Ecosyste.ms: Issues

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

GitHub / opencb/biodata issues and pull requests

#247 - TASK-1111 Add Pharmagenomics data to CellBase

Pull Request - State: open - Opened by jtarraga over 1 year ago - 1 comment

#246 - TASK-4163

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

#245 - TASK-4150 - Role in cancer info missing from gene-census disease panel

Pull Request - State: open - Opened by pfurio over 1 year ago - 1 comment

#244 - TASK-2241 Update Exomiser docker image to 13.1.0

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

#242 - TASK-3809 Fix variant annotation for consequence types

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

#241 - TASK-3809 Fix variant annotation for consequence types

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

#240 - TASK-3953 - CI/CD in task.yml to deploy project dependencies

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

#239 - TASK-2270

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

#238 - TASK-2549 - Role and modeOfInheritance changes in Panel data model

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

#237 - TASK-2274 HRDetect analysis for mutational signatures

Pull Request - State: closed - Opened by jtarraga almost 2 years ago - 1 comment

#236 - TASK-2242 Improve mutational signature analysis

Pull Request - State: closed - Opened by jtarraga almost 2 years ago - 1 comment

#235 - TASK-2294 - Include homalt count from aggregated vcf files

Pull Request - State: closed - Opened by j-coll almost 2 years ago - 1 comment

#234 - build(deps): bump htsjdk from 2.23.0 to 3.0.1

Pull Request - State: open - Opened by dependabot[bot] almost 2 years ago
Labels: dependencies

#233 - TASK-2342 - Error at variant-index "SQLException: ERROR 201 (22000): Illegal data"

Pull Request - State: closed - Opened by j-coll almost 2 years ago - 1 comment

#232 - remove VUS, it's a duplicate of uncertain significance

Pull Request - State: open - Opened by julie-sullivan almost 2 years ago

#231 - TASK-2242

Pull Request - State: open - Opened by jtarraga almost 2 years ago - 1 comment

#230 - TASK-2215 Fix family quality control (relatedness) when saving in OpenCGA catalog

Pull Request - State: closed - Opened by jtarraga almost 2 years ago - 1 comment

#229 - REVERT removing bigwig

Pull Request - State: closed - Opened by julie-sullivan almost 2 years ago

#228 - TASK-2152

Pull Request - State: closed - Opened by jtarraga about 2 years ago - 1 comment

#227 - build(deps): bump protobuf-java from 3.11.4 to 3.16.3

Pull Request - State: open - Opened by dependabot[bot] about 2 years ago
Labels: dependencies

#226 - TASK-1573

Pull Request - State: closed - Opened by jtarraga about 2 years ago - 1 comment

#225 - Hotfix 1.5.x - remove bigwig entirely

Pull Request - State: closed - Opened by julie-sullivan about 2 years ago

#224 - TASK-2103

Pull Request - State: closed - Opened by jtarraga about 2 years ago - 1 comment

#223 - TASK-1573 Show FUSION in Role In Cancer column

Pull Request - State: closed - Opened by jtarraga about 2 years ago - 2 comments

#222 - TASK-2094 - ClassNotFoundException: org.apache.commons.collections.CollectionUtils

Pull Request - State: closed - Opened by j-coll about 2 years ago - 1 comment

#221 - TASK-2041

Pull Request - State: closed - Opened by jtarraga about 2 years ago - 1 comment

#220 - TASK-1705

Pull Request - State: closed - Opened by jtarraga about 2 years ago - 1 comment

#219 - TASK-2017

Pull Request - State: closed - Opened by pfurio about 2 years ago - 1 comment

#218 - TASK-1988

Pull Request - State: closed - Opened by j-coll about 2 years ago - 1 comment

#217 - TASK-1935

Pull Request - State: closed - Opened by j-coll about 2 years ago - 1 comment

#216 - include common-lang3 and commons-collections in pox.xml #TASK-1625

Pull Request - State: closed - Opened by phamidko about 2 years ago - 1 comment

#215 - TASK-1194

Pull Request - State: closed - Opened by pfurio about 2 years ago - 1 comment

#214 - TASK-1472

Pull Request - State: closed - Opened by pfurio about 2 years ago - 1 comment

#213 - TASK-1092

Pull Request - State: closed - Opened by j-coll about 2 years ago - 1 comment

#212 - TASK-558

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

#211 - TASK-558

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

#210 - TASK-888

Pull Request - State: closed - Opened by jtarraga over 2 years ago - 1 comment

#209 - TASK-476

Pull Request - State: closed - Opened by pfurio over 2 years ago - 1 comment

#208 - upgrade log4j

Pull Request - State: closed - Opened by julie-sullivan over 2 years ago - 1 comment

