[BUG-84] Read sequence is not shown in sliced view; - JIRA UNCC

Details

Type: Bug
Status: Closed (View Workflow)
Priority: Major
Resolution: Fixed
Labels:
None

Description

Additionally, if sequence is loaded and read is right clicked, you are offered the option to 'restore read sequence' but it does not show sequence either.

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relates to

BUG-661 Sliced View

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Ascending order - Click to sort in descending order

Alyssa Gulledge (Inactive) created issue - 30/Mar/11 7:29 AM

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Hiral Vora (Inactive) added a comment - 30/Mar/11 10:55 AM

fixed on trunk. Will only merge after it is tested.

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Hiral Vora (Inactive) added a comment - 30/Mar/11 10:55 AM fixed on trunk. Will only merge after it is tested.

Hiral Vora (Inactive) made changes - 30/Mar/11 10:55 AM

Field	Original Value	New Value
Assignee	Hiral Vora [ hiralv ]	Alyssa Gulledge [ alyssa ]

Alyssa Gulledge (Inactive) made changes - 31/Mar/11 5:49 AM

Status	Open [ 1 ]	Resolved [ 5 ]
Resolution		Fixed [ 1 ]

Alyssa Gulledge (Inactive) made changes - 08/Apr/11 11:30 AM

Status

Resolved [ 5 ]

Closed [ 6 ]

Alyssa Gulledge (Inactive) made changes - 08/Apr/11 11:33 AM

Project	IGB6.5 [ 10010 ]	Bug Repository [ 10030 ]
Key	~~IGB-142~~	~~BUG-84~~

Alyssa Gulledge (Inactive) made changes - 31/Aug/11 5:48 AM

Resolution	Fixed [ 1 ]
Status	Closed [ 6 ]	Reopened [ 4 ]

David Norris (Inactive) made changes - 31/Aug/11 11:43 AM

Assignee

Alyssa Gulledge [ alyssa ]

David Norris (Inactive) made changes - 31/Aug/11 11:43 AM

Status	Reopened [ 4 ]	Resolved [ 5 ]
Resolution		Fixed [ 1 ]

David Norris (Inactive) made changes - 31/Aug/11 11:43 AM

Status

Resolved [ 5 ]

Closed [ 6 ]

Alyssa Gulledge (Inactive) made changes - 10/Jan/12 8:55 AM

Resolution	Fixed [ 1 ]
Status	Closed [ 6 ]	Reopened [ 4 ]
Assignee		Katharine Kubiak [ kkubiak ]

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Katharine Kubiak (Inactive) added a comment - 17/Jan/12 7:58 AM

Passed v9800 Windows

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Katharine Kubiak (Inactive) added a comment - 17/Jan/12 7:58 AM Passed v9800 Windows

Katharine Kubiak (Inactive) made changes - 17/Jan/12 7:58 AM

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Katharine Kubiak [ kkubiak ]

Anuj Puram [ anuj ]

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Anuj Puram (Inactive) added a comment - 20/Jan/12 3:45 AM

Passed 6.7.0 (9891) on Mac

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Anuj Puram (Inactive) added a comment - 20/Jan/12 3:45 AM Passed 6.7.0 (9891) on Mac

Anuj Puram (Inactive) made changes - 20/Jan/12 3:45 AM

Assignee

Anuj Puram [ anuj ]

Alyssa Gulledge [ alyssa ]

Alyssa Gulledge (Inactive) made changes - 23/Jan/12 4:06 AM

Status	Reopened [ 4 ]	Resolved [ 5 ]
Assignee	Alyssa Gulledge [ alyssa ]
Resolution		Fixed [ 1 ]

Alyssa Gulledge (Inactive) made changes - 23/Jan/12 4:07 AM

Status

Resolved [ 5 ]

Closed [ 6 ]

Richard Linchangco (Inactive) made changes - 13/Nov/12 9:32 AM

Resolution	Fixed [ 1 ]
Status	Closed [ 6 ]	Reopened [ 4 ]

Alyssa Gulledge (Inactive) made changes - 10/Dec/12 7:11 AM

Link

This issue relates to ~~BUG-661~~ [ ~~BUG-661~~ ]

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Richard Linchangco (Inactive) added a comment - 18/Dec/12 11:53 AM

FAILED V.13772, Mac, Java 1.7.0_09

'View Read Sequence in Read Sequence Viewer...' is a right-click option in both the main viewer and the 'Sliced View' Tab. This option works without issues in the main viewer but displays erratic behavior in the 'Sliced View' Tab.

