[IGBF-1342] Diff operation on 2 tracks is giving " no point" in ycord value in selection info in Graph Track Operations - JIRA UNCC

Details

Type: Bug
Status: Closed (View Workflow)
Priority: Major
Resolution: Done
Affects Version/s: None
Fix Version/s: 9.1.8 Major Release
Labels:
None

Story Points:
2
Epic Link:
Improve IGB for users
Sprint:
Fall 4 Oct 26 - Nov 6, Fall 5 Nov 9 - Nov 20, Fall 6 Nov 30 - Dec 11, Fall 7 Dec 14 - Dec 23, Winter 1 Dec 28 - Jan 8, Winter 2 Jan 11 - Jan 22, Winter 3 Jan 25 - Feb 5

Description

Diff operation on 2 tracks is giving " no point" in ycord value in selection info. Graph is not shown too.

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Attachments

graphWithNegative.bedgraph
0.2 kB
04/Jan/21 5:18 PM
graphWithNoZero.bedgraph
0.1 kB
04/Jan/21 5:18 PM
Screen Shot 2021-01-04 at 5.10.58 PM.png
57 kB
04/Jan/21 5:18 PM
Screen Shot 2021-01-04 at 5.11.16 PM.png
58 kB
04/Jan/21 5:18 PM

Issue Links

duplicates

IGBF-395 Negative values on a Graph say "No point" for the "Y Coord:" under the Selection Info tab

Closed

relates to

IGBF-1344 graph operations don't handle inverse 0 well

Closed

Activity

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Sneha Ramesh Watharkar (Inactive) created issue - 03/Jul/18 10:46 AM

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Ivory Blakley (Inactive) added a comment - 03/Jul/18 1:45 PM

It looks like the "no point" is only for negative values.

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Ivory Blakley (Inactive) added a comment - 03/Jul/18 1:45 PM It looks like the "no point" is only for negative values.

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Ivory Blakley (Inactive) added a comment - 03/Jul/18 1:46 PM

We discovered this in 9.0.1 and reproduced it in 9.0.0.

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Ivory Blakley (Inactive) added a comment - 03/Jul/18 1:46 PM We discovered this in 9.0.1 and reproduced it in 9.0.0.

Ivory Blakley (Inactive) made changes - 03/Jul/18 2:03 PM

Field	Original Value	New Value
Link		This issue relates to ~~IGBF-1344~~ [ ~~IGBF-1344~~ ]

Ann Loraine made changes - 27/Aug/19 4:58 PM

Workflow

Loraine Lab Workflow [ 18034 ]

Fall 2019 Workflow Update [ 18881 ]

Ann Loraine made changes - 16/Oct/19 5:48 PM

Workflow	Fall 2019 Workflow Update [ 18881 ]	Revised Fall 2019 Workflow Update [ 21008 ]
Status	Open [ 1 ]	To-Do [ 10305 ]

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Nowlan Freese added a comment - 05/Nov/20 10:27 AM

Check ~~IGBF-1344~~ for test graph files.

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Nowlan Freese added a comment - 05/Nov/20 10:27 AM Check IGBF-1344 for test graph files.

Ann Loraine made changes - 05/Nov/20 10:43 AM

Epic Link

IGBF-1765 [ 17855 ]

Ann Loraine made changes - 05/Nov/20 10:43 AM

Sprint

Fall 4 Oct 26 - Nov 6 [ 107 ]

Ann Loraine made changes - 05/Nov/20 10:44 AM

Assignee

Ann Loraine [ aloraine ]

Ann Loraine made changes - 05/Nov/20 10:44 AM

Assignee

Irvin Naylor [ inaylor ]

Ann Loraine made changes - 05/Nov/20 10:44 AM

Rank

Ranked higher

Ann Loraine made changes - 05/Nov/20 10:45 AM

Story Points

Ann Loraine made changes - 05/Nov/20 10:45 AM

Rank

Ranked higher

Irvin Naylor (Inactive) made changes - 06/Nov/20 12:04 PM

Status

To-Do [ 10305 ]

In Progress [ 3 ]

Irvin Naylor (Inactive) made changes - 06/Nov/20 3:55 PM

Status

In Progress [ 3 ]

To-Do [ 10305 ]

Ann Loraine made changes - 10/Nov/20 6:48 AM

Sprint

Fall 4 Oct 26 - Nov 6 [ 107 ]

