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Skip peddy if no hets are found in any samples.
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roryk committed Jan 9, 2021
1 parent 9c8ad93 commit 67b6310
Showing 1 changed file with 3 additions and 1 deletion.
4 changes: 3 additions & 1 deletion bcbio/variation/peddy.py
Original file line number Diff line number Diff line change
Expand Up @@ -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]):
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