BIOIN-2656 add indel category to report

[rinashalibo]

Note

Low Risk
Primarily reporting/test-schema changes and a small import refactor; risk is limited to downstream consumers expecting the old CSV column layout or category list.

Overview
Extends concordance/report outputs to include an aucpr (area under PR curve) metric in the generated expected.out.stats.csv test fixture, shifting the CSV schema accordingly.

Adds a new reporting category, non-hmer Indel + hmer Indel <=12, and implements its filter logic in report_utils.__filter_by_category, enabling combined indel performance summaries in createVarReport.ipynb.

Refactors run_no_gt_report.py to import and call annotate_concordance directly from ugbio_comparison.vcf_comparison_utils (instead of via comparison_utils).

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[Copilot]

Pull request overview

This PR adds a new indel category "non-hmer Indel + hmer Indel <=12" to the variant reporting system, combining non-homopolymer indels with short homopolymer indels (length ≤12).

Changes:

• Added filtering logic for the new combined indel category in the report utilities
• Extended the category list in the variant report notebook to include the new category
• Updated the ugbio_utils subproject commit reference

Reviewed changes

Copilot reviewed 3 out of 3 changed files in this pull request and generated no comments.

File	Description
ugvc/reports/report_utils.py	Implements filtering logic for the new combined indel category
ugvc/reports/createVarReport.ipynb	Adds the new category to the reporting categories list
ugbio_utils	Updates subproject commit reference

Comments suppressed due to low confidence (1)

ugvc/reports/report_utils.py:533

• This line exceeds 120 characters and contains complex nested boolean logic that is difficult to read. Consider breaking this into multiple lines or extracting the conditions into named variables for better readability.

            result = data[((data["indel"]) & (data["hmer_length"] == 0) & (data["indel_length"] > 0)) | ((data["indel"]) & (data["hmer_length"] > 0) & (data["hmer_length"] <= 12))]            

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[doron-st]

suggested simplification

[cursor]

Cursor Bugbot has reviewed your changes and found 1 potential issue.

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