IGV - how to show all bases in track in bash script

Question

[martinov.michael]

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?

[martinov.michael]

Thanks a lot!! It works in batch scrpit: preference SAM.SHOW_ALL_BASES 1

Answer 1

[Pierre Lindenbaum]

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

?

[Pierre Lindenbaum]

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