Release v0.4.0

CHANGELOG.md

@@ -4,7 +4,7 @@ Each release's binaries and full notes are on the
 [releases page](https://github.com/DylanCosto/bonefish/releases). "Output" means the alignment
 records. Each entry quotes the MD5 of the genome-wide HG001 sample's SAM output, `@PG` lines removed.
 
-## Unreleased
+## v0.4.0 (2026-10-28)
 
 **New: `-x hifi`** (alias `map-hifi`), for PacBio HiFi genomic DNA. It is the `dna` preset, plus
 one extra step: stretches of fragmented long gaps are realigned under minimap2 `map-hifi` scoring,

CITATION.cff

@@ -1,16 +1,17 @@
 cff-version: 1.2.0
 message: "If you use bonefish, please cite it as below, together with minimap2."
-title: "bonefish: a fast aligner for Oxford Nanopore DNA, RNA and cDNA reads"
+title: "bonefish: a fast aligner for Oxford Nanopore and PacBio HiFi reads"
 type: software
 authors:
   - family-names: Costo
     given-names: Dylan
-version: 0.3.0
-date-released: 2026-10-21
+version: 0.4.0
+date-released: 2026-10-28
 license: MIT
 repository-code: "https://github.com/DylanCosto/bonefish"
 keywords:
   - Oxford Nanopore
+  - PacBio HiFi
   - long reads
   - sequence alignment
   - variant calling

Cargo.toml

@@ -3,7 +3,7 @@ resolver = "2"
 members = ["bonefish-core", "bonefish"]
 
 [workspace.package]
-version = "0.3.0"
+version = "0.4.0"
 edition = "2024"
 license = "MIT"
 repository = "https://github.com/DylanCosto/bonefish"

bonefish/Cargo.toml

@@ -24,7 +24,7 @@ jemalloc = ["dep:tikv-jemallocator"]
 mimalloc = ["dep:mimalloc"]
 
 [dependencies]
-bonefish-core = { path = "../bonefish-core", version = "0.3.0", default-features = false }
+bonefish-core = { path = "../bonefish-core", version = "0.4.0", default-features = false }
 clap = { version = "4", features = ["derive"] }
 env_logger = "0.11"
 log = "0.4"