Merge pull request #86 from ArcInstitute/improve-namespace-of-codebase

Improve namespace of codebase

Author: noamteyssier

examples/network_streaming.rs

@@ -2,10 +2,10 @@ use std::io::{BufReader, BufWriter};
 use std::net::{TcpListener, TcpStream};
 use std::thread;
 
-use binseq::bq::{BinseqHeader, BinseqHeaderBuilder, StreamReader, StreamWriterBuilder};
+use binseq::bq::{FileHeader, FileHeaderBuilder, StreamReader, StreamWriterBuilder};
 use binseq::{BinseqRecord, Policy, Result};
 
-fn server(header: BinseqHeader, sequence: &[u8]) -> Result<()> {
+fn server(header: FileHeader, sequence: &[u8]) -> Result<()> {
     // Create a listener on localhost:3000
     let listener = TcpListener::bind("127.0.0.1:3000").expect("Failed to bind to address");
     println!("Server listening on 127.0.0.1:3000");
@@ -80,7 +80,7 @@ fn client() -> Result<()> {
 
 fn main() -> Result<()> {
     // Create a header for sequences of length 100
-    let header = BinseqHeaderBuilder::new().slen(100).build()?;
+    let header = FileHeaderBuilder::new().slen(100).build()?;
 
     // Create some example sequence data
     let sequence = b"ACGT".repeat(25); // 100 nucleotides

examples/streaming.rs

@@ -1,11 +1,11 @@
 use std::io::{BufReader, Cursor};
 
-use binseq::bq::{BinseqHeaderBuilder, StreamReader, StreamWriterBuilder};
+use binseq::bq::{FileHeaderBuilder, StreamReader, StreamWriterBuilder};
 use binseq::{BinseqRecord, Policy, Result};
 
 fn main() -> Result<()> {
     // Create a header for sequences of length 100
-    let header = BinseqHeaderBuilder::new().slen(100).build()?;
+    let header = FileHeaderBuilder::new().slen(100).build()?;
 
     // Create some example sequence data
     let sequence = b"ACGT".repeat(25); // 100 nucleotides

src/bq/header.rs

@@ -32,22 +32,22 @@ pub const SIZE_HEADER: usize = 32;
 pub const RESERVED: [u8; 17] = [42; 17];
 
 #[derive(Debug, Clone, Copy)]
-pub struct BinseqHeaderBuilder {
+pub struct FileHeaderBuilder {
     slen: Option<u32>,
     xlen: Option<u32>,
     bitsize: Option<BitSize>,
     flags: Option<bool>,
 }
-impl Default for BinseqHeaderBuilder {
+impl Default for FileHeaderBuilder {
     fn default() -> Self {
         Self::new()
     }
 }
 
-impl BinseqHeaderBuilder {
+impl FileHeaderBuilder {
     #[must_use]
     pub fn new() -> Self {
-        BinseqHeaderBuilder {
+        FileHeaderBuilder {
             slen: None,
             xlen: None,
             bitsize: None,
@@ -74,8 +74,8 @@ impl BinseqHeaderBuilder {
         self.flags = Some(flags);
         self
     }
-    pub fn build(self) -> Result<BinseqHeader> {
-        Ok(BinseqHeader {
+    pub fn build(self) -> Result<FileHeader> {
+        Ok(FileHeader {
             magic: MAGIC,
             format: FORMAT,
             slen: if let Some(slen) = self.slen {
@@ -93,13 +93,13 @@ impl BinseqHeaderBuilder {
 
