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nkindlon avatar nkindlon commented on August 23, 2024

On investigating, I found that not all files have been opened by the time the Context classes perform their validation via their isValidState() methods. I think the best solution here is to refactor the contexts to perform all file management. The various tools would then not need to do their own file management, but rather just access files through the context. The context would then be able to open and type check all files before or as part of it's validation step.

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arq5x avatar arq5x commented on August 23, 2024

Once this is refactored, we need to add a test to the Map tool to check if the -b file is BAM. If so, we should exit and issue an error. This will be needed until there is support for accessing fieldd by number ofr BAM files.

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nkindlon avatar nkindlon commented on August 23, 2024

Fixed with my latest pull request. This issue can be closed after merging.

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