GenomicsDB/GenomicsDB issues and pull requests

#336 - Expose a finalize from genomicsdb api for the processor callback

Pull Request - State: closed - Opened by nalinigans 4 months ago - 1 comment

#335 - Fix http links in Readme

Pull Request - State: open - Opened by nalinigans 5 months ago

#334 - Release memory associated with genomicsdb array from VariantQueryProcessor destructor

Pull Request - State: closed - Opened by nalinigans 5 months ago

#333 - Revert to jammy due to size issues

Pull Request - State: closed - Opened by mlathara 5 months ago

#332 - Allow for GT to be a nocall if GQ and PL[0] are zero instead of homref

Pull Request - State: closed - Opened by nalinigans 6 months ago - 2 comments

#331 - Docker build fixes

Pull Request - State: closed - Opened by mlathara 7 months ago - 1 comment

#330 - Support single cross architecture build for MacOS/htslib

Pull Request - State: closed - Opened by nalinigans 7 months ago - 1 comment

#329 - Moving to 24.04 for the docker builds is broken.

Issue - State: open - Opened by nalinigans 7 months ago

#328 - Link OpenSSL libraries right in the end to allow for various lib dependencies to be resolved

Pull Request - State: closed - Opened by nalinigans 7 months ago - 1 comment

#327 - Bump to ubuntu 24.05

Pull Request - State: closed - Opened by mlathara 7 months ago - 3 comments

#326 - Minor json format fix

Pull Request - State: closed - Opened by mlathara 7 months ago - 1 comment

#325 - Turn off HDFS support by default

Pull Request - State: closed - Opened by nalinigans 8 months ago - 1 comment

#324 - Check pointers before deferencing

Pull Request - State: closed - Opened by nalinigans 8 months ago - 1 comment

#323 - Support a samples list for json output in api queries

Pull Request - State: closed - Opened by nalinigans 9 months ago - 1 comment

#322 - Catch JNI importer exceptions and propagate them as java IOExceptions

Pull Request - State: closed - Opened by nalinigans 9 months ago - 1 comment

#321 - OpenJDK 17 seems to want explicit type match for Assert.assertEquals

Pull Request - State: closed - Opened by nalinigans 10 months ago - 1 comment

#320 - Add REF to payloads returned by the json processor api

Pull Request - State: closed - Opened by nalinigans 10 months ago - 1 comment

#319 - Build changes to support MacOS universal builds

Pull Request - State: closed - Opened by nalinigans 10 months ago - 2 comments

#318 - Support JSON output from genomicsdb api query_variant_calls()

Pull Request - State: closed - Opened by nalinigans 10 months ago - 1 comment

#317 - Ambiguous call to Assert in the tests

Issue - State: open - Opened by pgrt 10 months ago - 1 comment

#316 - Allow for a protobuf QueryConfiguration or ExportConfiguration arg to query_variant_calls

Pull Request - State: closed - Opened by nalinigans 11 months ago - 1 comment

#315 - The compatibility of array_schema.cc

Issue - State: open - Opened by MiyaaL 11 months ago - 1 comment

#314 - Cleanup compile warnings with both gcc and clang

Pull Request - State: closed - Opened by nalinigans 12 months ago - 2 comments

#313 - Use genomicsdb::version instead of deprecated genomicsdb_version()

Pull Request - State: closed - Opened by nalinigans 12 months ago - 1 comment

#312 - Move minimal support for MacOS to version 12 and set cmake visibility setting to honor the target types.

Pull Request - State: closed - Opened by nalinigans 12 months ago - 1 comment

#311 - get_files changes on genomicsdb side

Pull Request - State: open - Opened by eneskuluk 12 months ago - 1 comment

#310 - MacOS changes to minimize external dependencies at runtime

Pull Request - State: closed - Opened by nalinigans 12 months ago - 1 comment

#309 - Htslib azb support

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

#308 - Port the existing tests involving filter expressions to the underlying changes in TileDB

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

#307 - Minor Dockerfile fix

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

#306 - ERROR: failed to solve: failed to compute cache key

Issue - State: closed - Opened by youngbee12 about 1 year ago - 3 comments

#305 - Refactor create_genomicsdb_workspace to handle error messages and fit the pattern of the other tools

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

#304 - Small build fixes for Go bindings

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

#303 - Capture tiledb_errmsg for TileDBUtils methods returning errors

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

#302 - Generate protobuf bindings and support native installation from Go

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

#301 - Move has_annotation_sources() check before processing any annotation code

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

#300 - React to changed api in tiledb_array_evaluate_cell() and catch exceptions in GenomicsDB::query_variant_calls

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

#299 - Exclude annotation sources if not specified in protobuf for improved api query_variant_calls performance.

