I did download the code I posted, and it worked for me because I saved the input files as testReg.txt and testPos.txt respectively instead of reg.txt and pos.txt. Sorry about that. The beginning of the code is where I specify the file names.

The correct output should look like:

chr1    100    159    0    chr1    104    104    0    0    +
chr1    100    159    0    chr1    145    145    0    0    +
chr1    200    260    0    chr1    205    205    0    0    +
chr1    500    750    0    chr1    600    600    0    0    +
chr3    450    700    0    chr3    500    500    0    0    +
chr4    100    300    0    chr4    150    150    0    0    +
chr4    100    300    0    chr4    175    175    0    0    +
chr7    350    600    0    chr7    400    400    0    0    +
chr7    350    600    0    chr7    550    550    0    0    +
chr9    100    125    0    chr9    100    100    0    0    +
chr11    679    687    0    chr11    680    680    0    0    +
chr11    679    687    0    chr11    681    681    0    0    +
chr22    100    200    0    chr22    105    105    0    0    +
chr22    100    200    0    chr22    110    110    0    0    +
chr22    300    400    0    chr22    350    350    0    0    +
[download]

but as in my previous reply I can only get the first to lines to output at all (let alone correctly). Again, first 4 columns are from testReg.txt and last 6 columns are from testPos.txt. The "chr" column from testPos.txt isn't necessary in the output, but I was trying to include it as well.