#207 - TASK-552

Pull Request - State: closed - Opened by pfurio over 2 years ago - 1 comment

#206 - TASK-506

Pull Request - State: closed - Opened by imedina over 2 years ago - 1 comment

#205 - TASK-426

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

#204 - Support for clinical variant evidence reviews

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

#203 - build(deps): bump protobuf-java from 3.9.2 to 3.16.1

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 1 comment
Labels: dependencies

#202 - Add variant splice data models (e.g., SpliceAI scores)

Issue - State: open - Opened by jtarraga over 3 years ago
Labels: enhancement

#201 - Improve the mutational signature data model

Issue - State: open - Opened by jtarraga over 3 years ago
Labels: enhancement

#200 - Update the data models for alignment quality control metrics

Issue - State: closed - Opened by jtarraga over 3 years ago
Labels: enhancement, task

#199 - Create the Circos plot model

Issue - State: closed - Opened by jtarraga over 3 years ago
Labels: enhancement

#198 - merge in MNV fixes from hotfix 1.5.x branch

Pull Request - State: open - Opened by julie-sullivan over 3 years ago - 1 comment
Labels: bug

#197 - Hotfix 1.5.x - fix MNV coordinates

Pull Request - State: closed - Opened by julie-sullivan over 3 years ago
Labels: bug

#196 - fix Pair issue (again?)

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

#195 - Calculate and add VAF during variant normalisation

Issue - State: open - Opened by imedina over 3 years ago
Labels: enhancement

#194 - Do not decompose multiallelic Spanning Deletions when normalizing

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

#193 - Modify VariantType enum

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

#192 - build(deps): bump junit from 4.12 to 4.13.1

Pull Request - State: closed - Opened by dependabot[bot] almost 4 years ago
Labels: dependencies

#191 - Add VariantNormalizerExtensions

Issue - State: open - Opened by j-coll about 4 years ago
Labels: enhancement

#190 - add gnomad constraints and mirna targets to variant annotation

Pull Request - State: closed - Opened by julie-sullivan about 4 years ago

#189 - Implement new clinical objects

Issue - State: open - Opened by jtarraga about 4 years ago
Labels: enhancement

#188 - fix-mnv-protein-level-clinical-search: bugfix. Attributes now initial…

Pull Request - State: closed - Opened by javild over 4 years ago

#187 - Consolidate quality control stats

Issue - State: open - Opened by imedina over 4 years ago
Labels: task

#186 - Improve gene coverage stats

Issue - State: closed - Opened by jtarraga over 4 years ago
Labels: enhancement

#185 - Update clinical data models

Issue - State: closed - Opened by jtarraga over 4 years ago
Labels: enhancement

#184 - Data model for the alignment stats

Issue - State: open - Opened by jtarraga over 4 years ago
Labels: enhancement

#183 - Parse external panels to DiseasePanel

Issue - State: closed - Opened by pfurio over 4 years ago
Labels: enhancement

#182 - VariantSetStats and SampleVariantStats model changes

Issue - State: open - Opened by j-coll over 4 years ago

#181 - Upgrade htsjdk version to 2.21.3

Issue - State: closed - Opened by j-coll over 4 years ago
Labels: enhancement

#180 - avro/Cytoband and core/Cytoband - do we need both?

