11-17-2015
You're reading a 3/4 GB file four times - I don't know if disk I/O buffering will easily cater for that. Why dont you read your four .bed files into four different (multidimensional?) arrays ( 259 is not too large an array element count), then do your four independent calculations on each large file's input line, and then output to the four different result files?
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rl(1) User Commands rl(1)
NAME
rl - Randomize Lines.
SYNOPSIS
rl [OPTION]... [FILE]...
DESCRIPTION
rl reads lines from a input file or stdin, randomizes the lines and outputs a specified number of lines. It does this with only a single
pass over the input while trying to use as little memory as possible.
-c, --count=N
Select the number of lines to be returned in the output. If this argument is omitted all the lines in the file will be returned in
random order. If the input contains less lines than specified and the --reselect option below is not specified a warning is printed
and all lines are returned in random order.
-r, --reselect
When using this option a single line may be selected multiple times. The default behaviour is that any input line will only be
selected once. This option makes it possible to specify a --count option with more lines than the file actually holds.
-o, --output=FILE
Send randomized lines to FILE instead of stdout.
-d, --delimiter=DELIM
Use specified character as a "line" delimiter instead of the newline character.
-0, --null
Input lines are terminated by a null character. This option is useful to process the output of the GNU find -print0 option.
-n, --line-number
Output lines are numbered with the line number from the input file.
-q, --quiet, --silent
Be quiet about any errors or warnings.
-h, --help
Show short summary of options.
-v, --version
Show version of program.
EXAMPLES
Some simple demonstrations of how rl can help you do everyday tasks.
Play a random sound after 4 minutes (perfect for toast):
sleep 240 ; play `find /sounds -name '*.au' -print | rl --count=1`
Play the 15 most recent .mp3 files in random order.
ls -c *.mp3 | head -n 15 | rl | xargs --delimiter='
' play
Roll a dice:
seq 6 | rl --count 2
Roll a dice 1000 times and see which number comes up more often:
seq 6 | rl --reselect --count 1000 | sort | uniq -c | sort -n
Shuffle the words of a sentence:
echo -n "The rain in Spain stays mainly in the plain."
| rl --delimiter=' ';echo
Find all movies and play them in random order.
find . -name '*.avi' -print0 | rl -0 | xargs -n 1 -0 mplayer
Because -0 is used filenames with spaces (even newlines and other unusual characters) in them work.
BUGS
The program currently does not have very smart memory management. If you feed it huge files and expect it to fully randomize all lines it
will completely read the file in memory. If you specify the --count option it will only use the memory required for storing the specified
number of lines. Improvements on this area are on the TODO list.
The program uses the rand() system random function. This function returns a number between 0 and RAND_MAX, which may not be very large on
some systems. This will result in non-random results for files containing more lines than RAND_MAX.
Note that if you specify multiple input files they are randomized per file. This is a different result from when you cat all the files and
pipe the result into rl.
COPYRIGHT
Copyright (C) 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008 Arthur de Jong.
This is free software; see the license for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A
PARTICULAR PURPOSE.
Version 0.2.7 Jul 2008 rl(1)