Integrative Genomics Viewer Questions About Scaling and External Ports with Java

[jz...@tgen.org]

Dear Broad Institute,
Hello, my name is Justin.  I am asking as to whether the Integrative
Genomics Viewer (IGV) is able to automatically set the data range of
the BAM coverage to be the same for multiple BAM files within one IGV
session.  Specifically, is there a command that can allow me to
automatically scale and set the data range to be consistent for
multiple BAM files?

Secondly, my question arises as to whether I can save an IGV session
from an external port.  I am currently running Java from Eclipse right
now, and I am wondering if you offer specific functions or commands on
the IGV such as setting the data range constant and saving an IGV
session that can be used in addition to just taking photos as
mentioned in here: https://www.broadinstitute.org/igv/PortCommands

Third, I've been trying to set the "Coverage allele-fraction threshold" to 0.3 on a Java program, but when I type in the code, there is an unknown command:

out.println("preference Coverageallele-fractionthreshold " + 0.2);

response = in.readLine();

System.out.println(response);

Because the command for managing options is (preference key value), I was wondering specifically what I need to change to have the correct format for IGV: http://software.broadinstitute.org/software/igv/external_control

 And finally, I was wondering how I can access the methods and commands
inside IGVtools in reading in the recounts and variants from the
textbox display in the IGVtools GUI.  Is there an open source code for
the GUI?  If not, is there a method I can call within the jar file
that can extract the recounts and variants information?

Thank you so much for taking the time to answer my questions.  I look
hearing from you soon, and I hope you have a wonderful day.

Sincerely,
Justin Zhu

[Jim Robinson]

Hi Justin,

The answer to your questions in order are mostly no, with the exception of the preference question.   They key for that property is SAM.ALLELE_THRESHOLD.   The best way to discover keys is to change the preference in the UI, exit IGV, then look at prefs.properties in the igv folder.

Please enter issues for your other requests at our git repository, a separate issue for each request, at  github.com.igvteam.igv/issues.   Bear in mind that many requests compete for my time and port command enhancement is not currently a priority.   As you are also a developer I encourage you to submit pull requests,  I do review them and accept many.

Jim

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