Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / exomiser/svart issues and pull requests

#70 - Breakend unification

Pull Request - State: closed - Opened by julesjacobsen over 1 year ago

#69 - Add `VariantType.DELINS`

Issue - State: closed - Opened by julesjacobsen over 1 year ago - 2 comments

#66 - Improve GenomicAssemblies ergonomics

Issue - State: closed - Opened by julesjacobsen almost 2 years ago
Labels: enhancement

#65 - Maven central deployment error on Java 17

Issue - State: closed - Opened by julesjacobsen over 2 years ago - 1 comment

#64 - Some kind of breakend enhancement

Issue - State: closed - Opened by julesjacobsen over 2 years ago - 1 comment

#63 - Setup CI

Pull Request - State: closed - Opened by ielis over 2 years ago

#62 - Fix but in `BreakendVariant.mateId()`

Pull Request - State: closed - Opened by ielis over 2 years ago

#61 - `BreakendVariant.mateId()` returns `id()` of the right breakend.

Pull Request - State: closed - Opened by ielis over 2 years ago

#60 - `Bound` is no longer used

Issue - State: closed - Opened by ielis over 2 years ago - 1 comment
Labels: enhancement

#59 - `toString()` should include confidence interval data in default implementations

Issue - State: closed - Opened by ielis over 2 years ago
Labels: enhancement

#58 - Reduce `CoordinateSystem` to `ONE_BASED` and `ZERO_BASED`

Issue - State: closed - Opened by julesjacobsen almost 3 years ago - 1 comment

#57 - Rename `Variant` to `GenomicVariant`

Issue - State: closed - Opened by julesjacobsen almost 3 years ago

#56 - Bug in `VcfBreakendResolverTest`

Issue - State: closed - Opened by ielis almost 3 years ago - 1 comment
Labels: bug

#55 - Bug in `VariantTrimmer`

Issue - State: closed - Opened by ielis almost 3 years ago - 5 comments
Labels: bug

#54 - Use Coordinates instead of Position

Pull Request - State: open - Opened by ielis about 3 years ago - 4 comments

#53 - Bug in BreakendVariant?

Issue - State: closed - Opened by ielis over 3 years ago - 1 comment

#52 - MNV parse issue

Pull Request - State: open - Opened by ielis over 3 years ago

#51 - Change length calculation (or checking) might need a revision

Issue - State: closed - Opened by ielis over 3 years ago - 2 comments
Labels: bug

#50 - Thoughts about VcfConverter

Issue - State: closed - Opened by ielis over 3 years ago - 2 comments

#48 - Implement `distanceTo` for regions

Pull Request - State: closed - Opened by ielis over 3 years ago - 1 comment

#47 - Init the read the docs

Pull Request - State: closed - Opened by ielis over 3 years ago - 1 comment
Labels: documentation

#46 - Fix GenomicAssembly static constructor

Pull Request - State: closed - Opened by ielis over 3 years ago - 1 comment

#45 - Static constructor for GenomicAssembly should be static

Issue - State: closed - Opened by ielis over 3 years ago
Labels: bug

#44 - Setup Read the Docs

Issue - State: open - Opened by ielis over 3 years ago

#43 - Breakend creation

Issue - State: closed - Opened by ielis over 3 years ago - 4 comments

#42 - Open new issue on Nexus for Maven Central upload

Issue - State: closed - Opened by julesjacobsen over 3 years ago - 2 comments

#41 - Add a VcfVariantFactory class

Issue - State: closed - Opened by julesjacobsen over 3 years ago - 1 comment
Labels: enhancement

#40 - Define Variant.isSymbolic() and Variant.isBreakend() as different things?

Issue - State: closed - Opened by julesjacobsen over 3 years ago - 2 comments
Labels: question

#39 - Should BreakendVariants be able to implement 'withStrand'?

Issue - State: closed - Opened by julesjacobsen over 3 years ago - 2 comments
Labels: question

#37 - Add BreakendParser and tests

Pull Request - State: closed - Opened by ielis over 3 years ago - 3 comments

#36 - Add new VcfBreakendVariantParser/Builder

Issue - State: closed - Opened by julesjacobsen over 3 years ago - 1 comment

#32 - Remove SequenceVariant and SymbolicVariant classes

Issue - State: closed - Opened by julesjacobsen over 3 years ago

#31 - Should Contig *really* have an internal numeric id?

