Add category for error messages

[leexgh]

No description provided.

[gemini-code-assist]

Code Review

This pull request introduces an ErrorLevel enum (ERROR, WARN, INFO) to classify annotation errors and updates the error report format to include this level. It also adds handling for variants spanning coding/UTR boundaries, classifying them as expected INFO-level events, and improves error details for unknown annotations. The feedback suggests using StringUtils.isNotBlank to handle empty or whitespace-only error messages more robustly, and removing a redundant null check for the variant classification string.

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[gemini-code-assist]

If annotatedRecord.getErrorMessage() returns an empty string or whitespace, the resulting error message will be formatted as UNKNOWN_ANNOTATION_ERROR_MESSAGE + ";" + "", which is not very helpful. Using StringUtils.isNotBlank (from org.apache.commons.lang.StringUtils, which is already imported) ensures that we fall back to the default message if the error message is empty or blank.

Suggested change

	String errorDetail = annotatedRecord.getErrorMessage() != null
	? annotatedRecord.getErrorMessage()
	: "no error details available - check genome nexus logs";
	String errorDetail = StringUtils.isNotBlank(annotatedRecord.getErrorMessage())
	? annotatedRecord.getErrorMessage()
	: "no error details available - check genome nexus logs";

[gemini-code-assist]

The null check if (varClass == null) is redundant because getVARIANT_CLASSIFICATION() is guaranteed to return an empty string "" instead of null (as implemented in MutationRecord.java). We can simplify this method by removing the redundant null check.

    private boolean isVariantSpanningNonCodingRegion(AnnotatedRecord annotatedRecord) {
        String varClass = annotatedRecord.getVARIANT_CLASSIFICATION();
        return varClass.contains("Frame_Shift") || varClass.contains("In_Frame");
    }