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halelab / GBS-SNP-CROP

GBS SNP Calling Reference Optional Pipeline
GNU General Public License v2.0
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Creation of VerticalRefPos.txt file #30

Open fischuu opened 4 years ago

fischuu commented 4 years ago

Hi, I had some issues with the pipeline when I applied it to many samples. There I noticed that the creation of the file VerticalRefPos.txt in script GBS-SNP-CROP-6.pl lines 237 and 422 could be optimized by changing

system ( "cat *.ref.txt | uniq > VerticalRefPos.txt" );

to

system ( "sort -u -m -k2n *.ref.txt -o VerticalRefPos.txt" )

I think the uniq command requires the file to be sorted to remove all duplicated lines.

arthurmelobio commented 4 years ago

Hi Daniel Fischer,

Thank you for writing and I'm glad to know you're using GBS-SNP-CROP for your research. Also thank you so much for suggesting improvements to pipeline. I'll update the code!

Thanks. Best, Arthur