GenomicsDB / GenomicsDB

High performance data storage for importing, querying and transforming variants.

https://genomicsdb.readthedocs.io

GenomicsDB/GenomicsDB Issues

Moving to 24.04 for the docker builds is broken.
Updated 3 months ago
Porting to gcc-13
Updated 4 months ago2
Ambiguous call to Assert in the tests
Updated 6 months ago1
The compatibility of array_schema.cc
Updated 6 months ago1
Python library?
Closed 6 months ago3
Import should automatically increase buffer size as needed
Closed 6 months ago3
ERROR: failed to solve: failed to compute cache key
Closed 6 months ago3
Compilation on Ubuntu jammy fails in aws-cpp-sdk
Closed 8 months ago4
Support MacOS/Linux arm64 architecture
Updated 10 months ago7
Use unflattened genomic coordinates in GenomicsDB error messages
Closed a year ago
Changes to JsonFormat methods when building with protobuf-java-format 1.3 instead of 1.2
Closed a year ago
Dependencies missing in the pom
Updated 2 years ago2
Missing links to fmt
Updated 2 years ago
string_view needs c++-17
Updated 2 years ago
Allow for multiple inputs(bed, etc.) to be ingested into GenomicsDB
Updated 2 years ago
Api should allow for reference genome be optional
Closed 2 years ago1
plink support has introduced mpi dependency in test_gen.cc
Updated 2 years ago
Excessive logging with --max-alternate-alleles
Updated 2 years ago6
Annotation Service needs to be extended to support multiple alternate alleles
Updated 2 years ago1
Maven wget url invalid
Closed 3 years ago2
Add ID field and handle duplicate names in INFO/FMT/FILTER fields correctly in vcf2genomicsdb_init
Updated 3 years ago
protobuf version
Closed 3 years ago2
Explore using zstd as an optional alternative to using intel zlib from GenomicsDB
Updated 3 years ago
Move away from protobuf-v3.0.0-beta-1 and into later versions for GenomicsDB
Closed 3 years ago1
GenomicsDB api returns a null list when querying for variant calls with no rows specified
Updated 3 years ago
Extend Github Actions to run with cloud emulators - azurite, minio, etc.
Updated 3 years ago
Github action sporadic failure with spark
Closed 3 years ago11
ulimit issue isn't obvious from error message
Closed 4 years ago2
[TileDB::FileSystem] Error and FeatureReader to initialize with exception Error
Closed 4 years ago11
GenomicsDB IO exception has very limited debugging information
Closed 4 years ago2
GATK GenomicsDBImport - use list as input
Closed 4 years ago3
Compile error: ‘bcf_int64_missing’ was not declared in this scope
Closed 4 years ago4
Couldn't create GenomicsDBFeatureReader
Closed 4 years ago10
REF, ALT, QUAL, FILTER, INFO fields stored multiple times for each sample?
Closed 5 years ago2
ubuntu install help
Closed 5 years ago7
Add incremental support to GenomicsDBImport
Closed 5 years ago1
Improve (mainly java) logging in GenomicsDB
Updated 5 years ago1
Use Protobuf in the query api
Updated 5 years ago1
Extend query_variants() api to optionally return only shallow, top level variant info
Updated 5 years ago
Extend query_variants and query_variant_calls api to accept filter expressions.
Updated 5 years ago
Refine gt_mpi_gather and other tools
Updated 5 years ago1
Query based on attribute filters
Updated 5 years ago1
Referencing Issue "CSV Data Import in GenomicsDB" in new repository.
Updated 5 years ago9