Issue - State: open - Opened by julie-sullivan over 4 years ago - 1 comment
Labels: question

#179 - StudyEntry model changes

Issue - State: open - Opened by j-coll over 4 years ago
Labels: enhancement

#178 - update uniprot

Pull Request - State: closed - Opened by julie-sullivan over 4 years ago
Labels: enhancement

#177 - Add list of "IssueEntry" to StudyEntry

Issue - State: open - Opened by j-coll over 4 years ago
Labels: enhancement

#176 - Store VCF ID value as a FileEntry attribute

Issue - State: open - Opened by j-coll over 4 years ago - 1 comment
Labels: enhancement

#175 - Change Region.parse when missing END

Issue - State: closed - Opened by j-coll over 4 years ago

#174 - Add FilterCount and QualityAverage to VariantStats

Issue - State: open - Opened by j-coll over 4 years ago
Labels: enhancement

#173 - add equals() to make unit testing easier

Pull Request - State: closed - Opened by julie-sullivan almost 5 years ago
Labels: enhancement

#172 - Replace Pair with alternative class

Issue - State: open - Opened by julie-sullivan almost 5 years ago - 2 comments
Labels: question

#171 - Add constraint scores to the data model

Pull Request - State: closed - Opened by julie-sullivan almost 5 years ago

#170 - Generate missing reference blocks with missing genotypes

Issue - State: open - Opened by j-coll about 5 years ago
Labels: enhancement

#169 - Refactor reported variant creators (for clinical interpretations)

Issue - State: open - Opened by jtarraga over 5 years ago
Labels: enhancement

#168 - Feature 398 phased variants

Pull Request - State: closed - Opened by javild over 5 years ago

#167 - Feature 398 phased variants

Pull Request - State: closed - Opened by javild over 5 years ago - 1 comment

#166 - Ignore genotype phase when calculating VariantStats

Issue - State: closed - Opened by j-coll over 5 years ago
Labels: enhancement

#165 - CRAM support

Issue - State: closed - Opened by jtarraga over 5 years ago
Labels: enhancement, task

#164 - Implement variant sample stats

Issue - State: open - Opened by jtarraga almost 6 years ago
Labels: enhancement, task

#163 - Implement IBD algorithm

Issue - State: open - Opened by jtarraga almost 6 years ago
Labels: enhancement, task

#162 - Support symbolic alternate <*> and <NON_REF> as NO_VARIATION

Issue - State: open - Opened by j-coll about 6 years ago
Labels: enhancement

#161 - Use BlockCompressedIndexedFastaSequenceFile for LeftAlignment

Issue - State: closed - Opened by j-coll over 6 years ago - 1 comment
Labels: enhancement

#160 - Put repositories in an optional profile

Pull Request - State: closed - Opened by kevinpetersavage over 6 years ago

#159 - Implement a limit in BamIterators

Issue - State: closed - Opened by imedina over 6 years ago
Labels: task

#158 - Upgrade protobuf and gRPC

Issue - State: closed - Opened by imedina over 6 years ago
Labels: task

#157 - Remove deprecated and old code

Issue - State: open - Opened by imedina over 6 years ago
Labels: task

#156 - How to get a valid version?

Issue - State: closed - Opened by renyaoxiang almost 7 years ago - 8 comments
Labels: question

#155 - Improve BAM queries and coverage

Issue - State: closed - Opened by imedina almost 7 years ago
Labels: enhancement

#154 - Clean VariantStats and add VariantScore data models

Issue - State: closed - Opened by j-coll about 7 years ago
Labels: enhancement

#153 - Create VariantBuilder

Issue - State: closed - Opened by j-coll about 7 years ago
Labels: enhancement

#153 - Create VariantBuilder

Issue - State: closed - Opened by j-coll about 7 years ago
Labels: enhancement

#152 - VCF exporter implementation

Issue - State: closed - Opened by jtarraga about 7 years ago
Labels: enhancement, task

#151 - Improve and complete VariantMetadata models

Issue - State: closed - Opened by j-coll about 7 years ago
Labels: enhancement

#144 - Implement parsing of aggregated frequencies as provided by DiscovEHR

Issue - State: open - Opened by javild over 7 years ago
Labels: enhancement

#137 - Implement the functionality 'index' for Wig files

Issue - State: closed - Opened by jtarraga almost 8 years ago
Labels: enhancement