Use external gzip utilities for FASTQ IO

[Ulthran]

Summary

• open gzipped FASTQ files by shelling out to pigz when available and fall back to gzip or Python's gzip module
• wrap subprocess pipes so file-like interfaces remain compatible with existing code paths
• close CLI input and output streams after each run to flush compression pipelines and release resources

Testing

• pytest

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https://chatgpt.com/codex/tasks/task_e_68f12f6338608323a232b1100a4d1ca6

[Copilot]

Pull Request Overview

This PR introduces optimized gzip compression for FASTQ file I/O by leveraging external utilities (pigz/gzip) when available, falling back to Python's native gzip module otherwise. The changes wrap subprocess pipes in file-like interfaces to maintain compatibility with existing code paths and ensure proper resource cleanup.

• Adds subprocess-based gzip reading/writing using pigz (parallel) or gzip utilities
• Implements _SubprocessFileWrapper to provide file-like interface for subprocess pipes
• Adds stream cleanup logic to close input/output streams after command execution

Reviewed Changes

Copilot reviewed 2 out of 2 changed files in this pull request and generated 1 comment.

File	Description
src/heyfastqlib/argparse_types.py	Adds external gzip utility detection, subprocess wrapper class, and integration with GzipFileType for reading/writing compressed files
src/heyfastqlib/command.py	Adds stream cleanup logic with try-finally blocks and standard stream protection to ensure proper resource release

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[Copilot]

The subprocess return code check doesn't handle the case where wait() might raise an exception. Additionally, creating CalledProcessError without raising it immediately means subsequent exceptions could suppress this error. Consider raising the CalledProcessError immediately when detected.