rMATS turbo v4.3.0

• Add --individual-counts to enable individualCounts.[AS_Event].txt output files
• Add --darts-model
• Bug fix for missing values when counting reads
• Bug fix for strand based effective length for MXE fixed events
• Allow build to install more dependencies from conda

rMATS turbo v4.2.0

• Add EventTypeDescription column to summary output
• Bug fix for thread safe map lookup
• Add --twopassMode Basic to STAR command
• Update default alignSJDBoverhangMin for STAR
• Support building with Cython v3
• Handle exceptions when reading the gtf file
• Remove unnecessary numpy dependency
• Fix errors when building with clang

rMATS turbo v4.1.2

• Improve the performance of the FDR calculation
• Pass --nthread to STAR if starting with FASTQ files
• Add STAR to the Dockerfile
• Allow using string IDs for events with --fixed-event-set
• Remove buffer size limits in statistical model
• Handle Windows line endings
• Handle file systems that do not support colon in filenames
• Bug fix of single-end strand checking
• Bug fix of integer overflow for read outcome counts

rMATS turbo v4.1.1

Changes in v4.1.1:

• Add command line argument for running the statistical model separately (--task stat)
• Add command line argument for counting reads using a user supplied event set (--fixed-event-set)
• Add command line argument for handling clipped alignments (--allow-clipping)
• Add debug output to summarize any reads that were filtered out
• Add output file with a brief summary of event counts
• Add Dockerfile
• Support fastq.gz input files
• Bug fix of novel event classification
• Bug fix of strand specific read filtering

rMATS turbo v4.1.0

rmats_turbo_v4_1_0.tar.gz is just the source code. A build step is required before running.

rmats_turbo_v4_1_0_python_2_7.tar.gz and rmats_turbo_v4_1_0_python_3_6.tar.gz include the files produced when building in a python 2.7 or python 3.6 environment. It may be possible to run rMATS using those pre-built versions on compatible systems without running a build step.