Output fingerprinting results as csv

[gilhornung]

No description provided.

[Copilot]

Pull Request Overview

This PR changes the quick fingerprinting tool to output results in CSV format instead of plain text, while adding comprehensive documentation throughout the codebase.

• Converts output from text format to structured CSV with columns for cram_filename, sample_id, ground_truth_id, hit_fraction, and best_match
• Adds detailed docstrings and inline comments to improve code readability and maintainability
• Removes error checking and validation logic that was previously present in the comparison workflow

Reviewed Changes

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

File	Description
ugvc/pipelines/comparison/quick_fingerprinting.py	Added docstring to parser function and inline comments explaining each processing step
ugvc/comparison/quick_fingerprinter.py	Changed output format from text to CSV, added comprehensive documentation, and removed error validation logic

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[Copilot]

The file is opened without proper resource management. Consider using a context manager or ensure the file is closed in a finally block to prevent resource leaks if an exception occurs before reaching the close() call.

Suggested change

	self.output_file = open(f"{self.out_dir}/quick_fingerprinting_results.csv", "w")
	os.makedirs(out_dir, exist_ok=True)
	# Prepare ground truth VCFs for each sample
	self.ground_truths_to_check = self.prepare_ground_truth()
	self.output_file = open(f"{self.out_dir}/quick_fingerprinting_results.csv", "w")
	self._file_closed = False
	os.makedirs(out_dir, exist_ok=True)
	# Prepare ground truth VCFs for each sample
	self.ground_truths_to_check = self.prepare_ground_truth()
	def __enter__(self):
	return self
	def __exit__(self, exc_type, exc_val, exc_tb):
	self.close()
	def close(self):
	if hasattr(self, "output_file") and not self.output_file.closed:
	self.output_file.close()
	self._file_closed = True

[ilyasoifer]

@gilhornung - can you fix the test please?