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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