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updated grep bug #9

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merged 1 commit into from
Dec 4, 2024
Merged

updated grep bug #9

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2 changes: 1 addition & 1 deletion amplicov/amplicov
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Original file line number Diff line number Diff line change
Expand Up @@ -121,7 +121,7 @@ def convert_bedpe_to_amplicon_dict(input,cov_array,RefID="",unique=False, count_
amplicon=defaultdict(dict)
primers_pos=list()
RefID = '""' if RefID is None else RefID
cmd = 'grep %s %s | cut -f 2,3,5,6,7 ' % (RefID, input_bedpe)
cmd = 'grep -w %s %s | cut -f 2,3,5,6,7 ' % (RefID, input_bedpe)
proc = subprocess.Popen(cmd,shell=True,stdout=subprocess.PIPE)
previous_id=''
outs, errs = proc.communicate()
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