https://github.com/cdcgov/irma - IRMA v1.3.0

Release Notes for v1.3.0 : 2025-06

Added

• Created a Dockerfile for building Linux x86_64 and aarch64 containers
• Added Github actions for generating containers and packaged binaries on release

Changes

• IRMA has been relicensed under Apache 2. We have more clearly separated third party software that is distributed with IRMA under other licenses and conditions. See for more details.
• LABEL v0.7.0+ is now required to run IRMA.
• IRMA-core is now required to run IRMA and is packaged with it from now on. Certain read preprocessing and merging steps are now handled by IRMA-core.
• IRMA now provides automatic core detection for local execution mode. SINGLE_LOCAL_PROC can be still be used up to the available cores. LOCAL_PROCS_OVERRIDE can be set to pick any number of cores.
• Third-party binaries have been standardized to newer versions and generally support Linux, macOS on both aarch64 and x86_64. Use of LABEL classification on macOS still requires Rosetta.
• IRMA's updated, third-party SSW (v1.2.5M for modified) now provides soft clipping. This can slightly increase the size of intermediate data.
• Documentation has been updated for Github
• IRMA's QC_log.txt has been completely re-formatted and updated.

Fixes

• IRMA no longer uses which, which could sometimes cause warnings in some environments.
• The previously pinned version of SSW had a bug that shifted quality scores in reverse-complemented reads that were also clipped by the alignment (<8% observed). The newest version fixes this bug and another rare alignment correctness error (<0.01%).

Deprecations and Removals

• DOUBLE_LOCAL_PROC has been removed and will only issue a warning if set.
• USE_IRMA_CORE is deprecated and will be removed in a future version.

New Known Issues

• Some users have noted H1 swine misclassification via BLAT (LABEL can be used as a workaround). We will address this with a reference seed update.
• Merged-pair BAM files do not show clipping information. We will add clipping information for merged-pair reads in a future release.

v1.2.1 : 2024-10

Fixes

• The S-gene only SC2 configuration now has consensus padding turned off. The module is not compatible with this feature.
• IRMA had reported reads passing only the length filter as the observed raw reads. This has been fixed.

- Perl
Published by github-actions[bot] about 1 year ago

https://github.com/cdcgov/irma - IRMA v1.2.0

v1.2.0 : 2024-08

Feature

• First-party support for RSV has been added and tested. <!-- See acknowledgements. -->

v1.1.5 : 2024-04

Fixes

• Fixes an edge case where merging the read-pair quality scores of an 'N' and '-' allele could cause BAM file creation to fail.
• Upon disk size check failure, IRMA now reports the path it is checking for its scratch disk space to allow for better debugging and configuration.
• At the read level, IRMA now converts ambiguous base calls to 'n' or 'N' so that it will be handled properly downstream.

- Perl
Published by sammysheep over 1 year ago

https://github.com/cdcgov/irma - IRMA v1.1.4

v1.1.4 : 2024-02

Fixes

• Fixes a memory bottleneck for segmented modules (FLU) processing a large number of reads. Many thanks to T. Stark, K. Lacek, and M. Scotch for helping to diagnose the issue.

- Perl
Published by sammysheep over 1 year ago

https://github.com/cdcgov/irma - IRMA v1.1.3

v1.1.3 : 2023-11

Fixes

• Fixes a regression (fixed in v1.1.1 but reintroduced in v1.1.2) of the FASTQ header length issue for single-ended assemblies that can cause BAM files to not be written.
  

- Perl
Published by sammysheep over 1 year ago