Change Log¶

All notable changes to gNALI will be documented in this file.

1.1.0¶

2021-07-16

Added¶

• Add functionality to work with VCF records with multiple transcripts

Changed¶

• Changed detailed output file to have one line per transcript passing filtering
• Fixed an error in handling overlapping genes

1.0.5¶

2021-06-03

Changed¶

• Updated to work with gnomADv3.1.1
• Added verbose mode for error logging

1.0.4¶

2021-04-29

Changed¶

• Fixed an error in handling missing population frequency data

1.0.3¶

2021-03-12

Changed ###¶

• Improved verification of VEP cache
• Changed gnali_setup command to be able to select assembly to download reference files for
• Fixed issues with --force flag
• Updated pysam dependency to ensure that version < 0.16 is installed as pysam>=0.16 causes issues when installed from Bioconda
  • Bioconda version of pysam>=0.16 will segfault when initializing a TabixFile object with a remote database

1.0.2¶

2021-01-25

Changed ###¶

• Fixed installation/verification of VEP cache

Added¶

• Add error logging for genes not found in the Ensembl database

1.0.1¶

2021-01-11

Changed¶

• Fixed population frequency output column order

1.0.0¶

2020-11-06

Added¶

• Add support for custom databases using database configuration files
• Add support for GRCh38 databases
• Add support for remote/local and compressed/non-compressed databases
• Add support for databases without LOFTEE annotations
  • Add functionality to work with VEP/LOFTEE to add loss-of-function annotations
• Add new exceptions to exceptions.py

Commands: - VCF output command - Population frequencies output command - Additional filters command - Predefined filters command - GRCh37 database configuration template creation command - GRCh38 database configuration template creation command

Modules: - dbconfig.py: to work with database configuration files - Contains Config, RuntimeConfig, and DataFile classes - outputs.py: to write data to different formats - vep.py: to run VEP/LOFTEE on database files - Contains VEP class - gnali_setup.py: to install LOFTEE, download required files for VEP/LOFTEE - Contains Dependencies class

Changed¶

• Change database parameters to use a configuration file instead of being hard-coded

0.1.1¶

2020-04-16

Changed¶

• Fixed filtering for gene patches

0.1.0¶

2020-03-02

This is the initial release of gNALI.