0.10.2

Bug fixes

• Close file handles when not needed
• Fix dependencies
• Import fixed for INFO fields with sum as the combine operation

NOTE: this is the final release of GenomicsDB from Intel. Development will continue at https://github.com/GenomicsDB/GenomicsDB.

0.10.0

• Support to do I/O off HDFS/EMRFS(S3)/GCS
• Protobuf based API for import and query - Java tools that use these APIs
• Refactored Java modules
• Sites only query
• Bug fixes and improvements

0.9.2

• Allele specific annotation support
• Bug fixes

0.8.1

• Updated to TileDB v0.5.2
• Arrays and workspaces no longer need to maintain absolute paths - can be moved, copied etc to arbitrary locations using mv, cp
• GenomicsDBImporter stores merged VCF header to a file on disk which can be re-used during queries.
• Bug fixes

0.7.0

• Produce FILTER field
• Non-diploid genotypes
• Phasing information in genotypes
• Initial code for getting mapping data from a Postgresql DB using libdbi (not enabled by default/not documented)
• Bug fixes and error messages

0.6.4

• Minor updates for integration with GATK-4 - treat sampleMap as golden source for sample to TileDB row mapping
• Better error reporting/exception throws.
• ID field import from VCF files
• Bug fixes

0.5.0

• CMake based build - includes Protobuf regeneration
• Java GenomicsDBImporter to import data from FeatureReader<VariantContext> - to be used in GATK-4 import tool.
• Produce vid_mapping and callset_mapping from merged VCF header
• Flags and functions for creating TileDB workspace, deleting and re-creating array
• Version flag in GenomicsDB executables
• Batched import support in Java
• Bug fixes

0.4.0

• VariantContext write API in Java
• VariantContext read API for Spark in Java and Scala
• Obtain INFO field combine operations from the JSON
• ProtoBuf based implementation for information in callset_mapping_file and vid_mapping_file. Used in Java write API when sample, field and contig names are passed using the API.
• Split VCF files based on column partitions specified in the loader JSON
• Better error reporting
• Bug fixes

0.3.0

• Java VCF load API
• Deal with overlapping variant intervals at the start of a partition during loading
• Deal with large number of ALT alleles when producing combined gVCF
• Strictly enforce buffer limits when producing combined gVCF
• Bug fixes

0.2.0

• Build and run on MacOSX >=10.9 (see wiki for instructions on how to build)
• Java API for exporting data in a TileDB array as combined gVCF records represented as htsjdk.VariantContext objects (see this wiki section).
• Minor updates and fixes.