Add widowed read filtering and abstract shared behavior between trimmer and preprocess

Author: willchet

.gitlab-ci.yml

@@ -24,7 +24,7 @@ irma-test:
     - scicomp
   script:
     - perl -ne 'BEGIN { $/ = undef } if (/^## \[(.*?)\]/m) { if (! /<!-- Versions -->.*?^\[$1\]:/ms) { die "Version $1 not linked!\n"; } }' CHANGELOG.md
-    - perl -ne 'BEGIN { $/ = undef; $ver = shift @ARGV; } if (/^## \[(.*?)\] - \d{4}-\d{2}-\d{2}/m) { if ( $1 ne $ver) { die "Cargo.toml version is not latest!\n"; } }' "$(cargo pkgid|cut -f2 -d'#')" CHANGELOG.md
+    - perl -ne 'BEGIN { $/ = undef; ($v) = (shift @ARGV) =~ /#(\d+\.\d+\.\d+)/; } if (/^## \[(.*?)\] - \d{4}-\d{2}-\d{2}/m) { if ( $1 ne $v) { die "Cargo.toml version is not latest!\n"; } }' "$(cargo pkgid)" CHANGELOG.md
     - cargo test --verbose
 
 pages:

CHANGELOG.md

@@ -1,12 +1,19 @@
 # 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](VERSION_MATRIX.md).
+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](VERSION_MATRIX.md).
 
-## [0.4.4] - TBD
+## [0.5.0] - TBD
 
 ### Changed
 
 - Re-factor and specify dependencies.
+- The process `qc-trim-deflate` is now called `preprocess` and 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.
 
 ## [0.4.3] - 2025-05-01
 
@@ -49,11 +56,15 @@ All notable changes to this project will be documented in this file. The format
 
 ### Fixes
 
-- For `num-procs`, the environemntal var `LOCAL_PROCS_OVERRIDE` now caps at the max available cores, consistent with the warning message.
+- 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.
+- **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
 
@@ -86,7 +97,7 @@ All notable changes to this project will be documented in this file. The format
 - **Added**: custom inexact matching algorithm from [Zoe]
 
 <!-- Versions -->
-[0.4.4]: https://github.com/CDCgov/irma-core/compare/v0.4.3...v0.4.4
+[0.5.0]: https://github.com/CDCgov/irma-core/compare/v0.4.3...v0.5.0
 [0.4.3]: https://github.com/CDCgov/irma-core/compare/v0.4.2...v0.4.3
 [0.4.2]: https://github.com/CDCgov/irma-core/compare/v0.4.1...v0.4.2
 [0.4.1]: https://github.com/CDCgov/irma-core/compare/v0.4.0...v0.4.1

Cargo.lock

@@ -1,10 +1,10 @@
 [package]
 name = "irma-core"
-version = "0.4.3"
+version = "0.4.3-dev"
 edition = "2024"
 description = "A tool to aid virus sequencing and accelerating IRMA."
 license = "Apache-2.0"
-rust-version = "1.87"
+rust-version = "1.88"
 
 # Long-term maintainers of the IRMA-core
 authors = ["Samuel S. Shepard <sshepard@cdc.gov>"]