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Scenario: I have 4 FASTQ files in my current directory, and I want to print the first 10 seq names of each file. Ideally, the following command should work very quickly:
bioawk -c fastx 'FNR<11 {print $name} FNR==11{nextfile}' *.fastq
For example, with regular awk, the following works extremely fast:
awk 'FNR==1{print} FNR>1{nextfile}' *.fastq
But bioawk does not stop processing the file when it encounters nextfile. Instead, it seems to continue parsing the whole file, which is crazy when dealing with gigantic files. Plus, it seems to skip a file when running into the nextfile command, which is weird.
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