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Address Tranquillyzer hanging when error encountered during annotation. Will now empty queues and exit when an error is encountered.

Also did some refactoring to clean up some code and prepare for future changes/refactors.

Renamed to collect_prediction_stats to better reflect was is occurring
in this function. Also, moved function outside of outer function (to
global scope level) to untangle the two functions from one another.

More work may yet be needed to clean up this function and simplify
handling
Errors may occur during annotation or model building for visualization
that need to be caught and handled more gracefully than throwing a stack
trace.
allows logger to be shared across all functions. this will also allow
for an easier transition to creating a module that can be called by all
other modules for creating a logger
@AyushSemwal AyushSemwal merged commit 4b89e30 into huishenlab:main Nov 25, 2025
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codecov bot commented Nov 25, 2025

Codecov Report

❌ Patch coverage is 49.04459% with 80 lines in your changes missing coverage. Please review.

Files with missing lines Patch % Lines
wrappers/annotate_reads_wrap.py 39.09% 67 Missing ⚠️
wrappers/visualize_wrap.py 57.89% 8 Missing ⚠️
scripts/annotate_new_data.py 33.33% 2 Missing ⚠️
scripts/correct_barcodes.py 0.00% 1 Missing ⚠️
scripts/preprocess_reads.py 75.00% 1 Missing ⚠️
scripts/train_new_model.py 50.00% 1 Missing ⚠️
Files with missing lines Coverage Δ
scripts/deduplicate.py 40.72% <100.00%> (ø)
scripts/export_annotations.py 74.01% <100.00%> (ø)
scripts/plot_read_len_distr.py 78.04% <100.00%> (ø)
scripts/simulate_training_data.py 94.77% <100.00%> (ø)
wrappers/align_wrap.py 92.85% <100.00%> (ø)
wrappers/dedup_wrap.py 87.50% <100.00%> (ø)
wrappers/preprocess_wrap.py 75.00% <ø> (ø)
wrappers/read_length_distr_wrap.py 100.00% <100.00%> (ø)
wrappers/simulate_data_wrap.py 94.44% <100.00%> (ø)
wrappers/train_model_wrap.py 92.81% <100.00%> (ø)
... and 6 more

... and 1 file with indirect coverage changes

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@jamorrison jamorrison deleted the fix_hang branch December 3, 2025 20:10
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2 participants