Activity

From 10/20/2013 to 11/18/2013

11/18/2013

10:33 pm Bug #87 (Closed): SNP track showing all SNPs to be on reverse strand
* could observer SNPs in reverse strand! Daofeng Li
10:28 pm Bug #82 (Closed): crashed when restoring session
* cool fix Daofeng Li
10:27 pm Bug #74 (Closed): circlet plot generates wrong graph
* tested zoom in the circlet view, Fixed! Daofeng Li
10:22 pm Bug #71 (Closed): cannot handle irregularity in custom metadata
* cool error message! Daofeng Li
10:17 pm Feature #60 (Closed): "file type" category for custom facet table
* nice feature! Daofeng Li
10:15 pm Bug #66 (Closed): Save custom metadata vocabulary into session
* closed Daofeng Li
10:06 pm Bug #65 (Closed): Error rendering RRBS track
*fixed! Daofeng Li
10:01 pm Bug #73 (Closed): bam track in json hub set to show cause syntax error
fixed Daofeng Li
10:00 pm Feature #67 (Closed): change background color
Feature completed! Daofeng Li
09:59 pm Bug #88 (Closed): gene tracks are omitted in restored sessions
* closed Daofeng Li
09:58 pm Bug #91 (Closed): crashed when loading bam track
* tested loading custom bam file, works! Closed! Daofeng Li
09:56 pm Bug #92 (Closed): configuration of category track not 'apply to all' and 'apply background'
* nicely solved Daofeng Li
09:55 pm Bug #94 (Closed): Crashed when creating gene set on mm9
works well and closed Daofeng Li
09:54 pm Bug #95 (Closed): crashed when loading a hub with wrong metadata vocabulary
fixed and closed Daofeng Li
09:53 pm Feature #98 (Closed): multiple selection of tracks
* feature completed! Daofeng Li
09:51 pm Bug #102 (Closed): problem loading a datahub with no tracks shown by default
fixed and closed! Daofeng Li
09:51 pm Bug #104 (Closed): configuration of long range track missing height adjustment
nicely solved! Daofeng Li
09:49 pm Bug #107: handling of hub file errors
* this is cool
* how about adding an UCSC option for datahub type for loading UCSC hubs?
Daofeng Li
09:47 pm Bug #106 (Closed): gencodeV17 track cannot be saved in session
fixed and closed! Daofeng Li
12:05 pm Bug #59 (Closed): error filling contents for facet table of 2nd datahub
Xin Zhou
12:04 pm Bug #69 (Rejected): track name in svg
I may not be able to solve it soon, but user can either turn off track name on SVG output, or increase the track name... Xin Zhou
12:03 pm Bug #73 (Resolved): bam track in json hub set to show cause syntax error
Fixed in v27.3 on test browser
In the datahub, if a bam track is set to "show", it will be shown as a read density...
Xin Zhou
11:58 am Bug #92 (Resolved): configuration of category track not 'apply to all' and 'apply background'
Fixed in v27.3, on test browser
Both options "apply to all" and "background color" are now available for categoric...
Xin Zhou
11:57 am Bug #104 (Resolved): configuration of long range track missing height adjustment
Fixed in v27.3, on test browser
If the long range track is in heatmap mode, the height option will appear, otherwi...
Xin Zhou
11:54 am Bug #106 (Resolved): gencodeV17 track cannot be saved in session
Fixed in v27.3, on test browser Xin Zhou
11:54 am Bug #107 (Resolved): handling of hub file errors
Fixed in v27.3, on test browser Xin Zhou
11:53 am Bug #107 (Closed): handling of hub file errors
errors include:
non-existent hub file, e.g. http://vizhub.wustl.edu/hubSample/hg19/hub.missing
file with wrong ...
Xin Zhou
11:50 am Bug #102 (Resolved): problem loading a datahub with no tracks shown by default
Fixed in v27.3 on test browser Xin Zhou
10:19 am Bug #106 (Closed): gencodeV17 track cannot be saved in session
found by Rebecca on hg19, public browser Xin Zhou
07:25 am Bug #105 (Rejected): 'Remove all' button in Facet of public hub was not working
that's not an issue, that's a feature
One REMOVE ALL button controls the native tracks and will remove all native ...
Xin Zhou
07:19 am Bug #103 (Rejected): taking screen shot of genome snapshot
Don't know what you mean. The "screenshot" button IS DISABLED when you click it. Xin Zhou
07:17 am Feature #98: multiple selection of tracks
when you have multiple-selected some tracks, and then you right click on a new one that's not selected, the selection... Xin Zhou

