This is a test version of Biostars. For the public version, visit https://www.biostars.org.
IGV - how to show all bases in track in bash script

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?

igv bam viewer
• 2,304 views • link
updated by Jeremy Leipzig 2.3K • | written by martinov.michael 1

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

• 1 views • link
written by martinov.michael 1

1 answer

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

?

• 1 views • link
written by Pierre Lindenbaum 17K

If an answer was helpful you should upvote it, if the answer resolved your question you should mark it as accepted.

Upvote|Bookmark|Accept

• 1 views • link
written by Pierre Lindenbaum 17K

Log in to answer this question.

More posts like this