Version 0.8.0

Backward incompatible changes

• Default gsync worker type changed to gthread from gevent in docker-compose.yml. If you currently use the gevent worker type in your own docker-compose.override.yml, you will need to change it to gthread to avoid a critical worker timeout issue.
• Manual compilation now requires python 3.8.

New features

ldserver

• New LD format available - more compact, faster to generate server-side. Use format=compact parameter in API request.
• Support for msgpack, a binary serialization method. Use msgpack=1 in API request. This can also be used in conjunction with format=compact for a substantial reduction in payload size.
• Parallel computation of LD with OpenMP. Set environment variables OMP_NUM_THREADS=X and OPENBLAS_NUM_THREADS=X. These default to 1 when using the docker image.
• LD precision can be set using precision=X parameter. Precision can also be forced to a certain value server-side by adding LDSERVER_PRECISION = X in your config.py file.
• Added google benchmark + cases. There is now a new executable target generated benchmark-ldserver which can run a few simple benchmarks. These benchmarks can also be compared across commits.

playground

• Updated to support new format option.
• Number of visible lines of JSON increased.

raremetal

• Request covariance for an entire region, without having to specify individual variants or a mask.
• Support for filtering variants by MAF or p-value.
• Additional logging statements printed during add-yaml
• Performance improvements to loading phenotpye files.
• Support for MetaSTAAR summary statistic format (similar to RAREMETAL & rvtest format, but with much better on-disk compression and storage size.) Note that we only support MetaSTAAR parquet files, rather than the RData files.
• Added new endpoint /aggrevation/variants for retrieving a list of variants within a region from one of the summary statistic datasets.
• Add mean alt allele frequency across variants in each group to the /aggregation/covariance response.

Bug fixes

• Fix issue compiling on linux due to unsigned long vs unsigned long long

Version 0.7.0

Backward incompatible changes

• summaryStatDataset was changed to summaryStatisticDataset for consistency

New features

• Support for rvtest/raremetal files lacking a proper header
• Support for alternative variant format (such as CHR:POS:REF:ALT)
• Improved exception handling and error reporting code
  • More C++ errors are supported and properly reported
  • Better error messaging for when phenotype file is not able to be read
  • Better reporting of exactly where in a file an invalid value was encountered
• Reworked Dockerfile to better avoid cache misses

Bug fixes

• Properly handle edge case in rvtest where NaN allele frequency is reported for singletons observed in related samples
• Fixed two separate bugs causing file descriptors to be allocated but never released
• Return the empty set instead of throwing a server error if no variants exist within mask region in genotype or summary statistic file
• Only use SENTRY_DSN if it is actually populated with a value
• Redis version was previously unpinned in docker compose yaml, now pinned to 5.x

Version 0.6.0

Backward incompatible changes

• The raremetal app's SQLite DB schema changed to accommodate multiple score/covariance files per summary statistic "dataset". If you are not using the docker setup which re-creates the DB at each launch, you will need to remove and recreate the DB using the add-yaml command.

New features

• Allow providing score and covariance files split by chromosome using a glob pattern in the YAML. See the README for more details.

Bug fixes

• No bug fixes were made.

Version 0.5.0

Backward incompatible changes

• All python source has been upgraded to python 3, without backward support for python2

• CMake build process now only supports python 3

New features

• Support for serving pre-computed score statistics and covariance matrices generated by rvtest or raremetalworker

  • Brief summary
  • Configuration
  • API additions

• Slightly slimmer/faster docker image build

Bug fixes

• No bug fixes were made.