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Support for shared posix filesystems like NFS and Lustre. This turns on disable file locking and for import it minimizes writes to disks. The performance on some of the gatk datasets for the import of about 10 samples went from 23.72m to 6.34m on NFS which was comparable to importing to a local filesystem.
Use pre-compression filters for offset and compression files for new workspaces and genomicsdb arrays to help with reduced storage and increased performance on shared/distributed filesystems. The total sizes for a GenomicsDB workspace using the same dataset as above and the 10 samples went from 313MB to 170MB with no change in import and query times.
Support to handle MNVs similar to deletions as described in GATK Issue #6500.
Support in the GenomicsDBImporter to have multiple contigs in the same GenomicsDB partition/array. This will hopefully help import times in cases where users have many thousands of contigs.
Logging has been improved somewhat with the native C/C++ code using spdlog and fmt and the Java layer using apache log4j and log4j.properties provided by the application.
Improved loading of the native GenomicsDB library from the Java layer to directly use the library packaged in the jar file with java option genomicsdb.library.path=/path/to/library to override the library in the jar.
More improvements with the GenomicsDB api to make it usable with Java/Spark/Python/R.