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Description

This pull request includes changes to the ReferenceSequence class in the src/Snps/ReferenceSequence.php file and the addition of a new Resources class in the src/Snps/Resources.php file.

Summary

• Modified the ReferenceSequence class constructor to remove the readonly keyword from the property declarations.
• Modified the getID() and getChrom() methods in the ReferenceSequence class to return the correct property value.
• Modified the getUrl(), getPath(), getAssembly(), getSpecies(), and getTaxonomy() methods in the ReferenceSequence class to return the correct property value.
• Modified the getBuild() method in the ReferenceSequence class to use the correct property value.
• Modified the loadSequence() method in the ReferenceSequence class to use the correct property value.
• Added a new Resources class in the src/Snps/Resources.php file.
• Added a constructor to the Resources class to initialize the baseUrl, localResourceDir, and httpClient properties.
• Added a downloadResource() method to the Resources class to download a resource from a given URL to a specified destination path.
• Added a loadDataFromFile() method to the Resources class to load data from a file.
• Added a getReferenceSequence() method to the Resources class to get a ReferenceSequence object for a given ID.
• Added placeholder methods getAssemblyMappingData() and getExampleDataset() to the Resources class.
• Added a getLocalPathForResource() method to the Resources class to get the local path for a resource.

Fixes #110.

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Rollback Files For Sweep

• Rollback changes to src/Snps/ReferenceSequence.php
• Rollback changes to src/Snps/Resources.php

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Apply Sweep Rules to your PR?

• Apply: All new business logic should have corresponding unit tests.
• Apply: Refactor large functions to be more modular.
• Apply: Add docstrings to all functions and file headers.

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