bug report of the 'grep'

[Sen Li]

Hi,

Here I would like to report a bug of the command 'grep'. The case is:

I need to grab all lines which contains a string 'chr1' in the very big
text file (~1.2gb, I also send you an example of the file in the
attachment). So I apply this command

cut -f 2-9 var-${*variant_name*}-200-37-ASM.tsv | grep -vw 'no-call' | grep
-w chr1 | grep -vw 'no-ref'

In principle, this returns all lines only contain the string 'chr1' of the
certain file, right? But sometimes I can also get several lines with other
strings , such as 'chr12', 'chr22' etc. Well, there might be the invisible
'chr1' in those lines, but if I apply 'grep -w chr1' again, those lines are
removed. And I found that this case occurs randomly, you may not observe
this when you use my example file.

I am wondering whether you have received the similar problem before,
especially when the user apply 'grep' to a large file. Thanks for your time.

Best regards,
/Sen Li

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Sen Li
Ph.D. student
Section for Evolutionary Biology
Dept. of Ecology and Genetics
Evolutionary Biology Centre (EBC)
Uppsala University
Norbyvägen 18D
SE 752 36 Uppsala, Sweden

Cell: +46 (0)733 201818
Office: +46 (0)18 4712839
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var-NA18558-200-37-ASM.tsv.example
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