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Fix counting statistics with shorter trees#125

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ammarcsj merged 8 commits into
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fix_counting_stats_w_shorter_trees
May 25, 2026
Merged

Fix counting statistics with shorter trees#125
ammarcsj merged 8 commits into
mainfrom
fix_counting_stats_w_shorter_trees

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@ammarcsj ammarcsj commented Feb 13, 2026

The counting statistics module had an error on fragpipe data, because the tree format was not correctly recognized as reported here #105

Implemented a new function to determine the appropriate level for missing value statistical testing based on the tree structure, which is then used subsequently.

@ammarcsj ammarcsj requested a review from mschwoer February 13, 2026 12:28
@ammarcsj ammarcsj changed the title Fix_counting_stats_w_shorter_trees Fix counting statistics with shorter trees Feb 13, 2026
Comment thread alphaquant/config/quant_reader_config.yaml
Comment thread alphaquant/cluster/cluster_missingval.py Outdated
Comment thread alphaquant/cluster/cluster_missingval.py Outdated
Comment thread alphaquant/cluster/cluster_missingval.py Outdated
Comment thread alphaquant/cluster/cluster_missingval.py
ammarcsj and others added 6 commits May 25, 2026 11:32
File has no references anywhere in the codebase.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Not part of the public API; only called internally from _get_nodes_to_test.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Scenario 1 was missing an inline comment explaining why mod_seq_charge
is the test level when fragment data is present.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Return the level value instead of setting the global inside the function;
assign at the call site in _get_nodes_to_test.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
In short trees (no fragment data), the leaves are the precursors
themselves, making base-level testing the correct granularity.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
@ammarcsj ammarcsj merged commit 5e22dea into main May 25, 2026
@ammarcsj ammarcsj deleted the fix_counting_stats_w_shorter_trees branch May 25, 2026 09:38
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2 participants