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1 | 1 | #![doc = include_str!("../README.md")] |
2 | 2 | //! |
3 | | -//! # Overview |
| 3 | +//! # BINSEQ |
4 | 4 | //! |
5 | | -//! The `binseq` library provides efficient tools for working with binary-encoded |
6 | | -//! nucleotide sequences. It offers: |
| 5 | +//! The `binseq` library provides efficient tools for working with the [BINSEQ](https://www.biorxiv.org/content/10.1101/2025.04.08.647863v1) file format family. |
7 | 6 | //! |
8 | | -//! - Compact 2-bit encoding of nucleotide sequences |
| 7 | +//! It offers tools to read and write BINSEQ files, providing: |
| 8 | +//! |
| 9 | +//! - Compact 2-bit encoding and decoding of nucleotide sequences through [`bitnuc`](https://docs.rs/bitnuc/latest/bitnuc/) |
9 | 10 | //! - Memory-mapped file access for efficient reading |
10 | | -//! - Parallel processing capabilities |
11 | | -//! - Configurable policies for handling invalid nucleotides |
| 11 | +//! - Parallel processing capabilities for arbitrary tasks through the [`ParallelProcessor`] trait. |
| 12 | +//! - Configurable [`Policy`] for handling invalid nucleotides |
12 | 13 | //! - Support for both single and paired-end sequences |
| 14 | +//! - Abstract [`BinseqRecord`] trait for representing records from both `.bq` and `.vbq` files. |
| 15 | +//! |
| 16 | +//! ## Crate Organization |
13 | 17 | //! |
14 | | -//! # Core Components |
| 18 | +//! This library is split into 3 major parts. |
15 | 19 | //! |
16 | | -//! - [`BinseqWriter`]: Writes sequences to binary format |
17 | | -//! - [`MmapReader`]: Reads sequences using memory mapping |
18 | | -//! - [`BinseqHeader`]: Defines file format and sequence lengths |
19 | | -//! - [`Policy`]: Configures invalid nucleotide handling |
20 | | -//! - [`ParallelProcessor`]: Enables parallel sequence processing |
| 20 | +//! There are the [`bq`] and [`vbq`] modules, which provide tools for reading and writing `BQ` and `VBQ` files respectively. |
| 21 | +//! Then there are traits and utilities that are ubiquitous across the library which are available at the top-level of the crate. |
21 | 22 | //! |
22 | 23 | //! # Example |
23 | 24 | //! |
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