammyjava
Removed DEBUG output.
e1c45e9
@sammyjava
re-added licence handling
da97c31
@sammyjava
Update to allow additional optional GFF params in project.xml.
df7a77b
@sammyjava
Revert back to GOTerm for PR.
0ab9aaf
@sammyjava
Removed "HACK" comment which refers to something no longer here.
83d55a3
@sammyjava
Tweaked spacing for Travis.
44e2861
@sammyjava
Added Strain.identifier.
f73016f
@sammyjava
Strain.name -> Strain.identifier as key.
f94b596
@sammyjava
Bulk commit ahead of update to 4.1.2.
4142ab9
@sammyjava
Updated version to 4.1.2 (even though it's not yet).
783b480
@sammyjava
Removed conflicting files, to be restored.
52077c1
@sammyjava
Manual replacement of conflict files from 4.1.2.
ab5eead
@sammyjava
Merge pull request #1 from intermine/dev
8b3cc60 
Attempt to merge new 4.1.2 core into sammyjava
@sammyjava
My GFF3Converter.java.
c4fd505
@sammyjava
Added methods to return taxonId and strainIdentifier.
d370f3f
@sammyjava
Merge pull request #2 from intermine/dev
d8d2faf 
Merge from 4.1.3 patch
@sammyjava
Gotta have the Plant Ontology!
3b47e61
@sammyjava
Gotta have the plant trait ontology!
a2dd303
@sammyjava
Gotta have the soybean ontology!
4095e1d
@sammyjava
Include DataSet.description in properties file. We need it.
ea4bc83
@sammyjava
Added DataSet.description to properties file handling.
9ae0201
@sammyjava
Added assemblyVersion, annotationVersion and ontologyAnnotations.
3aa8eef
@sammyjava
Added Strain support; -FlyMine/ModMine; +DataSet.description.
e2c5238
@sammyjava
Added obo.ontology.description to properties.
71ba578
@sammyjava
Removed DEBUG.
1c15927
@sammyjava
Addtions of LENGTH and CONCAT to QueryExpression.
d5b8652
@sammyjava
Initial 5.1.0.3 updates.
dcf831d
@sammyjava
Add key for Chromosome/Supercontig.primaryIdentifier!
de0f4c2
@sammyjava
GenotypingPlatform as class.
be7e1f2
@sammyjava
Added gfa source.
9734fb0
@sammyjava
Delete existing flanking regions first to avoid dupes.
69d9c6d
@sammyjava
fasta/gfa/gff seem to be working with strain, assembly, annotation.
e7dde06
@sammyjava
gfa working as a proper BioFileConverter.
489bf42
@sammyjava
LinkageGroup, QTL identifier -> name
53b31ae
@sammyjava
Do both sides of GeneFamilyAssignment. Moved into method.
754e13b
@sammyjava
Removed geneFamilyAssignments reverse-reference (fixes bug).
4a3608e
@sammyjava
+SequenceFeature.ensemblName -Pathway.stableIdentifier +Trait.organism
9c1bdb8
@sammyjava
Moved PanGeneSet and collections from lis-pangeneset.
dec001c
@sammyjava
Yank some sources we aren't using that pollute the built datamodel.
874db71
@sammyjava
Yank chado-db which pollutes the built data model.
3fcccb5
@sammyjava
Don't need to yank actual code, just line in settings.gradle.
2de4a0d
@sammyjava
Just leave out of settings.gradle.
30f0450
@sammyjava
Only compile sources that LIS uses.
54a92f9
@sammyjava
Works for Chromosome and Supercontig features; no parallel.
7e1a1b9
@sammyjava
Merge pull request #12 from legumeinfo/transfer-sequences-supercontigs
2863e6f 
Works for Chromosome and Supercontig features; no parallel.
@sammyjava
Final serial version, mostly output cleanup, some code tidying.
217ee12
@sammyjava
Merge pull request #13 from legumeinfo/transfer-sequences-supercontigs
0aaf10d 
Final serial version, mostly output cleanup, some code tidying.
@sammyjava
Final housekeeping update. Fairly optimal, clean code.
a7d234a
@sammyjava
Don't transfer sequences for GeneticMarker.
c225a97
@sammyjava
Let's clean up deprecations.
9ae3867
@sammyjava
Final version methinks.
3383ed1
@sammyjava
Yanked CDSRegion.
ddc65da
@sammyjava
Cleaned up most compiler warnings.
2b3a120
@sammyjava
VASTLY faster handling of features on supercontigs.
05919ec
@sammyjava sammyjava closed this Dec 3, 2023
@sammyjava sammyjava deleted the supercontig-features-en-masse branch December 3, 2023 01:11
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers
No reviews
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.

None yet
2 participants
@sammyjava @adf-ncgr