From f3cba5dd4dd8a8726855b623236fe1c0b12325fe Mon Sep 17 00:00:00 2001 From: Magnus Wahlberg Date: Wed, 6 Dec 2023 14:56:22 +0100 Subject: [PATCH] Remoce joblib temporary --- deeprvat/preprocessing/preprocess.py | 17 ++++++++++++----- 1 file changed, 12 insertions(+), 5 deletions(-) diff --git a/deeprvat/preprocessing/preprocess.py b/deeprvat/preprocessing/preprocess.py index 46eba386..e9d4110a 100644 --- a/deeprvat/preprocessing/preprocess.py +++ b/deeprvat/preprocessing/preprocess.py @@ -299,12 +299,19 @@ def process_sparse_gt( logging.info(f"sparse gt chrom(es) are: {sparse_gt_chrom}") - processed = Parallel(n_jobs=threads, verbose=50)( - delayed(process_sparse_gt_file)( - f.as_posix(), variants_chrom, samples, calls_to_exclude + # processed = Parallel(n_jobs=threads, verbose=50)( + # delayed(process_sparse_gt_file)( + # f.as_posix(), variants_chrom, samples, calls_to_exclude + # ) + # for f in sparse_gt_chrom + # ) + processed = [] + for f in sparse_gt_chrom: + processed.append( + process_sparse_gt_file( + f.as_posix(), variants_chrom, samples, calls_to_exclude + ) ) - for f in sparse_gt_chrom - ) postprocessed_gt = postprocess_sparse_gt(processed, 1, len(samples)) postprocessed_variants = postprocess_sparse_gt(processed, 0, len(samples))