Fix freqency error in Legacy

[fuzhaoyuan]

Fix #10967
Describe changes proposed in this pull request:

1. Modified the getAlterationGeneCounts method to filter gene alteration data at the study level
2. Added a filtering step after the includeFrequencyFunction call, which is where matchingGenePanelIds gets populated
3. Created a filtered list for each study that only includes genes covered by gene panels in that specific study
4. Used the filtered list when merging results into the final collection

This implementation achieves the following benefits:

• Each study only contributes data for genes that are covered in its panels
• Genes not covered by panels in a particular study are excluded from that study's results
• The final result only contains genes that are covered by at least one panel in at least one study
• Preserves accurate profiled counts and alteration frequencies
• Maintains the proper processing flow without disrupting existing functionality

[sonarqubecloud]

Quality Gate passed

Issues
1 New issue
0 Accepted issues

Measures
0 Security Hotspots
100.0% Coverage on New Code
0.0% Duplication on New Code

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