Issue - State: closed - Opened by julesjacobsen over 3 years ago - 4 comments
Labels: question

#30 - Null pointer exception thrown when converting variant with * in ALT allele

Issue - State: closed - Opened by ielis over 3 years ago - 4 comments
Labels: bug

#29 - Issues with DefaultVariant and non-trimmed VCF records

Issue - State: closed - Opened by ielis over 3 years ago - 6 comments
Labels: bug

#28 - Add convenience methods to Contig

Pull Request - State: closed - Opened by ielis over 3 years ago

#27 - Add GenomeAssemblies with human 37 and 38 p13 defaults

Issue - State: closed - Opened by julesjacobsen over 3 years ago - 2 comments
Labels: enhancement

#26 - Allow to lookup contig by all accessions

Issue - State: closed - Opened by ielis over 3 years ago - 2 comments

#25 - Zero-length regions (again)

Issue - State: closed - Opened by julesjacobsen over 3 years ago - 2 comments

#23 - Update Contig and GenomicAssembly to include...

Issue - State: closed - Opened by julesjacobsen almost 4 years ago

#22 - Add convenience methods to Stranded

Pull Request - State: closed - Opened by ielis almost 4 years ago
Labels: enhancement

#21 - Add BaseBreakendVariant

Issue - State: closed - Opened by julesjacobsen almost 4 years ago - 10 comments
Labels: enhancement

#20 - Add extensible builder to Base classes?

Issue - State: closed - Opened by julesjacobsen almost 4 years ago - 1 comment

#19 - Implement serializable?

Issue - State: closed - Opened by julesjacobsen almost 4 years ago - 3 comments

#18 - UnknownContig should have length 1

Issue - State: closed - Opened by julesjacobsen almost 4 years ago - 1 comment

#17 - Rename as 'svart'?

Issue - State: closed - Opened by julesjacobsen almost 4 years ago - 2 comments

#16 - Update README

Issue - State: closed - Opened by julesjacobsen almost 4 years ago

#15 - Unexpected results after converting empty ZERO_BASED GenomicRegion to ONE_BASED

Issue - State: closed - Opened by ielis almost 4 years ago - 5 comments
Labels: bug

#14 - Update JavaDocs

Issue - State: closed - Opened by julesjacobsen almost 4 years ago

#13 - Ignore `.idea` folder

Pull Request - State: closed - Opened by ielis almost 4 years ago

#12 - Add sanity checks for positions used to create `GenomicRegion`

Pull Request - State: closed - Opened by ielis almost 4 years ago

#11 - Genomic coordinate sanity check during instantiation of GenomicRegion

Issue - State: closed - Opened by ielis almost 4 years ago - 1 comment
Labels: bug

#10 - Allow to turn a GenomicPosition into a GenomicRegion

Pull Request - State: closed - Opened by ielis almost 4 years ago - 1 comment

#8 - Add GenomicRegionFormatter/VariantFormatter?

Issue - State: open - Opened by julesjacobsen almost 4 years ago
Labels: enhancement

#7 - Add abstract base classes for GenomicRegion, GenomicPosition, Variant

Issue - State: closed - Opened by julesjacobsen almost 4 years ago - 1 comment

#6 - Properly modularise the package

Issue - State: closed - Opened by julesjacobsen almost 4 years ago - 2 comments

#5 - Delete unused classes? Adjacency and SequenceRearrangement

Issue - State: closed - Opened by julesjacobsen almost 4 years ago - 3 comments

#4 - Package-private scope prevents from running tests from command line

Issue - State: closed - Opened by ielis almost 4 years ago - 6 comments

#3 - Tweaks

Pull Request - State: closed - Opened by ielis almost 4 years ago - 2 comments

#2 - Pass through the code

Pull Request - State: closed - Opened by ielis almost 4 years ago

#1 - `ConfidenceInterval` needs to support flipping to the opposite strand

Issue - State: closed - Opened by ielis almost 4 years ago - 1 comment
Labels: enhancement