When the user wants to Color the reads based on SAMtags, the user must first select the SAMtag key that IGB should use as the parameter to compare (such as "CR" or "CB") and then add SAMtags values to the Edit Tag and Color window. If the user follows that order and presses the Save and Apply button in the table window and then click OK in the Color by window, things work as expected.
However, if the user forgets to choose the SAMtag key before saving the values then its too late. The only recourse then is to open Color by window, change the key and then open the Edit Tag and Color window, click on Save and Apply to register the change in SAMTags key.

Example Scenario:
1) User opens the Color by window
2) Does not notice the SAMtag key is default "CR" (and the user wants to compare "CB" values)
3) Opens Edit Tag and Color window
4) Adds values and clicks Save and Apply button
5) Clicks OK in Color by window
6) Waits for IGB to color the reads and it colors everything light grey
7) Realizes the mistake, goes back to Color by window, changes key to "CB", clicks OK
8) Nothing changes but user waits for a while expecting things to change.

This ticket is created to address this issue. In other Color by options such as Property, the value is not retained after the window is closed so this functionality is not needed for any other Color by options .This issue might require making changes to Color by methods that is used by other options but the changes should only apply to SAMtags.