v1.6.1

Changes:

• Added an output file which contains the summary report text in a .txt (this is to be used as an input to eggd_artemis).
• makefile changed to no longer download .whls from requirements.txt but instead use ready-downloaded .whls provided in the dnanexus/packages folder of the repo

v1.6.0

Summary

• Add code from eggd_athena into dnanexus/ directory in athena GitHub repository
• Add makefile to enable building as a DNAnexus app from current repository structure-
• Add additional optional input -iindication to pass clinical indication as a string to present in the clinical report summary text
• Fix bug introduced in v1.5.0 with new -ipanel_filters input not being optional

v1.5.0

Summary

Updated to add optional drop down filtering for the all genes plot section, as well as minor bug fixes.

Changes

• Optional drop down filtering added to all gene plots through use of --panel_filters, this allows for preset list of gene panels to be added for filtering of full gene plots (example here).
• enabled regex searching for all dataTables sections

Bug fixes

• Fixed #68
• Fixed #71

v1.4.1

Bug Fixes

• Correct natural sorting of full gene plots by exon number

v1.4.0

Improvements

• changes to allow multiple transcripts for a single gene
  • changed throughout to use transcript & exon as ‘unique’ regions for calculating coverage
• changes to make exon be non-integer type to allow intronic regions to be included in reports (denoted as ‘i1’ etc.)
• addition of copy button to gene, exon and SNP coverage tables
• improvement of summary gene plot text formatting for better readability
• addition of total unique transcript count to summary text
• added MIT license

Bug fixes

• #53 - update version no.
• #54 - fix potential index error on naming
• #62 - addition of copy table buttons

V1.3.0

Overview

Option added to include plots of coverage across each chromosome in the report.

Improvements

See above

Bug Fixes

Fixed #56 - Table headers did not scroll horizontally in sync with tabular data

v1.2.1

• Bug fix for specifying UTF8 encoding to fix rendering of em dashes in panel names
• Fixes #30

v1.2.0

Overview

Usability improvements through optimisation of tables and plots, with 50-90% smaller output reports. Addition of searching and filtering to all tables, with use of deferred rendering for all data to greatly improve loading times.

Improvements

• use of dataTables JS library for improved interaction with HTML tables. Also reduces file size through storing all tabular data in an array without HTML markup.
• reduced whole gene plot size by ~60%
• reduced interactive plot size from ~1MB to ~4KB per plot through storing data in array and plotting on render
• removal of all expandable sections, moved to fixed scrollable windows handled by dataTables
• replaced bed file annotation with Python script, now strips chr prefixes from all files if present to prevent bedtools intersect fail
• multiprocessing added to generating low exon plot data arrays to leverage available CPU cores
• improve clinical summary text section
• other minor visual improvements

Bug Fixes

• Fixes #30 - specify UTF8 in HTML to handle incorrectly rendering characters
• Fixes #20 - fix bug in having sys.exit() in multiprocess map, use of imap_unordered() with exception raised correctly terminates worker pool and no longer hangs indefinitely
• Fixes crashing on large panels due to no longer loading all data on initial rendering

v1.1.1

• fixed bug on intersecting panel bed file against exons_nirvana file in annotate_bed.sh where adjacent exons with a small overlap resulted in double entries in the resultant annotated bed file for those exons

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