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update script to handle missing values #2

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update script to handle missing values #2

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2 changes: 1 addition & 1 deletion depth_filter.py
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Original file line number Diff line number Diff line change
Expand Up @@ -85,7 +85,7 @@ def getFormatField(sample_name, field_name):
filter=False
for samp in args.sample_names.split(","):
depth = getFormatField(samp,args.site_depth_field)
if(depth=="NA"):
if(depth in ("NA", ".")):
if na_err:
print("WARNING: One or more sites lack the {} field. Those are being treated as zero and filtered".format(args.site_depth_field))
na_err=False
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