11/17/2013

09:23 pm Bug #105 (Rejected): 'Remove all' button in Facet of public hub was not working
* after loading one the public hub
* try to remove all tracks (native or tacks from hub)
* the two 'Remove all' but...
Daofeng Li
07:45 pm Bug #104 (Closed): configuration of long range track missing height adjustment
* seems the configuration of long track was not normal
** missing height adjustment
** adding font change like gene...
Daofeng Li
07:34 pm Bug #103 (Rejected): taking screen shot of genome snapshot
* Is it possisble to make this 'screenshot' button gray (not usable) after clicking it, now this button could always ... Daofeng Li
07:24 pm Feature #98: multiple selection of tracks
* few minor issues:
** after multiple selection, sometimes the yellow background of track name would disappear (like...
Daofeng Li
02:20 pm Bug #102 (Closed): problem loading a datahub with no tracks shown by default
Load a datahub (json) with all tracks set to "hide"
the loading GIF image never disappears, making it impossible f...
Xin Zhou

11/15/2013

10:59 pm Feature #98: multiple selection of tracks
* I tested the multiple selection on PC works pretty well
* might use check box instead of keyboard events would bri...
Daofeng Li

11/13/2013

10:03 am Bug #101: json syntax error when retrieving session
sorry for missing those info, hg19 on public server. Daofeng Li
09:49 am Bug #101: json syntax error when retrieving session
genome and server? Xin Zhou
09:48 am Bug #101 (Closed): json syntax error when retrieving session
* I have this session id: m4doLKKJHz with many status, only one of the status (id: 954222367) will give me 'Syntax er... Daofeng Li

11/11/2013

10:27 am washugb v27 release
* We have released v27 of WashU EpiGenome Browser.
h2. Updates:
* GENCODE V17 track for the human genome, for d...
Daofeng Li

11/10/2013

12:08 am Bug #100 (Closed): geneplot (lines plot) error
Fixed and closed. Daofeng Li

11/09/2013

07:37 am Bug #100 (Resolved): geneplot (lines plot) error
Fixed, thanks! Xin Zhou
12:05 am Bug #93 (Closed): new genecode v17 track not work with genome snapshot
* fixed Daofeng Li

11/08/2013

11:59 pm Bug #100 (Closed): geneplot (lines plot) error
* happened both at public and test server
* choose lines plot from geneplot panel, see screeshot for error message
Daofeng Li
06:46 am Bug #96 (Rejected): location jumping was not accurate
Xin Zhou
06:46 am Bug #96: location jumping was not accurate
reported in #46 Xin Zhou

11/07/2013

05:36 pm Feature #99 (New): function that move track(s) to top or bottom
* Is it useful to add a function that move track(s) to top or bottom of canvas? Daofeng Li
05:36 pm Feature #98 (Closed): multiple selection of tracks
* Is it possible to support multiple selection of tracks? Like I want to select 2 tracks from different samples or as... Daofeng Li
05:33 pm Feature #97 (New): user defined track color
* when changing track colors, is it possible to use other colors? Such as using RGB values or HEX values. Daofeng Li
05:32 pm Bug #96 (Rejected): location jumping was not accurate
* in the browser, if I want to jump to a location for example chr1:89443114-89943027
* the browser will give me chr1...
Daofeng Li
02:01 pm Bug #95 (Resolved): crashed when loading a hub with wrong metadata vocabulary
Fixed on public browser. The "Age" term which appears both as parent and child will be rejected. An error message wil... Xin Zhou
02:00 pm Bug #95 (Closed): crashed when loading a hub with wrong metadata vocabulary
the vocabulary contains following:
"Age":{
"Age":["1 year", "2 year"],
...
}
Xin Zhou
09:32 am Bug #94 (Resolved): Crashed when creating gene set on mm9
Fixed on public browser.
text descriptions of above items contain quote marks that need to be dealt with.
Xin Zhou
09:30 am Bug #94 (Closed): Crashed when creating gene set on mm9
With following text input:
Mir7675
Mir6387
Mir3066
Mir6937
Mir680
Mir5099
Mir1938
Mir5627
Mir1843a
Mir306...
Xin Zhou
08:26 am Bug #92: configuration of category track not 'apply to all' and 'apply background'
yes. Daofeng Li
07:34 am Bug #92: configuration of category track not 'apply to all' and 'apply background'
Do you mean the options "apply to all" and "apply background" are not available for categorical track? Xin Zhou

