When running batch file in IGV, how to set its oprion "Show all bases" for track? Or alternatively, is there an option to show all bases in tracks by default?
When running batch file in IGV, how to set its oprion "Show all bases" for track? Or alternatively, is there an option to show all bases in tracks by default?
not tested. In https://github.com/igvteam/igv/blob/master/src/main/java/org/broad/igv/batch/CommandExecutor.java there is a command: "preference"
which calls the PreferencesManager
There is a constant SAM.SHOW_ALL_BASES https://github.com/igvteam/igv/blob/da21278a6d8980e80a246c7934b549ffb407597c/src/main/java/org/broad/igv/prefs/Constants.java#L123
so I would try:
preference SAM.SHOW_ALL_BASES true
or
preference SAM.SHOW_ALL_BASES 1
?
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Thanks a lot!! It works in batch scrpit:
preference SAM.SHOW_ALL_BASES 1