BREAKING CHANGE: v0.16 -> CBQ input/output implementation

CHANGELOG.md

@@ -10,6 +10,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Added
 
 - `deacon filter --ordered` uses paraseq 0.5.0 order preservation for deterministic output. Also exposed as `ordered` in the Python bindings and JSON summary.
+- `deacon filter` accepts CBQ (BINSEQ) input, detected automatically, and writes CBQ when the output path ends in `.cbq`; paired reads are stored as native paired records in a single file.
 
 ### Changed
 

Cargo.toml

@@ -41,6 +41,8 @@ indicatif = { version = "0.18", optional = true }
 serde_json = { version = "1.0", optional = true }
 niffler = { version = "3.0.1", default-features = false, optional = true }
 paraseq = { version = "0.5.0", default-features = false, features = ["anyhow", "niffler"], optional = true }
+# Binary sequence format (CBQ) support. Defaults disabled: binseq's own paraseq integration is not needed.
+binseq = { version = "0.9.4", default-features = false, features = ["anyhow"], optional = true }
 ensure_simd = { version = "0.1.0", optional = true }
 
 # Compression deps (optional)
@@ -59,10 +61,11 @@ predicates = "3.0"
 tempfile = "3.20"
 rstest = "0.26"
 nix = { version = "0.31", features = ["fs"] }
+binseq = { version = "0.9.4", default-features = false, features = ["anyhow"] }
 
 [features]
 scalar = ["simd-minimizers/scalar", "packed-seq/scalar"]
-cli = ["rayon", "parking_lot", "indicatif", "paraseq", "ensure_simd", "clap", "niffler", "serde_json"]
+cli = ["rayon", "parking_lot", "indicatif", "paraseq", "binseq", "ensure_simd", "clap", "niffler", "serde_json"]
 # Disable for faster builds.
 compression = ["zstd", "liblzma", "flate2", "gzp", "paraseq/default"]
 # Use to still handle .gz files when "compression" is not enabled.

README.md

@@ -89,7 +89,7 @@ Prebuilt pangenome indexes are provided. These can be downloaded using the links
 
 ### Filtering
 
-The main command `deacon filter` accepts an index path followed by up to two FASTA/FASTQ file paths, depending on whether input sequences originate from stdin, a single file, or paired input files. Indexes are built with `deacon index build`.  Paired inputs are supported as either two separate or one interleaved file/stream when using `--interleaved`, and may be written either to separate paired output files or one interleaved file. For paired sequences, distinct minimizer hits originating from either mate are counted. By default, input sequences must meet both an absolute threshold of 2 minimizer hits (`-a 2`) and a relative threshold of 1% of minimizers (`-r 0.01`) to pass the filter. Filtering can be inverted for e.g. host depletion using the `--deplete` (`-d`) flag. Gzip, Zstandard, and xz compression formats are detected automatically by file extension. Paired read headers can be validated using `--check-pairs`. 
+The main command `deacon filter` accepts an index path followed by up to two FASTA/FASTQ file paths, depending on whether input sequences originate from stdin, a single file, or paired input files. Indexes are built with `deacon index build`.  Paired inputs are supported as either two separate or one interleaved file/stream when using `--interleaved`, and may be written either to separate paired output files or one interleaved file. For paired sequences, distinct minimizer hits originating from either mate are counted. By default, input sequences must meet both an absolute threshold of 2 minimizer hits (`-a 2`) and a relative threshold of 1% of minimizers (`-r 0.01`) to pass the filter. Filtering can be inverted for e.g. host depletion using the `--deplete` (`-d`) flag. Gzip, Zstandard, and xz compression formats are detected automatically by file extension. Paired read headers can be validated using `--check-pairs`. CBQ files (the columnar binary format of the [BINSEQ](https://www.biorxiv.org/content/10.1101/2025.04.08.647863v2) family) are detected on input by magic bytes, and written when the output path ends in `.cbq`; CBQ pairing is native, so paired reads stay in one file (do not pass `--output2`).
 
 #### Examples
 
@@ -130,6 +130,10 @@ zcat r12.fq.gz | deacon filter -d panhuman-1.k31w15.idx - - > filt12.fq
 # Save summary JSON
 deacon filter -d panhuman-1.k31w15.idx reads.fq.gz -o filt.fq.gz -s summary.json
 
+# CBQ (BINSEQ) input/output; paired reads stay in one CBQ file
+deacon filter panhuman-1.k31w15.idx reads.fq.gz -o filt.cbq
+deacon filter panhuman-1.k31w15.idx filt.cbq -o filt.fq.gz
+
 # Replace read headers with incrementing integers
 deacon filter -d -R panhuman-1.k31w15.idx reads.fq.gz > filt.fq
 

deacon-py/src/lib.rs

@@ -160,7 +160,7 @@ impl Index {
         let mins = Arc::clone(&self.minimizers);
         let (k, w) = (self.k, self.w);
         let summary = py
-            .detach(|| run_with_index(&mins, &IndexHeader::new(k, w), &cfg))
+            .detach(|| run_with_index(mins, &IndexHeader::new(k, w), &cfg))
             .map_err(to_pyerr)?;
         Ok(pythonize::pythonize(py, &summary)?.unbind())
     }