11/06/2013

09:43 pm Bug #93 (Closed): new genecode v17 track not work with genome snapshot
* an error "Uncaught TypeError: Cannot read property 'chr1' of undefined " Daofeng Li
09:30 pm Bug #92 (Closed): configuration of category track not 'apply to all' and 'apply background'
* not sure this was a bug or specific design though Daofeng Li

11/05/2013

07:29 pm Bug #91 (Resolved): crashed when loading bam track
Fixed in v26.2 on PUBLIC browser, still there on the test for you to see it
the error was because the code was try...
Xin Zhou
07:28 pm Bug #91 (Closed): crashed when loading bam track
try loading a bam track from submission panel, crashes Xin Zhou
06:26 pm Bug #90 (Resolved): long range track display runs into error
fixed in v26.2 on PUBLIC browser. Still there on test browser
it's the max score-calculating part that's causing t...
Xin Zhou
06:21 pm Bug #90 (Closed): long range track display runs into error
display a long range track. The track may not be able to show at all, or crashes when turning its display mode. Xin Zhou
01:26 pm Bug #89: mCRF tracks not recognized
Did a quick fix and added the error-reporting function, see this:
http://epgg-test.wustl.edu/browser/?genome=hg19&...
Xin Zhou
11:53 am Bug #89 (Resolved): mCRF tracks not recognized
Thanks for the report, following issues have been fixed.
* numerical hub tracks (bigwig or bedgraph) will be show...
Xin Zhou
11:16 am Bug #89 (Closed): mCRF tracks not recognized
When I load my dataHub, some of the mCRF tracks are not recognized by the browser. They are set to mode:"full" to app... Rebecca Lowdon
07:41 am Bug #88 (Resolved): gene tracks are omitted in restored sessions
Fixed on public browser. This problem still exists on test browser for you to see it.
BE SURE TO FULLY TEST THE BR...
Xin Zhou
07:40 am Bug #88 (Closed): gene tracks are omitted in restored sessions
save a session with numerical tracks and gene track
restore this session
the gene track is absent from tracks resto...
Xin Zhou

11/04/2013

10:04 pm Bug #86: 2nd panel didn't align top with main panel
* happens on the iMAC i am using, not on PC Daofeng Li

11/01/2013

11:05 am washugb v26 release
We have applied v26 source code to our public servers.
h2. updates:
* SNP information is a long-desired feature...
Daofeng Li

10/31/2013

10:46 am Bug #87 (Resolved): SNP track showing all SNPs to be on reverse strand
Fixed on public server, still visible on test server
Problem is that SNP track use +/- to indicate SNPs while the br...
Xin Zhou
10:44 am Bug #87 (Closed): SNP track showing all SNPs to be on reverse strand
happens to all SNPs in hg19 SNP track Xin Zhou
09:39 am Bug #86 (Closed): 2nd panel didn't align top with main panel
* minor display issue
* see screenshot
Daofeng Li
09:35 am Bug #84 (Closed): background in 2nd panel didn't apply to main panel automatically
Fixed! Daofeng Li
09:35 am Bug #85 (Closed): rmsk track configuration not available for subfamily tracks
Fixed Daofeng Li
08:52 am Bug #84 (Resolved): background in 2nd panel didn't apply to main panel automatically
Fixed in v25.5, thanks! Xin Zhou
08:51 am Bug #85 (Resolved): rmsk track configuration not available for subfamily tracks
fixed on test
in fact they are family-tracks, not subfamilies. Their parent tracks are TE classes.
the bug was be...
Xin Zhou

