Change Log

All notable changes to this project will be documented in this file. This project adheres to Semantic Versioning.

About changelog here

[2.7.7]

Fixed

Update to setuptools >= v.70 to address a security issue in the package_index module

[2.7.6]

Fixed

Updated issue templates

[2.7.4]

Changed

When using QUAL values, treat . as 0 quality

[2.7.3]

Added

Basic cli tests touching fixed deprecated code

Changed

Unfreezed PyMongo in requirements.txt
Replaced deprecated pymongo .count() function with count_documents() in code.

[2.7.2]

Fixed

Deprecated config in setup.cfg error when installing the package

[2.7.1]

Added

Script to correct contig name
Expanded instructions on how to set up an instance and load data into database

Changed

GitHub actions run tests using MongoDB versions 3.2, 4.4 and 5.0

Fixed

Restore command accepts custom database name
Restore command uses either database URI or host:port params

[2.5.2]

Changed

Convert version to string
Use Github Actions for running CI instead of Travis

[2.5.1]

Added

Option to add observation frequencies to exported VCF (--freq)

[2.5]

Added

Profiling feature added. Each sample gets a profile based on the genotypes for a set of high maf variants.
High maf variants used in profiling is loaded into DB via CLI
Reject loading a case if a similar profile already exists for any of the samples
Statistics of the profiles in DB can be generated through CLI
use bulk operations when deleting variants
Compatible with GRCh38
Option to include case count when querying for a variant

Fixed

Use correct fields in index

[2.3]

Added

Use bulk updates when inserting snvs

[2.2]

Added

CLI function to annotate variants
CLI functionality to dump and restore a database

[2.1]

Fixed

Fix bug with inserting variants

[2.0]

Added

Adds structural variants to loqus