Q:

I am trying to run the correlation java script and i get the following when I run the example:

java -jar EncodeTfCor2.jar human_genome_file.txt bedlist 1000000 0
Parsing genome chromosomes and tf bindings …
parsing human_genome_file.txt…
parsing lists in bedlist
Building data matrix …
Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: 0
at encodetfcor2.TfSitesDataMatrixBuilder.<init>(TfSitesDataMatrixBuilder.java:126)
at encodetfcor2.Main.main(Main.java:65)

Any idea whats going on? I have zero familiarity with Java so I am completely lost as to what is going on.

Well I got rid of it and installed a new version and this time I ran the snp data as the example and it worked. I have no idea what happened. One quick question though, I ran the example with the snp from the four individuals and I got the following matrix:

1.000000 0.984057 0.983579 0.941439
0.984057 1.000000 0.985570 0.956917
0.983579 0.985570 1.000000 0.952203
0.941439 0.956917 0.952203 1.000000

The track_names.txt says the following:

chinese.sites.chr1.parsed
korean.sites.parsed.chr1
venter.sites.parsed.chr1
watson.sites.parsed.chr1

so is the actual matrix then:

names chinese korean venter watson
chinese 1.000000 0.984057 0.983579 0.941439
korean 0.984057 1.000000 0.985570 0.956917
venter 0.983579 0.985570 1.000000 0.952203
watson 0.941439 0.956917 0.952203 1.000000

The readme file isnt very clear on that. Thanks.

A:
Yes, the matrix is labelled correctly.