I'd like eyes on the newest version of the script

[scoetzee]

There have been substantial changes to the layout and function of this script
start command with -h option to see how to set up a run. That information
has been copied here:
COMMAND LINE OPTIONS FOR FuncSNPi:
-c : max cpus availible (ex. -c 8)
-g : genome build to use (ex. -g hg19)
-r : location of risk SNP file (ex. -r ~/riskSNP.txt)
-b : location of of biological peaks file, in bed format (ex. -b ~/biopeaks.bed)

            riskSNP file must be in the following tab deliminated format
            <region>                <risk SNP id>   <ethnic group>
            10:122837334-123837335  rs2981579       EUR             <- example

[labrazil]

But remember the biological peaks should be a folder which contains all the bed files.

[scoetzee]

you're right i should make the help more clear. Right now i have it such that if you give it the name of a bed file, it uses the folder that it's in automatically, but if you give it the folder name, that's okay too.

[labrazil]

tabix does not contain chrX. need to include the chrX files as well. See original FTP site for location.

UPDATE: I added the chrX to the shared folder. just need to revamp the loop to check for chrX and then run tabix on it.

UPDATE: I added an if statement to take care of this event. Please check it.

[labrazil]

multicore function is still not working as expected. the LD tables aren't printing correctly.