Releases: mkirsche/Iris
Releases · mkirsche/Iris
1.0.5
1.0.4
1.0.3
v1.0.2
v1.0.1
Version 1.0.1
- Replaced Falconsense consensus module with Racon, improving speed and accuracy
- Added script for comparing refined variants to a ground truth set
- Fixed a few bugs and generally increased stability and robustness to different field names
- Added a number of additional command line flags to enable greater customization
- Renamed some scripts to reduce naming conflicts with common filenames such as Settings.java
- Add INFO fields to indicate whether variants have already been processed and/or refined.
Version 1.0
Improvements of IRIS over the original CrossStitch module include:
- Improved runtime (approximately 8x faster tested on a GIAB dataset with ~13k insertions)
- Less dependencies on external software (e.g., GNU Parallel)
- User-friendly help menu which IRIS outputs when run with incomplete or invalid parameters
- More flexibility in changing the parameters used in different stages of the pipeline
- Greater transparency in thread usage (entirely controlled through command line flag)
- Use of Minimap2 as the default aligner, with continued support for ngmlr
- Collection of external dependencies as submodules which can all be built with a single script if provided binaries are not compatible with a user's machine
- Simulation tests with accuracy metrics for insertion sequences compared to the ground truth
- An option to refine deletions
- Increased error checking and logging to more easily diagnose problems
- Creation of a tsv file which logs all refinements and edit distance from the original sequences
- More intelligent choice of which corrected read to extract the refined sequences from
- Robustness to nearby variants (i.e., checks to ensure that multiple variants are not collapsed into a single call)
- Ability to resume a failed run and avoid reprocessing variants