style: reformat code and add doc tests (#12)

<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->
## Summary by CodeRabbit

- **New Features**
- Introduced new error variants for enhanced error handling in regex
operations.
- Added a structured logging system to improve progress tracking and
message clarity.
- Implemented new `FastqReader` and `FastqWriter` for improved FASTQ
file handling.

- **Improvements**
	- Renamed functions for better clarity in compression type handling.
- Refactored command-line argument handling for improved organization
and readability.
- Enhanced documentation with clearer installation instructions and
project description.

- **Bug Fixes**
- Updated logging mechanism to replace print statements with structured
logger usage.

- **Refactor**
- Major refactor of barcode handling logic, simplifying structures and
methods.
- Consolidated parameters in the command-line interface for better
organization.
<!-- end of auto-generated comment: release notes by coderabbit.ai -->

Cargo.toml

@@ -3,7 +3,7 @@ name = "barkit"
 version = "0.1.0" # managed by release.sh
 edition = "2021"
 authors = ["Nikita Syzrantsev [email protected]"]
-description = "Tool to process barcodes in FASTQ"
+description = "BarKit — a cross-platform and ultrafast toolkit for barcodes manipulation in FASTQ files"
 license = "GPL-3.0"
 readme = "README.md"
 homepage = "https://github.com/nsyzrantsev/barkit"

README.md

@@ -1,21 +1,37 @@
 # BarKit
 
-> [!WARNING]  
-> This tool is under development. Please use the first release version when it becomes available.
-
-BarKit (Barcodes Toolkit) is a toolkit designed for manipulating FASTQ barcodes.
+BarKit (**Bar**codes Tool**Kit**) is a toolkit designed for manipulating FASTQ barcodes.
 
 ## Installation
 
+### From crates.io
+
+Barkit can be installed from [`crates.io`](https://crates.io/crates/barkit) using `cargo`. This can be done with the following command:
+
 ```bash
 cargo install barkit
 ```
 
-## Extract Command
+### Build from source
+
+1. Clone the repository:
+
+```bash
+git clone https://github.com/nsyzrantsev/barkit
+cd barkit/
+```
+
+2. Build:
+
+```bash
+cargo build --release && sudo mv target/release/barkit /usr/local/bin/
+```
+
+## Extract subcommand
 
-The extract command is designed to parse barcode sequences from FASTQ reads using approximate regex matching based on a provided pattern.
+The extract subcommand is designed to parse barcode sequences from FASTQ reads using approximate regex matching based on a provided pattern.
 
-All parsed barcode sequences are moved to the read header with base quality separated by colons:
+All parsed barcode sequences are moved to the read header with base quality, separated by colons:
 
 ```
 @SEQ_ID UMI:ATGC:???? CB:ATGC:???? SB:ATGC:????
@@ -34,7 +50,7 @@ Parse the first twelve nucleotides as a UMI from each forward read:
 barkit extract -1 <IN_FASTQ1> -2 <IN_FASTQ2> -p "^(?P<UMI>[ATGCN]{12})" -o <OUT_FASTQ1> -O <OUT_FASTQ2>
 ```
 
-Parse the first sixteen nucleotides as a cell barcode from each reverse read before the `atgccat` sequence:
+Parse the first sixteen nucleotides as a cell barcode from each reverse read before the `atgccat` adapter sequence:
 
 ```bash
 barkit extract -1 <IN_FASTQ1> -2 <IN_FASTQ2> -P "^(?P<CB>[ATGCN]{16})atgccat" -o <OUT_FASTQ1> -O <OUT_FASTQ2>

barkit-extract/Cargo.toml

@@ -3,7 +3,7 @@ name = "barkit-extract"
 version = "0.1.0" # managed by release.sh
 edition = "2021"
 authors = ["Nikita Syzrantsev [email protected]"]
-description = "Tool to extract barcodes"
+description = "Tool for extracting barcode nucleotide sequence according to a specified regex pattern"
 license = "GPL-3.0"
 readme = "../README.md"
 homepage = "https://github.com/nsyzrantsev/barkit"

barkit-extract/src/error.rs

@@ -12,10 +12,14 @@ pub enum Error {
     BarcodeCaptureGroupNotFound(String),
     #[error("Provided unexpected barcode capture group {0}")]
     UnexpectedCaptureGroupName(String),
-    #[error("Failed to read a file: {0}")]
-    FileRead(#[from] std::io::Error),
+    #[error("I/O error: {0}")]
+    IO(#[from] std::io::Error),
     #[error("No match")]
     PatternNotMatched,
+    #[error("Fancy regex error: {0}")]
+    FancyRegex(#[from] fancy_regex::Error),
+    #[error("Failed to choose permutation mask")]
+    PermutationMaskSize,
 }
 
 impl Clone for Error {
@@ -30,8 +34,10 @@ impl Clone for Error {
             Error::UnexpectedCaptureGroupName(capture_group) => {
                 Error::UnexpectedCaptureGroupName(capture_group.clone())
             }
-            Error::FileRead(err) => Error::FileRead(err.kind().into()),
+            Error::IO(err) => Error::IO(err.kind().into()),
             Error::PatternNotMatched => Error::PatternNotMatched,
+            Error::FancyRegex(err) => Error::FancyRegex(err.clone()),
+            Error::PermutationMaskSize => Error::PermutationMaskSize,
         }
     }
 }