How to read fastly files ( I/O operation)

bioinfornatics bioinfornatics at fedoraproject.org
Thu Feb 7 06:30:10 PST 2013


Little feed back
i named f the f's script and monarch the monarch's script

  gdmd -O -w -release f.d
~ $ time ./f bigFastq.fastq
['T':999786820, 'A':1007129068, 'N':39413, 'C':1350576504, 
'G':1353023772]

real	2m14.966s
user	0m47.168s
sys	0m15.379s
~ $ gdmd -O -w -release monarch.d
monarch.d:117: no identifier for declarator Lines
monarch.d:117: alias cannot have initializer
monarch.d:130: identifier or integer expected, not assert


i haven't take the time to look more

but in any case it seem memory mapped file is really slowly 
whereas it is said that is the faster way to read file. Create an 
index where reading the file need 12 min that is useless as for 
read and compute you need 2 min


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