Activity

From 11/08/2013 to 12/07/2013

12/06/2013

12:55 pm Bug #120 (Closed): custom bed track strand issue
* yes, indeed. Daofeng Li
12:48 pm Bug #120 (Resolved): custom bed track strand issue
fixed on public browser. Xin Zhou
12:18 pm Bug #120 (Closed): custom bed track strand issue
* the strand would display as 'reverse' when the strand was actually a dot '.'
* see Hyungjoo's hub (DMR tracks) fo...
Daofeng Li
07:00 am Bug #119: fixedscale and track height probem in json hub
tracks with "group:1" attribute all share a common scale range and the range is automatic. You cannot apply fixed sca... Xin Zhou
12:30 am Bug #83 (Closed): oversize text in SVG on Firefox
Daofeng Li
12:29 am Bug #116 (Closed): chromHMM tracks cannot be found by "chromhmm" keyword
Daofeng Li
12:29 am washugb v30 release
* We have released v30 of WashU EpiGenome Browser.
h2. Updates:
* custom gene tracks, more details please see: ...
Daofeng Li
12:27 am Bug #119 (Closed): fixedscale and track height probem in json hub
* I am working with Hyungjoo for his hub
* url: http://remc.wustl.edu/hyungjoo/hub_danRer7/hub_Zv9_DNAme.json
* pro...
Daofeng Li

11/29/2013

11:11 pm Feature #118 (New): search auto completion by right clicking from gene tracks
* Is it possible or useful to implement auto completion when we do gene name searching from right clicking of gene/SN... Daofeng Li
11:10 pm Feature #117 (New): add track name to genome snapshot
* I think it would be useful if the track name could be display when generating genome snapshot Daofeng Li

11/24/2013

09:17 pm Bug #112 (Closed): bam display as 'density' when specified as 'full' in UCSC hub
Daofeng Li
09:13 pm Bug #113 (Closed): retrieve session which contains USCS hub error
fixed and closed Daofeng Li
09:12 pm Bug #116: chromHMM tracks cannot be found by "chromhmm" keyword
* that's a useful update
* tested worked.
* so the search will perform against not just track name, also meta data ...
Daofeng Li
05:15 pm washugb v29 release
* We have released v29 of WashU EpiGenome Browser.
h2. Updates:
* access HTTPS resources, including Dropbox, fo...
Daofeng Li
03:44 pm Bug #114: Cannot read property 'cigar' of undefined
no clue... Xin Zhou
03:42 pm Bug #113 (Resolved): retrieve session which contains USCS hub error
fixed on public server Xin Zhou
03:25 pm Bug #111: Tracks disappear when using config panel
Sorry I just figured out the trouble. You must have used this in declaring the track in your hub:
height:"20",
...
Xin Zhou
01:47 pm Bug #112 (Resolved): bam display as 'density' when specified as 'full' in UCSC hub
fixed on public server Xin Zhou
11:55 am Bug #116 (Resolved): chromHMM tracks cannot be found by "chromhmm" keyword
fixed in v29 on public browser Xin Zhou
11:55 am Bug #116: chromHMM tracks cannot be found by "chromhmm" keyword
fixed in v29 on public browser Xin Zhou
10:22 am Bug #116 (Closed): chromHMM tracks cannot be found by "chromhmm" keyword
in hg19, search tracks by keyword "chromhmm" and found nothing
"chromhmm" should match a metadata term and should tu...
Xin Zhou

11/23/2013

04:19 pm Bug #115: tracks do not relocate and some disappear in GSV
When I load a new browser session (not from a saved session ID, but start over completely), then load the gene list, ... Rebecca Lowdon
04:07 pm Bug #115 (New): tracks do not relocate and some disappear in GSV
Loaded my browser session ID: L607cgtoI3
Then loaded attached regions into GSV via copy-paste.
Adjust to view "gen...
Rebecca Lowdon

11/22/2013

09:31 pm Bug #114 (Rejected): Cannot read property 'cigar' of undefined
* use the UCSC hub: http://vizhub.wustl.edu/hubSample/hg19/hg19/trackDb.txt
* open a 2nd panel
* switch to full
* ...
Daofeng Li
09:24 pm Bug #113 (Closed): retrieve session which contains USCS hub error
* session id: LvPDnsxtlZ (public hg19)
* use the UCSC hub mentioned before, save session, retrieve, an error happene...
Daofeng Li
09:20 pm Bug #112 (Closed): bam display as 'density' when specified as 'full' in UCSC hub
* minor issue
* when submit an UCSC hub, I have define the bam tracks display as 'full' mode
* the browser actually...
Daofeng Li

11/21/2013

11:17 am Bug #111 (New): Tracks disappear when using config panel
Tried adding three new tracks via Facet browser from my data hub. When I load them they appear with a huge track heig... Rebecca Lowdon
12:08 am Bug #90 (Closed): long range track display runs into error
* tested the long range tracks and could be displayed well.
* Closed and could re-opened if we found this issue again.
Daofeng Li

11/20/2013

03:13 pm Feature #110 (New): hub check button
* I think it would be great to add a 'check hub' button to the hub submission panel
* users could check the hub firs...
Daofeng Li
10:28 am Bug #109: Problem saving session
Saving session with many tracks and a large gene set will run into this error
mysql rejects a very long query by s...
Xin Zhou

11/19/2013

05:13 pm Bug #109 (Closed): Problem saving session
Tried to save my session (for the second time) but get an error. Rebecca Lowdon
05:13 pm washugb v28 release
h2. updates
* multiple track selection, for details please see: http://washugb.blogspot.com/2013/11/v28-1-of-2-mul...
Daofeng Li
08:06 am Feature #108 (New): compute pearson correlation in scatterplot
as requested by a user from MIT Xin Zhou

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
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