From becea828b3f011daea5848051bcde9529a98ca6a Mon Sep 17 00:00:00 2001 From: Magnus Wahlberg Date: Tue, 28 Nov 2023 10:54:24 +0100 Subject: [PATCH] Use exclude_calls_file_cols --- deeprvat/preprocessing/preprocess.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/deeprvat/preprocessing/preprocess.py b/deeprvat/preprocessing/preprocess.py index 2512d88f..3ac1adb8 100644 --- a/deeprvat/preprocessing/preprocess.py +++ b/deeprvat/preprocessing/preprocess.py @@ -253,12 +253,13 @@ def process_sparse_gt( logging.info(f"Processing chromosome {chrom}") logging.info("Reading in filtered calls") + exclude_calls_file_cols = ["chrom", "pos", "ref", "alt", "sample"] + calls_to_exclude = pd.DataFrame( - columns=["chrom", "pos", "ref", "alt", "sample"] + columns=exclude_calls_file_cols ) if exclude_calls is not None: - exclude_calls_file_cols = ["chrom", "pos", "ref", "alt", "sample"] exclude_calls_chrom = Path(exclude_calls).rglob("*.tsv*") exclude_calls_chrom_files = []