SplAdder version 2.4.1

This release adds experimental support for CRAM files and updates some dependencies.

SplAdder version 2.4.0

This release has the following changes:

• event IDs in text output are now more consistent (e.g., what previously was exon_skip.1 in gff and exon_skip_1 in txt output, now is consistently exon_skip.1)
• a command for the external chunked merge of many splicing graphs has been introduced (allowing for better distribution of large cohorts)
• some typos were fixed

SplAdder version 2.3.0

This release introduces a new visualisation mode

• splicing graphs, events, coverage, etc can now be visualised with individual tracks
• documentation was extended to describe new visualisation mode
• a bug that caused --validate-sg to be ignored was fixed
• a new feature to specific the support for edges in --validate-sg was added

SplAdder version 2.2.3

Bugfix / Doc Release

• fixed bug not correctly ordering isoforms in mutex exon events
• fixed bug inverting PSI computation for alt 3'/5' events
• extended and moved documentation onto separate platform

SplAdder version 2.2.2

Bugfix release

• changed requirements
• minor cleanups

SplAdder version 2.2.1

Bugfix release

• gracefully exit when attempting test of no-event output

SplAdder version 2.2.0

Bugfix release.

• fixes mistake in parallel mode, when very large alignment files are used
• fixes parsing of bam-file list in viz mode

SplAdder version 2.1.0

This release has the following changes:

• new option --set-mm-tag to customize the string for mismatch tags in alignment files for build mode
• restore compatibility to read files in test mode that were generated with previous SplAdder versions
• improved the internal re-use of quantified files in test mode when subsetting is selected

SplAdder version 2.0.1

Bugfix release addressing issue #78.

SplAdder version 2.0.0

This is the first release of SplAdder using Python 3. In addition to improved testing and the correction of minor bugs, we have re-designed the user interface. Following, we provide a list of the most notable changes:

• SplAdder now uses sub-commands. The previous scripts for graph building, visualization and testing have been replaced through three modes: build, viz and test
• the dash (-) is now consistently used in all parameters (e.g., --merge_strat has now become --merge-strat)
• binary flags have been re-introduced and can be directly switched on or off without an additional argument (e.g., --verbose y has become --verbose and --primary-only n has become --no-primary-only)
• -T has been replaced by --extract-ase

We also made some additional changes:

• SplAdder can now be installed via pip
• the concept of replicates was not used for the build phase and has been removed from the code
• the Matlab code has been removed
• additional test cases have been introduced and test coverage was increased
• some new settings previously only accessibly through changes in the code have been made available to the user
• the code has been cleaned up further