Sorry - this is complicated! As always, feel free to re-assign (or not) as you see fit.

In IGB 6.7, it is now possible to set Stack Height for minus and plus strands independently. That is, I can change the setting for plus strand and minus strand and observe how features change their stack height.

However, when I try to change Stack Height for minus strand – after changing it for plus strand – I see that the Max Stack Height is reported as the old value even though in order to get the new value to apply, I have to change it.

To repeat:

• reset preferences to default
• launch IGB, load H sapiens latest genome (click Mona Lisa face)
• right-click RefSeq + track label, change stack height to 1
• observe that + strand changes it's appearance - now there all regions have only 2 models stacked
• observe that - strand doesn't change
• now right-click RefSeq - track label, choose Stack height
• observe window opens and the current value of Stack height is now 0, even though the change did not affect the minus strand features

Here's what I recommend should happen:

When users right-click a track label and set stack height, the change should apply JUST to the track they clicked (minus or plus strand tier separately if plus/minus tracks are being shown separately or BOTH if they are being shown together in +/- mode.)

if a user has set stack height differently for the plus and minus tracks of the same feature, and then combines them so that plus and minus strand features appear together in the same track (+/- mode), then the minimum value should take effect for both. That is, if one track setting is "1" and another is "10", then the newly combined track's minimum stack depth should be 1.