OpenCGA v0.6.0

Most important changes include:

• Upgrade java version from 1.7 to 1.8
• Change license to Apache License 2.0
• Variant Storage study-oriented, instead of file-oriented
• MongoDB variants data model optimizations
• Sample annotations with complex structures
• Implemented missing catalog methods
• Added RestWS tests
• Many small bugfixes and improvements

OpenCGA v0.5.0 Sample Cohort Stats

Most important changes include:

• New data model Cohort in Catalog to create groups of samples
• New stats per cohort, apart from the statistics for all samples
• Stats calculation done in postLoad ETL step, not in transform
• Multi-thread implementation for transformation and load
• Lots of bugfixes

OpenCGA v0.4.0 "Storage Refactoring"

Most important changes include:

• OpenCGA Storage module has been converted in a real framework and split in several Maven modules: opencga-storage-app, opencga-storage-core, opencga-storage-mongodb, opencga-storage-hbase
• OpenCGA Catalog module has reached a usable point, it still lacks some extra functionality but it is usable. JUnit tests have also been implemented
• New Variant Annotation pipeline using CellBase Variant Annotator has been developed. This annotate selected variants in the different storage engines
• OpenCGA Server has learnt some new RESTful web services
• Many small fixes and improvements

See OpenCGA wiki for more details.

OpenCGA v0.3.3, improvements in MongoDB Variant storage engine

This version includes patches and improvements over the stable version 0.3.2:

• Better support for aggregated files
• Better support for multi-allelic variants
• Mongo collections to query can now be configured
• Improved options for genotype storage (compressed or uncompressed)
• More complex variant files meta-data

Version 0.4 will be released in 2015 (see milestones).

Genotype compression for great reduction in disk usage

This version includes patches and improvements on the stable version 0.3.1:

• Disk usage greatly reduced with an option to compress genotypes from a VCF file
• Tool for variant accession IDs creation
• Improved API for study and files information retrieval
• Dependencies upgraded to Biodata 2.0 and Variant 1.2