Pull Request - State: closed - Opened by nalinigans about 1 year ago - 2 comments

#298 - Porting to gcc-13

Issue - State: open - Opened by pgrt about 1 year ago - 2 comments

#297 - Pull fix for issues with crc32c while building gcssdk

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

#296 - Remove incompatible log4j in pom.xml and surefire causing build issues and cleanup mvn warnings

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

#295 - Finalize release sonatype flow

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

#294 - Remove mpi dependencies from vcf2genomicsdb

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

#293 - Build genomicsdb-spark.jar with no dependencies

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

#292 - Add overlapping contigs in vidmap test

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

#291 - Fix typos, formatting and links in import-etl docs and update README.md

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

#290 - Install genomicsdb_status.h, update snapshot version and copyrights

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

#289 - upgrade spark version to 3.4.0

Pull Request - State: closed - Opened by eneskuluk over 1 year ago - 4 comments

#288 - Run ubuntu 22.04 on the installed openssl 3 for continuous builds and minor cleanup

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

#287 - Compilation on Ubuntu jammy fails in aws-cpp-sdk

Issue - State: closed - Opened by lima1 over 1 year ago - 4 comments

#286 - Minimize image size

Pull Request - State: closed - Opened by mlathara over 1 year ago - 2 comments

#285 - Use the new tiledb_array_evaluate_cell to apply filter expressions for the SingleCellTileDBIterator

Pull Request - State: closed - Opened by nalinigans over 1 year ago - 3 comments

#284 - java 17 support

Pull Request - State: closed - Opened by eneskuluk over 1 year ago - 11 comments

#283 - Java 17 support

Pull Request - State: closed - Opened by eneskuluk over 1 year ago - 2 comments

#282 - Use GENOMICSDB_TAG to test with a version compatible GenomicsDB for smoke testing with TestGenomicsDBJar

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

#281 - Exclude spark from core jar

Pull Request - State: closed - Opened by eneskuluk over 1 year ago - 3 comments

#280 - Explicit Coverage Step for C++ sources as codecov/codecov-action@v3 not handling it well

Pull Request - State: closed - Opened by nalinigans over 1 year ago - 2 comments

#279 - Bump testng from 6.10 to 7.7.0

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

#278 - Get Dockerfiles to use the BUILD_DISTRIBUTABLE_LIBRARY env instead of bash position args.

Pull Request - State: closed - Opened by nalinigans over 1 year ago - 4 comments

#277 - Removal of spark2 support

Pull Request - State: closed - Opened by eneskuluk over 1 year ago - 2 comments

#276 - Support building and testing of GenomicsDB on ubuntu 22.04

Pull Request - State: closed - Opened by nalinigans over 1 year ago - 4 comments

#275 - cmake argument fix for readthedocs

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

#274 - Fixed cmake command argument at readthedocs

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

#273 - Update base docker image

Pull Request - State: closed - Opened by mlathara over 1 year ago - 2 comments

#272 - React to codecov's need for explicit gcov specification for C/C++

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

#271 - Use unflattened genomic coordinates in error messages from GenomicsDB queries.

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

#270 - Allow for resize/retry if size_per_column_partition specified to vcf2genomicsdb is too small

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

#269 - Update python notebook for docs

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

#268 - Protobuf cleanup to allow for import/export from other languages via prototype buffers

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

#267 - Use azure lite client from OmicsDataAutomation

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

#266 - Expose some of the TileDB filesystem functionality in GenomicsDB for use in Python/R and probably Java bindings

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

#265 - readthedocs

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

#264 - Disable gatk IT for release pipeline

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

#263 - Use unflattened genomic coordinates in GenomicsDB error messages

Issue - State: closed - Opened by nalinigans almost 2 years ago

#262 - Bump htsjdk from 2.23.0 to 3.0.1

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

#261 - Use ubuntu 20.04 explicitly for GitHub Actions and other release specific cleanup

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

#260 - Pull in underlying support for hierarchical namespaces in Azure Blob Storage

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

#259 - Fixes for Mac and new cmake option for usecases that do not need testing

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

#258 - Bump scala-maven-plugin from 4.4.0 to 4.7.2

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago - 3 comments
Labels: dependencies

#257 - Bump protobuf-java from 3.21.7 to 3.21.9

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago - 4 comments
Labels: dependencies

#256 - Bump maven-compiler-plugin from 3.8.1 to 3.10.1

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago - 3 comments
Labels: dependencies

#255 - Bump scalatest-maven-plugin from 2.1.0 to 2.2.0

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago - 3 comments
Labels: dependencies

#254 - Bump testng from 6.10 to 7.6.1

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

#253 - Pull in dependabot pom.xml suggestions

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

#252 - Move GenomicsDB version to 1.4.5 and Github Action changes to migrate CI builds on Ubuntu 20.04 runners

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

#251 - Bump maven-compiler-plugin from 3.8.1 to 3.10.1

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

#250 - First pass at implementing a bypass mechanism for intersecting intervals mode for fast, fuzzy queries based on just simple traversal

Pull Request - State: closed - Opened by nalinigans almost 2 years ago - 3 comments

GitHub / GenomicsDB/GenomicsDB issues and pull requests