yttria-aniseia / fastq-lengths Goto Github PK

time wc -l ../fastq/ERR1415401_1.fastq
6922240 ../fastq/ERR1415401_1.fastq

real    0m0.068s
user    0m0.000s
sys     0m0.063s

time fastq-lengths/bin/fastq-lengths count ../fastq/ERR1415401_1.fastq
1730560

real    0m0.631s
user    0m0.546s
sys     0m0.037s

fgetc is the wrong way to do this, read into a buffer instead.

there may be speedups to be had if we use libdeflate to handle compressed inputs internally instead of requiring either pre-decompression or zcat piping

however, this complicates the implementation significantly relative to its current state.