Fall 4 Oct 26 - Nov 6, Fall 5 Nov 9 - Nov 20 [ 107, 108 ]

Ann Loraine made changes - 10/Nov/20 6:48 AM

Rank

Ranked higher

Irvin Naylor (Inactive) made changes - 13/Nov/20 2:37 PM

Status

To-Do [ 10305 ]

In Progress [ 3 ]

Ann Loraine made changes - 17/Nov/20 10:19 AM

Fix Version/s

9.1.6 Major Release [ 10604 ]

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Irvin Naylor (Inactive) added a comment - 19/Nov/20 4:24 PM

Log 11/19 -

'No point' is still appearing in 9.1.6.
Combed through the AbstractFloatTransformer and GraphGlyph.java to try and isolate instances where 'no point' should and should not come up in normal operations

Steps to replicate:

1) Open human genome (H_sapiens_Dec_2013)
2) Navigate to: chr1:0-550
3) Load the grapgWithNegative.bedgraph file (found in ~~IGBF-1344~~)
4) Click the graphWithNegative.bedgraph track label to select it.
5) Click in the center of the graph where the values are negative.
6) Navigate to the selection info to display coordinates (noting y-coordinate as 'no point').

Show

Irvin Naylor (Inactive) added a comment - 19/Nov/20 4:24 PM Log 11/19 - 'No point' is still appearing in 9.1.6. Combed through the AbstractFloatTransformer and GraphGlyph.java to try and isolate instances where 'no point' should and should not come up in normal operations Steps to replicate: 1) Open human genome (H_sapiens_Dec_2013) 2) Navigate to: chr1:0-550 3) Load the grapgWithNegative.bedgraph file (found in IGBF-1344 ) 4) Click the graphWithNegative.bedgraph track label to select it. 5) Click in the center of the graph where the values are negative. 6) Navigate to the selection info to display coordinates (noting y-coordinate as 'no point').

Irvin Naylor (Inactive) made changes - 19/Nov/20 4:24 PM

Status

In Progress [ 3 ]

To-Do [ 10305 ]

Irvin Naylor (Inactive) made changes - 19/Nov/20 4:41 PM

Assignee

Irvin Naylor [ inaylor ]

Irvin Naylor (Inactive) made changes - 19/Nov/20 4:41 PM

Assignee

Irvin Naylor [ inaylor ]

Irvin Naylor (Inactive) made changes - 25/Nov/20 10:11 AM

Assignee

Irvin Naylor [ inaylor ]

Ann Loraine made changes - 30/Nov/20 10:47 AM

Sprint

Fall 4 Oct 26 - Nov 6, Fall 5 Nov 9 - Nov 20 [ 107, 108 ]

Fall 4 Oct 26 - Nov 6, Fall 5 Nov 9 - Nov 20, Fall 6 Nov 23 - Dec 4 [ 107, 108, 109 ]

Ann Loraine made changes - 30/Nov/20 10:47 AM

Rank

Ranked higher

Ann Loraine made changes - 30/Nov/20 12:11 PM

Fix Version/s

9.1.6 Major Release [ 10604 ]

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Ann Loraine added a comment - 04/Dec/20 7:10 AM - edited

Potentially helpful suggestions:

Make a short screencast video demonstrating the above steps
Describe what the proper behavior should be in the comments text and/or in the video

Once you determine what the proper behavior should be:

Search the code base for text "no point" to find code implementing the "no point" behavior
Use debugger figure out the logic flow and identify places to implement a change

Show

Ann Loraine added a comment - 04/Dec/20 7:10 AM - edited Potentially helpful suggestions: Make a short screencast video demonstrating the above steps Describe what the proper behavior should be in the comments text and/or in the video Once you determine what the proper behavior should be: Search the code base for text "no point" to find code implementing the "no point" behavior Use debugger figure out the logic flow and identify places to implement a change

Irvin Naylor (Inactive) made changes - 04/Dec/20 2:13 PM

Assignee

Irvin Naylor [ inaylor ]

Irvin Naylor (Inactive) made changes - 04/Dec/20 2:13 PM

Status

To-Do [ 10305 ]

In Progress [ 3 ]

Ann Loraine made changes - 14/Dec/20 4:12 AM

Sprint

Fall 4 Oct 26 - Nov 6, Fall 5 Nov 9 - Nov 20, Fall 6 Nov 30 - Dec 11 [ 107, 108, 109 ]

