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awk changing numbering in output file

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# 1  
Old 08-17-2016
awk changing numbering in output file
The below awk is supposed filter $8 of example.txt using the each line in gene.txt. I think it is but why is it renumbering the 1,2,3 in $1 to 28,29,394? I have attached the data as it is large, example.txt is the file to be searched, gene.txt has the lines to match, and filtered.txt is the current output. The desured output is just that but with $1 or R_Index sequentially numbered. Thank you Smilie.

awk
Code:
awk 'NR==FNR{for (i=1;i<=NF;i++) a[$i];next} FNR==1 || ($8 in a)' gene.txt example.txt | awk '{split($2,a,"-"); print a[1] "\t" $0}' | cut -f2-> filtered.txt

example.txt (2.38 MB) 
gene.txt (136 Bytes) 
filtered.txt (27.6 KB) 
# 2  
Old 08-17-2016
How about this:

Code:
awk 'NR==FNR{for (i=1;i<=NF;i++) a[$i];next} $8 in a {$1=++n; print} FNR==1' gene.txt example.txt > filtered.txt

These 3 Users Gave Thanks to Chubler_XL For This Post:
cmccabe rbatte1 vgersh99
# 3  
Old 08-18-2016
Thank you very much Smilie
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