graph LR
Utility_Functions["Utility Functions"]
Data_Types_and_Schemas["Data Types and Schemas"]
Error_Handling_Framework["Error Handling Framework"]
Date_and_Time_Utilities["Date and Time Utilities"]
Support_Utilities["Support Utilities"]
Utility_Functions -- "depends on" --> Data_Types_and_Schemas
Utility_Functions -- "depends on" --> Error_Handling_Framework
Date_and_Time_Utilities -- "depends on" --> Error_Handling_Framework
Error_Handling_Framework -- "provides base exceptions to" --> Date_and_Time_Utilities
Error_Handling_Framework -- "provides base exceptions to" --> Support_Utilities
Data_Types_and_Schemas -- "provides data structures to" --> Utility_Functions
Data_Types_and_Schemas -- "provides data structures to" --> Date_and_Time_Utilities
Data_Types_and_Schemas -- "provides data structures to" --> Support_Utilities
This foundational component provides a collection of common helper functions, reusable data structures, and robust error handling mechanisms that are utilized across all other augur components. It includes utilities for generic file reading/writing, date parsing and handling, and fundamental data manipulation, ensuring consistency and reducing code duplication throughout the project.
This component provides a wide array of general utility functions for common operations like file handling, data manipulation, and string processing. It acts as a central hub for reusable code snippets, ensuring consistency and reducing code duplication across the augur project.
Related Classes/Methods:
This component defines the core data structures, enumerations (like ArgparseEnum), and type definitions used throughout the augur project. It ensures data consistency and facilitates clear communication and validation between different modules, which is crucial for a data-centric bioinformatics pipeline.
Related Classes/Methods:
This component centralizes the definition of custom exception classes, such as AugurError and its various specialized subclasses (e.g., InvalidDate, CyclicGeolocationRulesError), specific to augur's operations. It provides a structured and consistent approach to error handling across the pipeline, allowing for more specific and informative error reporting.
Related Classes/Methods:
This component specializes in parsing, validating, and resolving ambiguous date formats, which is crucial for epidemiological and phylogenetic data often characterized by varying date granularities. It provides specialized functions for date-related operations, ensuring temporal accuracy.
Related Classes/Methods:
This component provides additional general-purpose utility functions and helper classes that support various functionalities across the augur project. This may include more specialized data handling or file processing capabilities that complement the broader Utility Functions component.
Related Classes/Methods:
augur.util_support(1:1000)