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IRMA-core Changelog

All notable changes to this project will be documented in this file. The format is roughly based on Keep a Changelog, and this project tries to adheres to Semantic Versioning. For IRMA vs IRMA-core compatibility, please see the version matrix.

0.9.1 - TBD

Fixes

  • Fixes error in aligner tally diagnostics when reverse complement is not enabled

Changed

  • Adds more context to paired read errors

0.9.0 - 2026-03-06

Added

  • Adds verbose flag to sampler for printing total number of reads in original input and number of downsampled records to stderr
  • Adds verbose flag to trimmer for printing diagnostic output on number of reads trimmed to stderr
  • Adds phase process for phase clustering assignment and labeling of single nucleotide variants of genes
  • Adds more detailed error messages with more context, including file paths for many IO errors

Fixes

  • Adds requirement in sampler arguments to provide either a --subsample-target or a --percent-target, fixing unreachable error when neither is provided
  • Fixes a bug where leading whitespace in a record file can cause the program to stall (in sampler and aligner)
  • Allows repeated input/output files from processes if they are device files (e.g., /dev/null)
  • merge-sam now respects the seed set in the environmental variable IRMA_SEED
  • Fixes a bug where not all paired headers were being checked in preprocess, sampler, trimmer, and xleave

0.8.1 - 2025-12-02

Fixes

  • aligner with --rev-comp and --best-match now produces the correct positions and CIGAR strings

0.8.0 - 2025-11-21

Added

  • Adds standalone aligner process for performing pairwise local sequence alignment with the Striped Smith Waterman algorithm

Changed

  • The trimmer process now can perform deinterleaving, as well as widow filtering with interleaved inputs and outputs

0.7.0 - 2025-09-17

Added

  • Adds standalone xleave process for interleaving and de-interleaving paired-end FastQ and FASTA files

0.6.2 - 2025-09-25

Fixes

  • xflate recently produced invalid FASTQ during inflation. This has been fixed. This bug was not surfaced in IRMA.

0.6.1 - 2025-09-09

Changed

  • The fastq-converter process has been removed.
  • More context is added for IO errors in sampler

Fixes

  • Fixes bug where SRA paired-end headers could be could be incorrectly flagged as unmated when --filter-widows was selected in trimmer, or with paired reads in sampler
  • Fixes a reproducibility issue in sampler where the seed wasn't being used in one case

0.6.0 - 2025-08-29

Added

  • Adds a new standalone process called sampler that provides support for randomly downsampling FastQ or FASTA files. Deinterleaving is also supported.

Changed

  • Use threads and anonymous pipes (in Rust) when decompressing zipped inputs
  • Improve error messages to include file names in trimmer and preprocess
  • Other dependencies updated, such as a faster foldhash.

Fixes

  • mergeSAMpairs: updated Zoe dependency (in v0.0.19, using v0.0.20) fixes hard clipping in merged reads. Reader error messages are also improved generally.

0.5.1 - 2025-06-03

Fixes

  • Fixes a bug where --polyg-trim would trim the sequence but not the quality scores.

0.5.0 - 2025-05-30

Added

  • preprocess (formerly qc-trim-deflate) now supports zipped inputs (fastq.gz files).

Changed

  • Re-factor and specify dependencies.
  • The process qc-trim-deflate is now called preprocess, and it includes most of the same functionality as trimmer (note that its arguments have been conformed to match trimmer rather than the legacy fastq_converter process).
  • The deprecated fastq_converter will be removed in the next version.
  • For trimmer/preprocess, --filter-widows can no longer be specified when there is only a single input file.
  • For fastq_converter/preprocess, --keep-header has been removed since IRMA has made this an unmodifiable default since v1.1.2.

0.4.3 - 2025-05-01

Fixes

  • Fixed bug in trimmer to allow handling of multi-member fastq.gz files

0.4.2 - 2025-04-30

Changed

  • The Dockerfile has been updated for nextflow compatibility (it currently needed: awk, grep, ps, sed)
  • The num-procs process now allows LOCAL_PROCS_OVERRIDE to be greater than the available cores. Use IFX_LOCAL_PROCS if you would like it capped at the available cores.

0.4.1 - 2025-04-28

Added

  • The trimmer process now supports compressed fastq.gz files for both input and output.
  • Adds flate2 crate as a dependency for handling .gz files

Changed

  • The release process has been improved to produce better and more artifacts.

0.4.0 - 2025-04-16

Added

  • trimmer now supports -f, --filter-widows for filtering widowed/orphaned reads in a paired-end context, with support for two input and two output fastq files.
  • Github actions added to generate downloadable releases

Changed

  • Updates dependencies, particularly with foldhash and zoe improvements
  • For trimmer, long argument --fastq-output-file is now --fastq-output

Fixes

  • For num-procs, the environemntal var LOCAL_PROCS_OVERRIDE now caps at the max available cores, consistent with the warning message.

0.3.1 - 2025-03-21

  • Added: The num-procs process now has the option --cap-cores-using-env so environmental variables like NSLOTS and IFX_LOCAL_PROCS can further cap resources. The var LOCAL_PROCS_OVERRIDE trumps other settings up to the available cores.

0.3.0 - 2025-03-18

Added

  • Adds trimmer standalone process. Read the docs.
  • Adds integrated num-procs process for portable core counts.
  • Adds documents for open-sourcing.

Changed

  • Refactors into integrated / standalone processes.
  • Updates dependencies.

Fixes

  • Incorporates fix for Zoe that affected IUPAC base recoding.

0.2.0 - 2024-10-30

  • Added: Updates the new qc-trim-deflate (name subject to change) process with various fixes and improvements.
  • Changed: Slims down and corrects raw read counts in the the fastq-converter process.

0.1.6 - 2024-10-11

  • Added: xflate and qc-trim-deflate processes (initial sketch) and rewritten the flow for the fastq-converter process.

0.1.5 - 2024-09-04

  • Added: custom inexact matching algorithm from Zoe