Fall 4 Oct 26 - Nov 6, Fall 5 Nov 9 - Nov 20, Fall 6 Nov 30 - Dec 11, Fall 7 Dec 14 - Dec 23 [ 107, 108, 109, 110 ]

Ann Loraine made changes - 14/Dec/20 4:13 AM

Rank

Ranked higher

Irvin Naylor (Inactive) made changes - 18/Dec/20 4:04 PM

Status

In Progress [ 3 ]

Needs 1st Level Review [ 10005 ]

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Irvin Naylor (Inactive) added a comment - 18/Dec/20 4:04 PM

Fork Link: https://bitbucket.org/Inaylor01/integrated-genome-browser/src/IGBF-1342/

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Irvin Naylor (Inactive) added a comment - 18/Dec/20 4:04 PM Fork Link: https://bitbucket.org/Inaylor01/integrated-genome-browser/src/IGBF-1342/

Irvin Naylor (Inactive) made changes - 18/Dec/20 4:05 PM

Assignee

Irvin Naylor [ inaylor ]

Ann Loraine made changes - 27/Dec/20 12:34 PM

Sprint

Fall 4 Oct 26 - Nov 6, Fall 5 Nov 9 - Nov 20, Fall 6 Nov 30 - Dec 11, Fall 7 Dec 14 - Dec 23 [ 107, 108, 109, 110 ]

Fall 4 Oct 26 - Nov 6, Fall 5 Nov 9 - Nov 20, Fall 6 Nov 30 - Dec 11, Fall 7 Dec 14 - Dec 23, Winter 1 Dec 28 - Jan 8 [ 107, 108, 109, 110, 111 ]

Ann Loraine made changes - 27/Dec/20 12:35 PM

Rank

Ranked higher

Nowlan Freese made changes - 04/Jan/21 12:13 PM

Assignee

Nowlan Freese [ nfreese ]

Nowlan Freese made changes - 04/Jan/21 5:02 PM

Status

Needs 1st Level Review [ 10005 ]

First Level Review in Progress [ 10301 ]

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Nowlan Freese added a comment - 04/Jan/21 5:18 PM

Tested jar on Mac.

The y coord value is now showing correctly for negative graph values.

However, I noticed that values that should read no point, where there is no y coord value (no graph data), now show as -1.0. The code change Irvin made makes sense to me, so I think there is some further digging required to identify why a value with -1.0 is being recorded where there is no graph data.

[~aloraine] - I'm unsure of whether we should move forward with a pull request or investigate further.

Show

Nowlan Freese added a comment - 04/Jan/21 5:18 PM Tested jar on Mac. The y coord value is now showing correctly for negative graph values. However, I noticed that values that should read no point, where there is no y coord value (no graph data), now show as -1.0. The code change Irvin made makes sense to me, so I think there is some further digging required to identify why a value with -1.0 is being recorded where there is no graph data. [~aloraine] - I'm unsure of whether we should move forward with a pull request or investigate further.

Nowlan Freese made changes - 04/Jan/21 5:18 PM

Attachment		Screen Shot 2021-01-04 at 5.10.58 PM.png [ 15099 ]
Attachment		Screen Shot 2021-01-04 at 5.11.16 PM.png [ 15100 ]
Attachment		graphWithNegative.bedgraph [ 15101 ]
Attachment		graphWithNoZero.bedgraph [ 15102 ]

Nowlan Freese made changes - 04/Jan/21 5:19 PM

Status

First Level Review in Progress [ 10301 ]

To-Do [ 10305 ]

Nowlan Freese made changes - 04/Jan/21 5:19 PM

Assignee

Nowlan Freese [ nfreese ]

Irvin Naylor [ inaylor ]

Irvin Naylor (Inactive) made changes - 05/Jan/21 11:04 AM

Status

To-Do [ 10305 ]

In Progress [ 3 ]

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Irvin Naylor (Inactive) added a comment - 05/Jan/21 12:54 PM

I've done a bit of digging into the code and found that the only time -1.0 comes up is in the Graph Strand Minus variable as an assigned constant.
I have updated some of my solution code as well to make it a bit cleaner and have a specific time when "No Point" should show up (AKA when Y is neither greater than, less than, or equal to 0).

