Speedy tool for counting reads in fastq / fastq.gz files
A c++ fastq read counter with openMP multithreading
Core functionality derived from
https://github.com/billzt/readfq
which was modified from
http://lh3lh3.users.sourceforge.net/parsefastq.shtml.
Usage: fqcounter <*fastq>
fqcounter -b -t <int> <*fastq.gz>
-b Add a basecount column
-l Add basecount and mean length columns
-t <int> [2] Select number of threads
(one fastq file/thread)
-o Delayed ordered output
-h This message
Note: No fastq format checking is performed
Also counts fasta files
To compile use make or:
g++ -o fqcounter -fopenmp fqcounter.cpp -lz