Ecosyste.ms: Issues

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GitHub / Ferlab-Ste-Justine/datalake-lib issues and pull requests

#225 - Spark 3.5.1

Pull Request - State: closed - Opened by jecos 11 months ago

#224 - feat: BG-32 Update spark and java version

Pull Request - State: closed - Opened by jecos 12 months ago

#223 - Unic 1390

Pull Request - State: closed - Opened by laurabegin about 1 year ago

#222 - fix: SKFP-793 fix INFO_ANN filter for multi allelic

Pull Request - State: closed - Opened by celinepelletier about 1 year ago

#221 - fix(split): Use full join to keep all variants in case of filters

Pull Request - State: closed - Opened by laurabegin about 1 year ago

#220 - feat: BG-28 Refactor Frequencies to allow SimpleSplit computation

Pull Request - State: closed - Opened by laurabegin about 1 year ago

#219 - fix: CQDG-502 Enriched variants should left join with freqs

Pull Request - State: closed - Opened by laurabegin about 1 year ago

#218 - fix: Add companion object for all RuntimeETLContexts

Pull Request - State: closed - Opened by laurabegin about 1 year ago

#217 - feat: Add exists method to FileSystem trait

Pull Request - State: closed - Opened by laurabegin about 1 year ago

#216 - feat: Parse steps into a Seq of RunStep

Pull Request - State: closed - Opened by laurabegin about 1 year ago

#215 - Restore ETLSingleDestination in v2

Pull Request - State: closed - Opened by laurabegin about 1 year ago

#214 - feat: BG-26 Make ETL compatible with ID-based cdc

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

#213 - fix: Frequencies should filter input dataframe

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

#212 - feat: Add extraAggregations option + fix: package names

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

#211 - fix: Remove broadcasts from withPickedCsqPerLocus

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

#210 - feat: Add compact method to DeltaUtils

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

#209 - fix: BaseConsequences should allow subtype with any instance of BaseE…

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

#208 - feat: CLIN-2162 Add missing external references in enriched variants

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

#207 - fix: CLIN-1478 Rollback cosmic gene set to previous version

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

#206 - feat: UNIC-2182 Enrich variants with cosmic data

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

#205 - feat: CLIN-2182 Normalize Cosmic Mutation Set

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

#204 - fix(cosmic gene set): CLIN-1478 Cast start to Long

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

#203 - feat: CLIN-2182 New CosmicGeneSet Version

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

#202 - feat: CLIN-2152 Pass groupByColumns to BaseConsequences

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

#201 - fix: BG-24 pass basic auth to es client

Pull Request - State: closed - Opened by adipaul1981 over 1 year ago

#200 - feat/bg-22 Adding ClinVar Vep table

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

#199 - feat: BG-23 CreateTableAndView job

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

#198 - feat: Move spark3.file to commons + Add SparkSpec testutil

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

#197 - feat: Add some supported ReadOptions

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

#196 - feat: BG-20 Implement cacheRDD method

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

#195 - feat/bg-18 ACMG - Adding PP2

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

#194 - fix/clin-2119 Correctly separate MC in ClinVar parsing

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

#193 - feat/bg-17 ACMG - Adding BS2

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

#191 - feat/bg-16 ACMG - Adding PM2

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

#190 - feat: Refactor ETL classes and use command line parser for main classes

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

#189 - feat: Move models and class generator into test lib

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

#188 - Feat/get alias

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

#187 - feat: BG-12 Create a lib for test utils

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

#186 - fix: use sbt cache in setup-java

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

#185 - feat: adding BA1 criteria

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

#184 - feat: BG-10 use sttp for ES client

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

#183 - Es sttp

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

#182 - feat: CLIN-2026 - optional VCF

Pull Request - State: closed - Opened by creativeyann17 over 1 year ago

#181 - fix: UNIC-1134 Optionally clean replacement value in table name

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

#180 - Add search_text into gene_centric

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

#179 - HadoopFileSystem list + DatasetConf implicits

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

#178 - Add refseq protein id into enriched csq

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

#177 - Remove unnecessary fields from csq

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

#176 - Add filter on SNV

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

#175 - Max impact score

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

#174 - Calculate AF / PF in frequencies

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

#173 - Exclude chromosome M in gnomadV3

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

#172 - Fix ensembl mapping

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

#171 - Ensembl repartition

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

#170 - fix: CLIN-1946

Pull Request - State: closed - Opened by creativeyann17 over 1 year ago

#169 - cosmic

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

#168 - Fix Public tables

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

#167 - fix: CLIN-1946

Pull Request - State: closed - Opened by creativeyann17 over 1 year ago

#166 - Repartition for all ETL

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

#165 - fix: CLIN-1946 version

Pull Request - State: closed - Opened by creativeyann17 over 1 year ago

#164 - fix: CLIN-1946

Pull Request - State: closed - Opened by creativeyann17 over 1 year ago

#163 - Enrich variant and preapre variant centric

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

#162 - feat: CLIN-1946

Pull Request - State: closed - Opened by creativeyann17 over 1 year ago

#161 - feat: Utilities for frequencies

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

#160 - Removing file artifacts generated from tests

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

#159 - feat: Utilities for genomic consequences

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

#158 - UNIC-1067: add HL7 format

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

#157 - feat: UNIC-1041 Create database if not existing in ETL load

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

#156 - Add some genomic features from clin

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

#155 - fix: CLIN-1648 Set parental_origin to unknown for solo proband

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

#154 - feat(GenomicImplicits): CLIN-1756 Add withPickedCsqPerLocus

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

#153 - fix: CLIN-1788 DeltaLoader upsert isin condition

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

#153 - fix: CLIN-1788 DeltaLoader upsert isin condition

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

#152 - fix: CLIN-1788 Use <=> to check equality in DeltaLoader merge + scd1

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

#152 - fix: CLIN-1788 Use <=> to check equality in DeltaLoader merge + scd1

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

#151 - feat(datasetconf): update datasetconf signature

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

#150 - feat(datasetconf): update signature of datasetconf add new param

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

#150 - feat(datasetconf): update signature of datasetconf add new param

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

#149 - fix: eliminate duplicate into rare variant table

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

#149 - fix: eliminate duplicate into rare variant table

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

#148 - fix: typo in locusColumnNames

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

#148 - fix: typo in locusColumnNames

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

#147 - feat: CLIN-1758 Compound heterozygous and rare variants

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

#147 - feat: CLIN-1758 Compound heterozygous and rare variants

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

#146 - feat(upsert): dynamically build merge condition

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

#146 - feat(upsert): dynamically build merge condition

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

#145 - feat: UNIC-1071 Implement OverWritePartitionDynamic LoadType for Delta

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

#145 - feat: UNIC-1071 Implement OverWritePartitionDynamic LoadType for Delta

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

#143 - CLIN-1669

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

#143 - CLIN-1669

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

#142 - fix(spliceai): CLIN-1601 Increase enriched etl partition number

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

#142 - fix(spliceai): CLIN-1601 Increase enriched etl partition number

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

#141 - refactor(spliceai): CLIN-1601 Add Enriched ETL + Organize testmodels

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

#141 - refactor(spliceai): CLIN-1601 Add Enriched ETL + Organize testmodels

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

#140 - feat: CLIN-1601 Bump version to 5.1.0

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

#140 - feat: CLIN-1601 Bump version to 5.1.0

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

#139 - feat(spliceai): CLIN-1601 Import spliceai public tables

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