Details
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Type:
Bug
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Status: Closed (View Workflow)
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Priority:
Major
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Resolution: Fixed
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Labels:None
Description
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.
Attachments
Issue Links
- relates to
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BUG-658 'Stack Height' function bugs
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- Closed
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Activity
| Field | Original Value | New Value |
|---|---|---|
| Description |
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 Max 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 Max 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 max stack depth to 1 - observe that + strand changes it's appearance - now there are regions with more only 2 models stacked - observe that - strand doesn't change - now right-click RefSeq - track label, choose Adjust Max Stack Depth - observe window opens and the current value of Max Stack Depth 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 change max stack depth, 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.) However, when users use the Preferences tab to change max stack depth, e.g., by clicking a row and modifying the settings, then the change should apply to BOTH plus and minus tracks, since there is currently no way to specify whether the user means plus or minus strand (or both) in the Preferences interface. Also, if the user has set the max depth differently for the plus and minus tracks, the track preferences window should report a null value for the max depth, similar to what happens if the user has selected multiple rows in the Preferences table. Lastly, if a user has set max depth 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 "0" and another is "10", then the newly combined track's minimum stack depth should be 0. |
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 Max 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 Max 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 max stack depth 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 Adjust Max Stack Depth - observe window opens and the current value of Max Stack Depth 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 change max stack depth, 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.) However, when users use the Preferences tab to change max stack depth, e.g., by clicking a row and modifying the settings, then the change should apply to BOTH plus and minus tracks, since there is currently no way to specify whether the user means plus or minus strand (or both) in the Preferences interface. Also, if the user has set the max depth differently for the plus and minus tracks, the track preferences window should report a null value for the max depth, similar to what happens if the user has selected multiple rows in the Preferences table. Lastly, if a user has set max depth 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 "0" and another is "10", then the newly combined track's minimum stack depth should be 0. |
| Environment | IGB 6_6_7 branch | IGB 6_7 branch |
| Assignee | Hiral Vora [ hiralv ] | Alyssa Gulledge [ alyssa ] |
Everything described works well. There is a minor bug remaining. If I change the depth of one strand (- let's say) to 2, when I select the + track, the max depth popup box shows the max depth setting for the most recently adjusted strand as opposed to the value for the CURRENTLY selected strand... This is only within the same data set (other loaded sets show their current max depth)
| Assignee | Alyssa Gulledge [ alyssa ] | Hiral Vora [ hiralv ] |
Nevermind 
Bug is fixed.
| Status | Open [ 1 ] | Closed [ 6 ] |
| Assignee | Hiral Vora [ hiralv ] | |
| Resolution | Fixed [ 1 ] |
| Resolution | Fixed [ 1 ] | |
| Status | Closed [ 6 ] | Reopened [ 4 ] |
| Assignee | Fuquan Wang [ fwang4 ] |
Passed on 7.0.0 (11884) Mac.
| Status | Reopened [ 4 ] | Resolved [ 5 ] |
| Assignee | Fuquan Wang [ fwang4 ] | |
| Resolution | Fixed [ 1 ] |
| Resolution | Fixed [ 1 ] | |
| Status | Resolved [ 5 ] | Reopened [ 4 ] |
| Summary | adjust max stack depth - plus/minus independently set, out of sync | stack height - plus/minus independently set, out of sync |
| Environment | IGB 6_7 branch | |
| Description |
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 Max 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 Max 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 max stack depth 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 Adjust Max Stack Depth - observe window opens and the current value of Max Stack Depth 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 change max stack depth, 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.) However, when users use the Preferences tab to change max stack depth, e.g., by clicking a row and modifying the settings, then the change should apply to BOTH plus and minus tracks, since there is currently no way to specify whether the user means plus or minus strand (or both) in the Preferences interface. Also, if the user has set the max depth differently for the plus and minus tracks, the track preferences window should report a null value for the max depth, similar to what happens if the user has selected multiple rows in the Preferences table. Lastly, if a user has set max depth 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 "0" and another is "10", then the newly combined track's minimum stack depth should be 0. |
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. |
| Status | Reopened [ 4 ] | Closed [ 6 ] |
| Resolution | Fixed [ 1 ] |
Allowing individual max expand was intended. It was a bug.
Fixed in r9745.