 /// Header structure for binary sequence files
 ///
-/// The `BinseqHeader` contains metadata about the binary sequence data stored in a file,
+/// The `FileHeader` contains metadata about the binary sequence data stored in a file,
 /// including format information, sequence lengths, and space for future extensions.
 ///
 /// The total size of this structure is 32 bytes, with a fixed layout to ensure
 /// consistent reading and writing across different platforms.
 #[derive(Debug, Clone, Copy, PartialEq, Eq)]
-pub struct BinseqHeader {
+pub struct FileHeader {
     /// Magic number to identify the file format
     ///
     /// 4 bytes
@@ -135,7 +135,7 @@ pub struct BinseqHeader {
     /// 17 bytes
     pub reserved: [u8; 17],
 }
-impl BinseqHeader {
+impl FileHeader {
     /// Creates a new header with the specified sequence length
     ///
     /// This constructor initializes a standard header with the given sequence length,
@@ -150,7 +150,7 @@ impl BinseqHeader {
     ///
     /// # Returns
     ///
-    /// A new `BinseqHeader` instance
+    /// A new `FileHeader` instance
     #[must_use]
     pub fn new(bits: BitSize, slen: u32, flags: bool) -> Self {
         Self {
@@ -178,7 +178,7 @@ impl BinseqHeader {
     ///
     /// # Returns
     ///
-    /// A new `BinseqHeader` instance with extended sequence information
+    /// A new `FileHeader` instance with extended sequence information
     #[must_use]
     pub fn new_extended(bits: BitSize, slen: u32, xlen: u32, flags: bool) -> Self {
         Self {
@@ -214,7 +214,7 @@ impl BinseqHeader {
     ///
     /// # Returns
     ///
-    /// * `Ok(BinseqHeader)` - A valid header parsed from the buffer
+    /// * `Ok(FileHeader)` - A valid header parsed from the buffer
     /// * `Err(Error)` - If the buffer contains invalid header data
     ///
     /// # Errors
@@ -266,7 +266,7 @@ impl BinseqHeader {
     ///
     /// # Returns
     ///
-    /// * `Ok(BinseqHeader)` - A valid header parsed from the buffer
+    /// * `Ok(FileHeader)` - A valid header parsed from the buffer
     /// * `Err(Error)` - If the buffer is too small or contains invalid header data
     ///
     /// # Errors
@@ -324,7 +324,7 @@ impl BinseqHeader {
     ///
     /// # Returns
     ///
-    /// * `Ok(BinseqHeader)` - A valid header read from the reader
+    /// * `Ok(FileHeader)` - A valid header read from the reader
     /// * `Err(Error)` - If reading from the reader failed or the header data is invalid
     ///
     /// # Errors

src/bq/mod.rs

@@ -2,9 +2,9 @@
 //!
 //! *.bq files are BINSEQ variants for **fixed-length** records and **does not support quality scores**.
 //!
-//! For variable-length records and optional quality scores use the [`vbq`](crate::vbq) module.
+//! For variable-length records and optional quality scores use the [`cbq`](crate::cbq) or [`vbq`](crate::vbq) modules.
 //!
-//! This module contains the utilities for reading, writing, and interacting with BINSEQ files.
+//! This module contains the utilities for reading, writing, and interacting with BQ files.
 //!
 //! For detailed information on the file format, see our [paper](https://www.biorxiv.org/content/10.1101/2025.04.08.647863v1).
 //!
@@ -46,11 +46,11 @@
 //! // Create an in-memory buffer for output
 //! let output_handle = Cursor::new(Vec::new());
 //!
-//! // Initialize our BINSEQ header (64 bp, only primary)
-//! let header = bq::BinseqHeaderBuilder::new().slen(64).build().unwrap();
+//! // Initialize our BQ header (64 bp, only primary)
+//! let header = bq::FileHeaderBuilder::new().slen(64).build().unwrap();
 //!
-//! // Initialize our BINSEQ writer
-//! let mut writer = bq::BinseqWriterBuilder::default()
+//! // Initialize our BQ writer
+//! let mut writer = bq::WriterBuilder::default()
 //!     .header(header)
 //!     .build(output_handle)
 //!     .unwrap();
@@ -79,11 +79,11 @@
 //! // Create an in-memory buffer for output
 //! let output_handle = Cursor::new(Vec::new());
 //!
-//! // Initialize our BINSEQ header (64 bp and 128bp)
-//! let header = bq::BinseqHeaderBuilder::new().slen(64).xlen(128).build().unwrap();
+//! // Initialize our BQ header (64 bp and 128bp)
+//! let header = bq::FileHeaderBuilder::new().slen(64).xlen(128).build().unwrap();
 //!
-//! // Initialize our BINSEQ writer
-//! let mut writer = bq::BinseqWriterBuilder::default()
+//! // Initialize our BQ writer
+//! let mut writer = bq::WriterBuilder::default()
 //!     .header(header)
 //!     .build(output_handle)
 //!     .unwrap();
@@ -109,12 +109,12 @@
 //!
 //! ```
 //! use binseq::{Policy, Result, BinseqRecord, SequencingRecordBuilder};
-//! use binseq::bq::{BinseqHeaderBuilder, StreamReader, StreamWriterBuilder};
+//! use binseq::bq::{FileHeaderBuilder, StreamReader, StreamWriterBuilder};
 //! use std::io::{BufReader, Cursor};
 //!
 //! fn main() -> Result<()> {
 //!     // Create a header for sequences of length 100
-//!     let header = BinseqHeaderBuilder::new().slen(100).build()?;
+//!     let header = FileHeaderBuilder::new().slen(100).build()?;
 //!
 //!     // Create a stream writer
 //!     let mut writer = StreamWriterBuilder::default()
@@ -150,7 +150,7 @@
 //!
 //! ## BQ file format
 //!
-//! A BINSEQ file consists of two sections:
+//! A BQ file consists of two sections:
 //!
 //! 1. Fixed-size header (32 bytes)
 //! 2. Record data section
@@ -241,6 +241,6 @@ mod header;
 mod reader;
 mod writer;
 
