IRMA-core v0.9.1

Release Notes for v0.9.1 - 2026-04-15

Fixes

• Fixes error in aligner tally diagnostics when reverse complement is not enabled
• Fixes error in phase when trying to read matrix file when no variants are present

Changed

• Adds more context to paired read errors in trimmer, xleave, preprocess,
  and sampler processes
• Hardens Dockerfile using dhi.io (requires login)

IRMA-core v0.9.0

Release Notes for v0.9.0 - 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 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

IRMA-core v0.8.1

Release Notes for v0.8.1 - 2025-12-02

Fixes

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

IRMA-core v0.8.0

Release Notes for v0.8.0 - 2025-11-21

Added

• Adds standalone aligner process for perform 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

IRMA-core v0.7.0

Release Notes for v0.7.0 - 2025-10-09

Added

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

IRMA-core v0.6.2

Release Notes for v0.6.2 - 2025-09-25

Fixes

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

IRMA-core v0.6.1

Release Notes for v0.6.1 - 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

IRMA-core v0.6.0

Release Notes for v0.6.0 - 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.

IRMA-core v0.5.1

Release Notes for v0.5.1 - 2025-06-03

Fixes

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

v0.5.0

Release Notes for v0.5.0 - 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.