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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:
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.
The text was updated successfully, but these errors were encountered:
Agreed. I concur. Calling nextfile as in the example above causes every other .fastq file to be processed (e.g. files in even positions in ARGV will be skipped).
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:
For example, with regular awk, the following works extremely fast:
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 thenextfile
command, which is weird.The text was updated successfully, but these errors were encountered: