v1.5.0

Summary

Packages Athena v1.5.0

Changes

Addition of --panel_filters argument for adding drop down list of gene panels for filtering all gene plots

v1.4.0

Improvements

• Adds Athena v1.4.1
  • ability to handle multiple transcripts, intronic regions and copy buttons to tables
• Bump app top Ubuntu 20, removes requirement for bundled miniconda3.8
• Switch packages for pybedtools, pandasql and retrying from source tars to pre-built wheels
  • reduces run time by ~1 minute
• Compress annotated bed file for output to reduce size by ~90%
• Change exons_nirvana input name to exons_file

v1.3.0

• Includes Athena v1.3.0
• Adds optional chromosomal level coverage plots

v1.2.2

• make use of --chunk_size for annotate_bed.py to reduce required memory for instance
• change to mem1_ssd1_v2_x16 instance to increase cpu core count to 16, leveraged by multiprocess to reduce run time

v1.2.1

• Release of DNAnexus applet for Athena.
• Includes bug fix for specifying UTF8 encoding to fix rendering of em dashes in panel names

v1.2.0

Release of DNAnexus applet for Athena.

Various usability improvements and bug fixes, full release notes may be found here.

v1.1.2

• includes Athena v1.1.1 with bug fix for correct bed intersecting

v1.1.1

• Fix missing version tags in dxapp.json from v1.1.0 release

v1.1.0

• Refactored code into multiple new functions and classes for better structure
• Improved speed of generating coverage stats and plots through using multiprocessing library to utilise multicore processors
• Improved styling of summary plot for low numbers of genes
• Added number genes <90% coverage at threshold value to summary text

v1.0.3

Adds new Athena v1.0.5 release, includes following:

• Improve colouring of threshold column in sub-optimal exons table
• Added source of VCF to variant tables - this is derived from the input VCF file name, split on the first "_"
• Added fixed uuids for tables where pd.Styler used, this aids in testing as it stops random unique ids being generated for each report
• Added check for multiple regions for one exon from input bed file in coverage_single_stats.py - catches errors if exon split into more than one region and => would result in wrongly calculating coverage
• Fixes bug where coverage bin values at the threshold weren't included in the threshold calculations resulting in under calculating coverage