Calling BBMerge from Java program

[maxbio]

Hi,

I have a handful of metatranscriptome sequences that I would like to merge using BBMerge, and I've sorted them together into bidimensional file arrays using a java program using code like this;

public static void example(){
File[][]example = new File[1][2]; // in reality, this would be 4 arrays long
example[0][0] = new File("example_file_R1.fastq");
example[0][1] = new File("example_file_R2.fastq");
}

Now what I'm trying to do is figure out how I can send the files to BBMerge from here from within the code; I'm familiar with calling other methods within the same class, as such:

for(int i = 0; i < example.length; i++){
bbmerge(example[i][0], example[i][1]);
}

but since BBMerge is outside the class (but still on the computer and still a java program, meaning it should be able to take the 2 files from the array as parameters) I'm not sure how I would go about this from within the program. Would anyone have any idea how to do this?

Thanks,

[GenoMax]

I suggest that you email Brian Bushnell directly about this. You can find his email address in the bbmap source.