Load BAM files with a space character in pathname via port control

[stefandi...@googlemail.com]

Hello,

I have written a Java program, which is comunicating with IGV via port 60151. It`s working fine up to now. But when I try to load a BAM file with a space character or a coma in its filepath IGV cuts up at the first space in filepath.

Is there any way to encode this path to make sure IGV will find the file. Renaming th file will not be an option, because everything is automated.
Thanks a lot for your help!

Regards
Stefan

[James Robinson]

Try quoting the filename, as in the example below

private static void testFileWithSpaces(PrintWriter out, BufferedReader in) throws IOException {
    String response;
    String command = "load \"/Users/jrobinso/projects/Version_1.5_rc2/test/data/gct/file with spaces.gct\"";
    System.out.println("asking igv to " + command);
    out.println(command);
    System.out.println("waiting for response");
    response = in.readLine();
    System.out.println(response);
}

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[stefandi...@googlemail.com]

Hi Jim,

thanks a lot! It is working. I tried it with single quotes ( ' ) before, which did not work. I did not come up with the idea trying it with double quotes.

Thanks again!
Stefan