Fork link: https://bitbucket.org/Inaylor01/integrated-genome-browser/src/IGBF-1342/

Show

Irvin Naylor (Inactive) added a comment - 05/Jan/21 12:54 PM I've done a bit of digging into the code and found that the only time -1.0 comes up is in the Graph Strand Minus variable as an assigned constant. I have updated some of my solution code as well to make it a bit cleaner and have a specific time when "No Point" should show up (AKA when Y is neither greater than, less than, or equal to 0). Fork link: https://bitbucket.org/Inaylor01/integrated-genome-browser/src/IGBF-1342/

Irvin Naylor (Inactive) made changes - 05/Jan/21 2:50 PM

Status

In Progress [ 3 ]

To-Do [ 10305 ]

Irvin Naylor (Inactive) made changes - 05/Jan/21 2:52 PM

Status

To-Do [ 10305 ]

In Progress [ 3 ]

Irvin Naylor (Inactive) made changes - 05/Jan/21 2:52 PM

Status

In Progress [ 3 ]

Needs 1st Level Review [ 10005 ]

Irvin Naylor (Inactive) made changes - 05/Jan/21 2:53 PM

Assignee

Irvin Naylor [ inaylor ]

Ann Loraine made changes - 11/Jan/21 9:40 AM

Sprint

Fall 4 Oct 26 - Nov 6, Fall 5 Nov 9 - Nov 20, Fall 6 Nov 30 - Dec 11, Fall 7 Dec 14 - Dec 23, Winter 1 Dec 28 - Jan 8 [ 107, 108, 109, 110, 111 ]

Fall 4 Oct 26 - Nov 6, Fall 5 Nov 9 - Nov 20, Fall 6 Nov 30 - Dec 11, Fall 7 Dec 14 - Dec 23, Winter 1 Dec 28 - Jan 8, Winter 2 Jan 11 - Jan 22 [ 107, 108, 109, 110, 111, 112 ]

Ann Loraine made changes - 11/Jan/21 9:40 AM

Rank

Ranked higher

Ann Loraine made changes - 25/Jan/21 9:20 AM

Sprint

Fall 4 Oct 26 - Nov 6, Fall 5 Nov 9 - Nov 20, Fall 6 Nov 30 - Dec 11, Fall 7 Dec 14 - Dec 23, Winter 1 Dec 28 - Jan 8, Winter 2 Jan 11 - Jan 22 [ 107, 108, 109, 110, 111, 112 ]

Fall 4 Oct 26 - Nov 6, Fall 5 Nov 9 - Nov 20, Fall 6 Nov 30 - Dec 11, Fall 7 Dec 14 - Dec 23, Winter 1 Dec 28 - Jan 8, Winter 2 Jan 11 - Jan 22, Winter 3 Jan 25 - Feb 5 [ 107, 108, 109, 110, 111, 112, 113 ]

Ann Loraine made changes - 25/Jan/21 9:20 AM

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Ann Loraine added a comment - 27/Jan/21 9:40 AM

Nowlan Freese - Could you please review?

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Ann Loraine added a comment - 27/Jan/21 9:40 AM Nowlan Freese - Could you please review?

Ann Loraine made changes - 27/Jan/21 9:40 AM

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Nowlan Freese [ nfreese ]

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Nowlan Freese added a comment - 27/Jan/21 9:52 AM - edited

I requested a change to the code from Irvin.

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Nowlan Freese added a comment - 27/Jan/21 9:52 AM - edited I requested a change to the code from Irvin.

Nowlan Freese made changes - 27/Jan/21 3:05 PM

Status

Needs 1st Level Review [ 10005 ]

First Level Review in Progress [ 10301 ]

Nowlan Freese made changes - 27/Jan/21 4:47 PM

Assignee

Nowlan Freese [ nfreese ]

Irvin Naylor [ inaylor ]

Nowlan Freese made changes - 27/Jan/21 4:47 PM

Status

First Level Review in Progress [ 10301 ]

To-Do [ 10305 ]

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Irvin Naylor (Inactive) added a comment - 27/Jan/21 5:49 PM

Nowlan Freese - here are the changes.
Fork Link: https://bitbucket.org/Inaylor01/integrated-genome-browser/src/IGBF-1342/

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Irvin Naylor (Inactive) added a comment - 27/Jan/21 5:49 PM Nowlan Freese - here are the changes. Fork Link: https://bitbucket.org/Inaylor01/integrated-genome-browser/src/IGBF-1342/

Nowlan Freese made changes - 28/Jan/21 9:11 AM

Status

To-Do [ 10305 ]

