How to read fastly files ( I/O operation)

bioinfornatics bioinfornatics at fedoraproject.org
Mon Feb 4 06:04:37 PST 2013


Dear,

I am looking to parse efficiently huge file but i think D lacking 
for this purpose.
To parse 12 Go i need 11 minutes wheras fastxtoolkit (written in 
c++ ) need 2 min.

My code is maybe not easy as is not easy to parse a fastq file 
and is more harder when using memory mapped file.

I do not see where i can get some perf as i do not do many copy 
and i use mmfile.
fastxtoolkit do not use mmfile and store his result into a  
struct array for each sequences but is is still faster!!!

thanks to any help i hope we can create a faster parser otherwise 
that is too slow to use D instead C++


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