From 67b6310efe1cb3fe7bb5a11368246bcc4b14e623 Mon Sep 17 00:00:00 2001 From: roryk Date: Fri, 8 Jan 2021 12:59:10 -0500 Subject: [PATCH] Skip peddy if no hets are found in any samples. --- bcbio/variation/peddy.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/bcbio/variation/peddy.py b/bcbio/variation/peddy.py index e2bca36b5..8b565e930 100644 --- a/bcbio/variation/peddy.py +++ b/bcbio/variation/peddy.py @@ -112,7 +112,9 @@ def allowed_errors(l): return ((l.find("IndexError") >= 0 and l.find("is out of bounds for axis") >= 0) or (l.find("n_components=") >= 0 and l.find("must be between 1 and n_features=") >= 0) or (l.find("n_components=") >= 0 and l.find("must be between 1 and min") >= 0) or - (l.find("Input contains NaN, infinity or a value too large for dtype") >= 0)) + (l.find("Input contains NaN, infinity or a value too large for dtype") >= 0) or + (l.find("peddy: no hets found for sample") >= 0) or + (l.find("ValueError: need at least one array to concatenate") >= 0)) def all_line_errors(l): return (l.find("no intervals found for") >= 0) if any([allowed_errors(l) for l in to_show]) or all([all_line_errors(l) for l in to_show]):