10/29/2013

10:13 pm Bug #85 (Closed): rmsk track configuration not available for subfamily tracks
* the new display was not configurable for subfamily tracks
* see screenshot
* (might be not a bug?)
Daofeng Li

10/28/2013

10:44 pm Bug #84 (Closed): background in 2nd panel didn't apply to main panel automatically
* might be not an issue
* in 2nd panel, if you apply smoothing, the effect will also apply to main panel
* if you a...
Daofeng Li
11:07 am Bug #81 (Rejected): lineplot information not contain in 'making url'
lineplot may be too complicated to fit in URL parameter, its intended use is: you first bring up a numerical track on... Xin Zhou
10:16 am Bug #83 (Resolved): oversize text in SVG on Firefox
Fixed on public server. The trouble can still be seen on TEST. Xin Zhou
10:16 am Bug #83 (Closed): oversize text in SVG on Firefox
SVG graph displayed on Firefox shows oversize text, as pointed out by a user Xin Zhou
09:20 am Bug #82 (Resolved): crashed when restoring session
Solved by allowing the code to tolerate the non-existent tracks and wrong metadata color map term information.
In ...
Xin Zhou
09:18 am Bug #82 (Closed): crashed when restoring session
this happens to sessions that were created a while ago, before September 2013. Xin Zhou

10/26/2013

11:47 pm Bug #81 (Rejected): lineplot information not contain in 'making url'
* after making a track to line, making a url
* click the url didn't show the lineplot
Daofeng Li
11:45 pm Bug #80 (New): session with lineplot TypeError
* save a session with lineplot
* reload, TypeError happened
Daofeng Li
11:39 pm Bug #79 (New): browser background color
* sometimes when removed 2nd panel, the main panel will expand, the background color of rightmost part will not be th... Daofeng Li
11:30 pm Bug #78 (New): 2nd panel lineplot not applied to main panel
* see screenshot Daofeng Li
11:25 pm Bug #77 (New): track background color not applied on 2nd panel of line plot
* see screenshot please Daofeng Li

10/25/2013

08:36 am Bug #75 (Closed): smoothing window doesn't work well on tracks in secondary panel
fixed! Daofeng Li
08:36 am Bug #76 (Closed): circlet view not work at test
* yeah, seems my web browser cashed the old code, after refresh everything goes well Daofeng Li
06:59 am Bug #76: circlet view not work at test
It works for me. Did you refresh page? If the error still happens can you provide some description? Xin Zhou

10/24/2013

10:50 pm Bug #76 (Closed): circlet view not work at test
* a TypeError happened Daofeng Li
11:40 am Bug #75 (Resolved): smoothing window doesn't work well on tracks in secondary panel
fixed on test browser Xin Zhou
11:39 am Bug #75 (Closed): smoothing window doesn't work well on tracks in secondary panel
Apply smoothing window to a track in main panel, open a secondary panel, got error Xin Zhou
08:49 am Bug #74 (Resolved): circlet plot generates wrong graph
Has been fixed on public server as soon as the problem was found out.
It is still left unfixed on test server.
Xin Zhou
08:48 am Bug #74 (Closed): circlet plot generates wrong graph
After running circlet view on a long range track, zoom in on the circlet view and find the wrong graph Xin Zhou

10/23/2013

04:02 pm Bug #73 (Closed): bam track in json hub set to show cause syntax error
* Use bam track in a json hub, the hub works when all bam tracks set to 'hide' mode
* while any of the bam track set...
Daofeng Li
04:00 pm Bug #72 (Closed): error when click 'smooth window' after check 'apply to all'
FIxed! Daofeng Li
07:27 am Bug #72 (Resolved): error when click 'smooth window' after check 'apply to all'
Fixed. Thanks a lot for finding out this bug! Xin Zhou

10/22/2013

10:57 pm Bug #72 (Closed): error when click 'smooth window' after check 'apply to all'
* on test server, load hg19 default tracks
* select one of the track, apply smoothing, then check 'apply to all trac...
Daofeng Li
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