"sort alignments by" function not working on PC

[amanda....@gmail.com]

I just downloaded the new PC version of IGV yesterday (IGV 2.3.x ) and am trying to work with .bam files that contain PacBio IsoSeq data.  I need  to be able to sort these tracks by "start location", however, when I right click on the track and go to "sort alignments by" and select "start location", nothing changes.  There is no error message, however, the program fails to "check" any of the options for that tab to show that it is selected and the individual alignments are sort of randomly stacked.  I am attaching an image of what the data looks like and the lack of a check mark beside "start location" when I go to make this selection.  Advice on how to get this function to work properly is much appreciated.  A colleague is able to get this function to work on her Mac version with the same dataset.  Thank you.

Amanda

Iowa State University

[Jim Robinson]

Could you check your version (use "Help > About"), as well as your colleagues version and report them here?

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[amanda....@gmail.com]

Version 2.7.79 (118) for mine (PC that is not working).

Version 2.3.67 (96) for hers (Mac that is working).

Thanks.

Amanda

[Jim Robinson]

Hi,

I can't find any problem with 2.3.79.   Could you share that portion of the file that you are showing in the screenshot?   You can extract it by right-clicking and selecting "Export Alignments".  This will create a SAM file, that is enough for me to try.   I will send you a drop box link to upload it.

Its normal that no option is checked,  sorting is an "action" not a state,  so the menu items are not check boxes.   Also, its important to understand that sorting just rearranges the alignment rows based on the chosen property of the alignment intersecting the center line of the view.    Below is an example of a "alignment start" sorted bam