Steps to reproduce:

Open a fresh IGB
Select A_thaliana_Jun_2009
Load bam file linked below
- Zoom in on a span of 5 or so genes
- Click 'Load Data'
Click on the 'Sliced View' Tab
Click on any read in the main viewer and it will appear in the 'Sliced View' Tab
- Right-click and choose to 'View Read Sequence...' and the 'Sequence Viewer' should open and display the read
NOW click anywhere in the main viewer that IS NOT a read (the background).
- The 'Sliced View' Tab view should remain the same as before but now when you right-click and try to 'View Read Sequence...' NOTHING HAPPENS

Expected behavior would be that, regardless of the read/read section being selected in the main viewer, any reads visible in the 'Sliced View' Tab viewer should be able to be seen in the 'Sequence Viewer'.

Tested with:
http://igbquickload.org/lorainelabrnaseq/A_thaliana_Jun_2009/heat_drought/CoolHT2.bam
(Need authentication information, retrieve from Dr. Loraine or Hiral)

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Richard Linchangco (Inactive) added a comment - 18/Dec/12 11:53 AM FAILED V.13772, Mac, Java 1.7.0_09 'View Read Sequence in Read Sequence Viewer...' is a right-click option in both the main viewer and the 'Sliced View' Tab. This option works without issues in the main viewer but displays erratic behavior in the 'Sliced View' Tab. Steps to reproduce: Open a fresh IGB Select A_thaliana_Jun_2009 Load bam file linked below Zoom in on a span of 5 or so genes Click 'Load Data' Click on the 'Sliced View' Tab Click on any read in the main viewer and it will appear in the 'Sliced View' Tab Right-click and choose to 'View Read Sequence...' and the 'Sequence Viewer' should open and display the read NOW click anywhere in the main viewer that IS NOT a read (the background). The 'Sliced View' Tab view should remain the same as before but now when you right-click and try to 'View Read Sequence...' NOTHING HAPPENS Expected behavior would be that, regardless of the read/read section being selected in the main viewer, any reads visible in the 'Sliced View' Tab viewer should be able to be seen in the 'Sequence Viewer'. Tested with: http://igbquickload.org/lorainelabrnaseq/A_thaliana_Jun_2009/heat_drought/CoolHT2.bam (Need authentication information, retrieve from Dr. Loraine or Hiral)

Richard Linchangco (Inactive) made changes - 18/Dec/12 11:53 AM

Assignee

Hiral Vora [ hiralv ]

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Hiral Vora (Inactive) added a comment - 19/Dec/12 5:13 AM

Remove Open Read in Sequence Viewer from sliced view.

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Hiral Vora (Inactive) added a comment - 19/Dec/12 5:13 AM Remove Open Read in Sequence Viewer from sliced view.

Hiral Vora (Inactive) made changes - 19/Dec/12 5:13 AM

Assignee

Hiral Vora [ hiralv ]

Fuquan Wang [ fwang4 ]

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Fuquan Wang (Inactive) added a comment - 19/Dec/12 11:28 AM

Done in 13790:

Removed right click menu in slice view.

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Fuquan Wang (Inactive) added a comment - 19/Dec/12 11:28 AM Done in 13790: Removed right click menu in slice view.

Fuquan Wang (Inactive) made changes - 19/Dec/12 11:28 AM

Assignee

Fuquan Wang [ fwang4 ]

Richard Linchangco [ richard ]

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Richard Linchangco (Inactive) added a comment - 19/Dec/12 11:53 AM

Passed V.13790, Mac, Java 1.7.0_10

Right-click options no longer exist in 'Sliced View' Tab.

Double clicking on a read centers the 'Sliced View' viewer on that read.

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Richard Linchangco (Inactive) added a comment - 19/Dec/12 11:53 AM Passed V.13790, Mac, Java 1.7.0_10 Right-click options no longer exist in 'Sliced View' Tab. Double clicking on a read centers the 'Sliced View' viewer on that read.

Richard Linchangco (Inactive) made changes - 19/Dec/12 11:53 AM

Status	Reopened [ 4 ]	Resolved [ 5 ]
Assignee	Richard Linchangco [ richard ]
Resolution		Fixed [ 1 ]

Richard Linchangco (Inactive) made changes - 19/Dec/12 11:54 AM

Status

Resolved [ 5 ]

Closed [ 6 ]

People

Assignee:

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Reporter:

Alyssa Gulledge (Inactive)

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Dates

Created:

30/Mar/11 7:29 AM

Updated:

19/Dec/12 11:54 AM

Resolved:

19/Dec/12 11:53 AM