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remove sample_class_filter function
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danlu1 committed Nov 25, 2024
1 parent 9a3ba06 commit 1a38f45
Showing 1 changed file with 0 additions and 18 deletions.
18 changes: 0 additions & 18 deletions genie/database_to_staging.py
Original file line number Diff line number Diff line change
Expand Up @@ -501,24 +501,6 @@ def seq_date_filter(clinicalDf, processingDate, consortiumReleaseCutOff):
return removeSeqDateSamples


def sample_class_filter(clinical_df: pd.DataFrame) -> list:
"""Filter samples by SAMPLE_CLASS
Args:
clinical_df (pd.DataFrame): Clinical dataframe
Returns:
list: List of samples to filter out
"""
if clinical_df.get("SAMPLE_CLASS") is not None:
remove_samples = clinical_df["SAMPLE_ID"][
clinical_df["SAMPLE_CLASS"] == "cfDNA"
].tolist()
else:
remove_samples = []
return remove_samples


# TODO: Add to transform.py
def mutation_in_cis_filter(
syn,
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