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Question: IGV - how to show all bases in track in bash script
1
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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?

ADD COMMENTlink 15 months ago martinov.michael • 10 • updated 15 months ago Jeremy Leipzig 18k
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Thanks a lot!! It works in batch scrpit: preference SAM.SHOW_ALL_BASES 1

ADD REPLYlink 15 months ago
martinov.michael
• 10
3
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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

?

ADD COMMENTlink 15 months ago Pierre Lindenbaum 120k
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If an answer was helpful you should upvote it, if the answer resolved your question you should mark it as accepted.

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ADD REPLYlink 15 months ago
Pierre Lindenbaum
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