-pub use header::{BinseqHeader, BinseqHeaderBuilder, SIZE_HEADER};
+pub use header::{FileHeader, FileHeaderBuilder, SIZE_HEADER};
 pub use reader::{MmapReader, RefRecord, StreamReader};
-pub use writer::{BinseqWriter, BinseqWriterBuilder, Encoder, StreamWriter, StreamWriterBuilder};
+pub use writer::{Encoder, StreamWriter, StreamWriterBuilder, Writer, WriterBuilder};

src/bq/reader.rs

@@ -17,7 +17,7 @@ use bitnuc::BitSize;
 use bytemuck::cast_slice;
 use memmap2::Mmap;
 
-use super::header::{BinseqHeader, SIZE_HEADER};
+use super::header::{FileHeader, SIZE_HEADER};
 use crate::{
     BinseqRecord, DEFAULT_QUALITY_SCORE, Error, ParallelProcessor, ParallelReader,
     error::{ReadError, Result},
@@ -298,12 +298,12 @@ impl RecordConfig {
     ///
     /// # Arguments
     ///
-    /// * `header` - A reference to a `BinseqHeader` containing sequence lengths
+    /// * `header` - A reference to a `FileHeader` containing sequence lengths
     ///
     /// # Returns
     ///
     /// A new `RecordConfig` instance with the sequence lengths from the header
-    pub fn from_header(header: &BinseqHeader) -> Self {
+    pub fn from_header(header: &FileHeader) -> Self {
         Self::new(
             header.slen as usize,
             header.xlen as usize,
@@ -411,7 +411,7 @@ pub struct MmapReader {
     mmap: Arc<Mmap>,
 
     /// Binary sequence file header containing format information
-    header: BinseqHeader,
+    header: FileHeader,
 
     /// Configuration defining the layout of records in the file
     config: RecordConfig,
@@ -456,7 +456,7 @@ impl MmapReader {
         let mmap = unsafe { Mmap::map(&file)? };
 
         // Read header from mapped memory
-        let header = BinseqHeader::from_buffer(&mmap)?;
+        let header = FileHeader::from_buffer(&mmap)?;
 
         // Record configuraration
         let config = RecordConfig::from_header(&header);
@@ -491,7 +491,7 @@ impl MmapReader {
     ///
     /// The header contains format information and sequence length specifications.
     #[must_use]
-    pub fn header(&self) -> BinseqHeader {
+    pub fn header(&self) -> FileHeader {
         self.header
     }
 
@@ -580,7 +580,7 @@ pub struct StreamReader<R: Read> {
     reader: R,
 
     /// Binary sequence file header containing format information
-    header: Option<BinseqHeader>,
+    header: Option<FileHeader>,
 
     /// Configuration defining the layout of records in the file
     config: Option<RecordConfig>,
@@ -659,7 +659,7 @@ impl<R: Read> StreamReader<R> {
     ///
     /// # Returns
     ///
-    /// * `Ok(&BinseqHeader)` - A reference to the validated header
+    /// * `Ok(&FileHeader)` - A reference to the validated header
     /// * `Err(Error)` - If reading or validating the header fails
     ///
     /// # Panics
@@ -672,7 +672,7 @@ impl<R: Read> StreamReader<R> {
     /// * There is an I/O error when reading from the source
     /// * The header data is invalid
     /// * End of stream is reached before the full header can be read
-    pub fn read_header(&mut self) -> Result<&BinseqHeader> {
+    pub fn read_header(&mut self) -> Result<&FileHeader> {
         if self.header.is_some() {
             return Ok(self
                 .header
@@ -687,7 +687,7 @@ impl<R: Read> StreamReader<R> {
 
         // Parse header
         let header_slice = &self.buffer[self.buffer_pos..self.buffer_pos + SIZE_HEADER];
-        let header = BinseqHeader::from_buffer(header_slice)?;
+        let header = FileHeader::from_buffer(header_slice)?;
 
         self.header = Some(header);
         self.config = Some(RecordConfig::from_header(&header));