03-19-2009
might help to see some of what the input file looks like. I have a feeling this line is wrong:
if ($chrom[$i] =~ /chrd+/) {
unless you really are looking for "chr" followed by one or more "d". Probably should be:
if ($chrom[$i] =~ /chr\d+/) {
in which case its searching for "chr" followed by one or more digits.
Use the perl highlighter to post perl code. The php highlighter will mangle some perl code.
Besides that, I also don't understand what you are wanting to do.
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RAND(3) Linux Programmer's Manual RAND(3)
NAME
rand, srand - random number generator.
SYNOPSIS
#include <stdlib.h>
int rand(void);
void srand(unsigned int seed);
DESCRIPTION
The rand() function returns a pseudo-random integer between 0 and RAND_MAX.
The srand() function sets its argument as the seed for a new sequence of pseudo-random integers to be returned by rand(). These sequences
are repeatable by calling srand() with the same seed value.
If no seed value is provided, the rand() function is automatically seeded with a value of 1.
RETURN VALUE
The rand() function returns a value between 0 and RAND_MAX. The srand() returns no value.
NOTES
The versions of rand() and srand() in the Linux C Library use the same random number generator as random() and srandom(), so the lower-
order bits should be as random as the higher-order bits. However, on older rand() implementations, the lower-order bits are much less ran-
dom than the higher-order bits.
In Numerical Recipes in C: The Art of Scientific Computing (William H. Press, Brian P. Flannery, Saul A. Teukolsky, William T. Vetterling;
New York: Cambridge University Press, 1992 (2nd ed., p. 277)), the following comments are made:
"If you want to generate a random integer between 1 and 10, you should always do it by using high-order bits, as in
j=1+(int) (10.0*rand()/(RAND_MAX+1.0));
and never by anything resembling
j=1+(rand() % 10);
(which uses lower-order bits)."
Random-number generation is a complex topic. The Numerical Recipes in C book (see reference above) provides an excellent discussion of
practical random-number generation issues in Chapter 7 (Random Numbers).
For a more theoretical discussion which also covers many practical issues in depth, please see Chapter 3 (Random Numbers) in Donald E.
Knuth's The Art of Computer Programming, volume 2 (Seminumerical Algorithms), 2nd ed.; Reading, Massachusetts: Addison-Wesley Publishing
Company, 1981.
CONFORMING TO
SVID 3, BSD 4.3, ISO 9899
SEE ALSO
random(3), srandom(3), initstate(3), setstate(3)
GNU
1995-05-18 RAND(3)