sv_classifier.py crash at calc_params if no del in training data. #321
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jasonbhn wants to merge 2 commits intohall-lab:masterfrom
Open
sv_classifier.py crash at calc_params if no del in training data. #321jasonbhn wants to merge 2 commits intohall-lab:masterfrom
jasonbhn wants to merge 2 commits intohall-lab:masterfrom
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svtools classify cannot handle cases where input vcf has no deletions. Added conditions to skip deletion length adjustment if no deletions is present.
updated sv_classifier.py to fit into sv-pipeline
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Hi,
I was trying to modify sv-pipeline to be able to classify variant calls of a smaller cohort. calc_params would fail if deletions are not present in the naive Bayes training call set, contradicting the post-merge WDL script's logic. Edits are made so this could run classifications of svtypes other than deletions without crashing due to an empty deletion dataframe. Please review. Thanks
Bohan