IGV session loading with error when session includes track generated by "Search Motif" menu item and saved in session

[namra1]

On Wednesday, June 23, 2021 at 10:36:18 AM UTC-4 nasi...@gmail.com wrote:
When loading a saved IGV session, I get the following error:
" Unexpected error: java.lang.NullPointerException.
See igv.log for more details ".

The igv.log is attached as well as the session xml.
It seems to be related to tracks in xml file such as this track:

Note that I had to change .xml extension to _xml.txt since GitHub does not support .xml attachments.

igv.log

Fusion_gene_primers-igv_session copy_xml.txt

[jrobinso]

I can reproduce the problem. Apparently no on has ever tried this (saving session with motifs), or hasn't in a very long time. Working on a solution.

[jrobinso]

I have pushed a fix, it will be available in the next release scheduled for the week of July 12. If you need it in the meantime you can try the development snapshot build (follow link from downloads page).

Unfortunately the fix requires a change to the XML, if you want to convert existing session files 2 changes are required

1. Change the "classz" attribute from org.broad.igv.track.FeatureTrack. to org.broad.igv.track.MotifTrack
2. add pattern and strand attributes to the track element.

An example follows

        <Track attributeKey="tata" clazz="org.broad.igv.track.MotifTrack" displayMode="SQUISHED" featureVisibilityWindow="10000000" fontSize="10" groupByStrand="false" id="tata" name="tata" pattern="TATA" strand="POSITIVE" visible="true"/>
        <Track attributeKey="tata Negative" clazz="org.broad.igv.track.MotifTrack" color="255,0,0" displayMode="SQUISHED" featureVisibilityWindow="10000000" fontSize="10" groupByStrand="false" id="tata Negative" name="tata Negative" pattern="TATA" strand="NEGATIVE" visible="true"/>