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"

https://github.com/igvteam/igv/blob/master/src/main/java/org/broad/igv/batch/CommandExecutor.java#L173

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

?

