From 34bd2c3e88b51550a7320a765b63029e1b9c74a7 Mon Sep 17 00:00:00 2001 From: Susanna Kiwala Date: Wed, 18 Dec 2024 15:50:05 -0600 Subject: [PATCH] Fix bug with pVACsplice aggregate_inclusion_count_limit --- pvactools/lib/aggregate_all_epitopes.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/pvactools/lib/aggregate_all_epitopes.py b/pvactools/lib/aggregate_all_epitopes.py index 6a044b83..edb48bf3 100644 --- a/pvactools/lib/aggregate_all_epitopes.py +++ b/pvactools/lib/aggregate_all_epitopes.py @@ -1123,6 +1123,7 @@ def __init__( percentile_threshold=None, allele_specific_binding_thresholds=False, aggregate_inclusion_binding_threshold=5000, + aggregate_inclusion_count_limit=15, top_score_metric="median", trna_vaf=0.25, trna_cov=10, @@ -1137,6 +1138,7 @@ def __init__( percentile_threshold=percentile_threshold, allele_specific_binding_thresholds=allele_specific_binding_thresholds, aggregate_inclusion_binding_threshold=aggregate_inclusion_binding_threshold, + aggregate_inclusion_count_limit=aggregate_inclusion_count_limit, top_score_metric=top_score_metric, ) self.tumor_purity = tumor_purity