In Progress [ 3 ]

Nowlan Freese made changes - 28/Jan/21 9:11 AM

Status

In Progress [ 3 ]

Needs 1st Level Review [ 10005 ]

Nowlan Freese made changes - 28/Jan/21 9:11 AM

Status

Needs 1st Level Review [ 10005 ]

First Level Review in Progress [ 10301 ]

Nowlan Freese made changes - 28/Jan/21 9:11 AM

Assignee

Irvin Naylor [ inaylor ]

Nowlan Freese [ nfreese ]

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Nowlan Freese added a comment - 28/Jan/21 11:59 AM

Tested Irvin's dmg for 1342 on Mac using the attached bedgraph files.

Selection Info now shows "no point" where there is no data and negative values are showing correctly.
Single-Graph operations are working correctly and saving the bedgraph from IGB works correctly.

Recommend pull request.

Show

Nowlan Freese added a comment - 28/Jan/21 11:59 AM Tested Irvin's dmg for 1342 on Mac using the attached bedgraph files. Selection Info now shows "no point" where there is no data and negative values are showing correctly. Single-Graph operations are working correctly and saving the bedgraph from IGB works correctly. Recommend pull request.

Nowlan Freese made changes - 28/Jan/21 11:59 AM

Assignee

Nowlan Freese [ nfreese ]

Irvin Naylor [ inaylor ]

Nowlan Freese made changes - 28/Jan/21 12:00 PM

Status

First Level Review in Progress [ 10301 ]

Ready for Pull Request [ 10304 ]

Irvin Naylor (Inactive) made changes - 28/Jan/21 4:19 PM

Status

Ready for Pull Request [ 10304 ]

Pull Request Submitted [ 10101 ]

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Irvin Naylor (Inactive) added a comment - 28/Jan/21 4:20 PM

Nowlan Freese - Here's the pull request: https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/860/igbf-1342-diff-operations-on-2-tracks

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Irvin Naylor (Inactive) added a comment - 28/Jan/21 4:20 PM Nowlan Freese - Here's the pull request: https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/860/igbf-1342-diff-operations-on-2-tracks

Irvin Naylor (Inactive) made changes - 28/Jan/21 4:21 PM

Assignee

Irvin Naylor [ inaylor ]

Ann Loraine made changes - 29/Jan/21 9:08 AM

Status

Pull Request Submitted [ 10101 ]

Reviewing Pull Request [ 10303 ]

Ann Loraine made changes - 29/Jan/21 9:08 AM

Status

Reviewing Pull Request [ 10303 ]

Merged Needs Testing [ 10002 ]

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Ann Loraine added a comment - 29/Jan/21 9:08 AM

Merged and master branch installers are built. Please test.

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Ann Loraine added a comment - 29/Jan/21 9:08 AM Merged and master branch installers are built. Please test.

Nowlan Freese made changes - 03/Feb/21 10:02 PM

Status

Merged Needs Testing [ 10002 ]

Post-merge Testing In Progress [ 10003 ]

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Nowlan Freese added a comment - 03/Feb/21 10:24 PM

Tested master dmg on Mac 10.14.6 (18G7016)

Everything working correctly, nothing odd in the logs. Closing issue.

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Nowlan Freese added a comment - 03/Feb/21 10:24 PM Tested master dmg on Mac 10.14.6 (18G7016) Everything working correctly, nothing odd in the logs. Closing issue.

Nowlan Freese made changes - 03/Feb/21 10:24 PM

Assignee

Irvin Naylor [ inaylor ]

Nowlan Freese made changes - 03/Feb/21 10:24 PM

Resolution		Done [ 10000 ]
Status	Post-merge Testing In Progress [ 10003 ]	Closed [ 6 ]

Nowlan Freese made changes - 26/Mar/21 10:18 AM

Link

This issue duplicates ~~IGBF-395~~ [ ~~IGBF-395~~ ]

Nowlan Freese made changes - 26/Mar/21 2:34 PM

Fix Version/s

9.1.8 Major Release [ 10605 ]

People

Assignee:

Irvin Naylor (Inactive)

Reporter:

Sneha Ramesh Watharkar (Inactive)

Votes:

0 Vote for this issue

Watchers:

5 Start watching this issue

Dates

Created:

03/Jul/18 10:46 AM

Updated:

26/Mar/21 2:34 PM

Resolved:

03/Feb/21 10:24 PM