Update Zoe to v0.0.19

Author: sammysheep

.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 { $/ = undef; ($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
+    - perl -ne 'BEGIN { $/ = undef; ($v) = (shift @ARGV) =~ /#(.+)/; } if (/^## \[(.*?)\] - (\S+)/m) { if ( (length $2 eq 10 && $1 ne $v) || ($2 eq 'TBD' && $v !~ /dev$/) ) { die "Cargo.toml ($v) mismatches changelog ($1 / $2)!\n"; } }' "$(cargo pkgid)" CHANGELOG.md
     - cargo test --verbose
 
 pages:

CHANGELOG.md

@@ -5,6 +5,17 @@ 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).
 
+## [0.5.2] - TBD
+
+### Changed
+
+- Use threads and anonymous pipes (in Rust) when decompressing zipped inputs
+
+### Fixes
+
+- Updated Zoe dependency (v0.0.19) fixes hard clipping in merged reads. Reader
+  error messages are also improved generally.
+
 ## [0.5.1] - 2025-06-03
 
 ### Fixes
@@ -112,6 +123,7 @@ is roughly based on [Keep a Changelog], and this project tries to adheres to
 - **Added**: custom inexact matching algorithm from [Zoe]
 
 <!-- Versions -->
+[0.5.2]: https://github.com/CDCgov/irma-core/compare/v0.5.1...v0.5.2
 [0.5.1]: https://github.com/CDCgov/irma-core/compare/v0.5.0...v0.5.1
 [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

Cargo.lock

@@ -1,19 +1,19 @@
 [package]
 name = "irma-core"
-version = "0.5.1-dev"
+version = "0.5.2-dev"
 edition = "2024"
 description = "A tool to aid virus sequencing and accelerating IRMA."
 license = "Apache-2.0"
 rust-version = "1.88"
 
-# Long-term maintainers of the IRMA-core
 authors = ["Samuel S. Shepard <sshepard@cdc.gov>"]
 categories = [
     "science::bioinformatics::sequence-analysis",
     "science::bioinformatics::genomics",
 ]
 keywords = ["sequencing", "influenza", "trimming", "qc"]
 repository = "https://github.com/CDCgov/irma-core"
+homepage = "https://github.com/CDCgov/irma-core"
 readme = "README.md"
 
 
@@ -22,7 +22,7 @@ clap = { version = "4.5", features = ["derive"] }
 foldhash = "0.1.5"
 num_cpus = "1.16"
 flate2 = "1.1"
-zoe = { version = "0.0.18", default-features = false, features = [
+zoe = { version = "0.0.19", default-features = false, features = [
     "multiversion",
 ] }
 
@@ -32,3 +32,4 @@ opt-level = 1
 [profile.release]
 strip = true
 lto = "fat"
+# Long-term maintainers of the IRMA-core

Cargo.toml

@@ -79,7 +79,7 @@ pub fn merge_sam_pairs_process(args: MergeSAMArgs) {
                 if d.rname != reference.name {
                     continue;
                 }
-                *d
+                d
             }
             Ok(SamRow::Header(h)) => {
                 writeln!(sam_writer, "{h}").unwrap_or_die(&format!(