Handle empty inputs in parsing and mapping

[Ulthran]

Summary

• ensure parsers gracefully handle empty or header-only inputs and preserve expected columns
• reindex mapped outputs so final summaries include required fields even when inputs are empty
• add regression tests covering empty inputs for parsers and map helpers

Testing

• pytest (fails: missing pandas dependency in environment)

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Codex Task

[Copilot]

Pull request overview

This PR enhances the robustness of data parsing and mapping functions by ensuring they gracefully handle empty and header-only input files while preserving expected column structures. The changes prevent downstream failures when processing empty datasets by using DataFrame.reindex() to guarantee consistent schemas even when all inputs are empty.

Key Changes

• Added empty-case handling in parse_sylph() and parse_mash_winning_sorted_tab() to return DataFrames with complete column definitions after filtering operations
• Updated all mapping functions to use DataFrame.reindex() instead of direct column selection, ensuring required columns exist even with empty inputs
• Added comprehensive regression tests covering empty inputs for both parsers and mapping helpers

Reviewed changes

Copilot reviewed 5 out of 5 changed files in this pull request and generated 3 comments.

File	Description
scripts/test_parse.py	Added tests for header-only TSV files and empty sylph files to verify column structure preservation
scripts/test_map.py	Added comprehensive test verifying all mapping functions handle empty parsed outputs correctly
scripts/parse.py	Enhanced parse_mash_winning_sorted_tab() and parse_sylph() to return DataFrames with expected columns when inputs become empty after filtering
scripts/map.py	Replaced direct column selection with DataFrame.reindex() in all mapping functions to guarantee column presence regardless of input emptiness

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