Activity
From 01/23/2014 to 02/21/2014
02/19/2014
- 11:19 am Bug #165 (Closed): browser frozen when panning of BAM tracks
- * Thanks for fixing!
- 11:07 am Bug #165 (Resolved): browser frozen when panning of BAM tracks
- Fixed in v32.1.8!
- 10:15 am Bug #165 (Closed): browser frozen when panning of BAM tracks
- * using this hub: http://epigenomegateway.wustl.edu/browser/?genome=hg19&datahub_jsonfile=http://cgs.wustl.edu/~dli/C...
- 10:13 am Bug #164 (Closed): UI frozen when click 'remove all' from json hub
- 10:11 am Bug #164 (Resolved): UI frozen when click 'remove all' from json hub
- Fixed in v32.1.7. Thanks!
- 09:58 am Bug #164 (Closed): UI frozen when click 'remove all' from json hub
- * loading this hub: http://epigenomegateway.wustl.edu/browser/?genome=hg19&datahub_jsonfile=http://cgs.wustl.edu/~dli...
02/18/2014
- 03:39 pm Bug #163 (New): long responsive time while track missed in hub
- * see Junchen's hub at http://remc.wustl.edu/jgu/human/remc/methylomes/methylomes_all_hub.json
* apache error log sh... - 08:02 am Feature #162 (Resolved): Tooltip information
- Implemented in v32.1.4. Thanks!
02/15/2014
- 01:09 pm Bug #160 (Resolved): Custom PE BAM files unstable
- Fixed in v32.1.4
http://epigenomegateway.wustl.edu/browser/?genome=danRer7&custombam=xx,http://cgs.wustl.edu/~rlow... - 08:00 am Bug #153: track information display error
- Missing GEO accession has been fixed.
02/14/2014
- 10:18 pm Bug #147 (Closed): crash when track file not exist in json hub
- fixed.
- 10:17 pm Bug #153: track information display error
- GEO links also could not be recovered?
- 04:46 pm Bug #159 (Closed): Session not saving
- 04:45 pm Bug #155: browser url parameter for coordinate not working
- Use the "native_track" keyword and add gene track to your JSON datahub.
Find example in this hub:
http://vizhub... - 04:43 pm Bug #155: browser url parameter for coordinate not working
- OK. I see.
Then how do I include the gene annotation track by default with my own data? When I uploaded my own tr... - 04:43 pm Bug #157: refSeq gene position didn't keep in session
- refSeq is a "native track". Current design only keeps order of custom tracks. Native tracks are all piled to the bottom.
- 04:29 pm Bug #155 (Rejected): browser url parameter for coordinate not working
- When the "session" and "statusId" parameters are in use, the "coordinate" parameter is disregarded, since the view ra...
- 04:25 pm Bug #153 (Resolved): track information display error
- Fixed in v32.1.3, but the track details from previous saved sessions cannot be recovered.
- 03:58 pm Bug #147 (Resolved): crash when track file not exist in json hub
- can you try again with the new code?
- 03:31 pm Feature #162 (Closed): Tooltip information
- Would be great if the tooltip could include per-read CIGAR strings, mapping quality scores, and maybe insert size inf...
02/13/2014
- 05:59 pm Feature #158: wrapping for tooltip read information
- good suggestion :)
- 05:58 pm Bug #159: Session not saving
- my bad, wrong permission for the session folder. Should be fixed now. Please let me know if problem still exists.
- 03:32 pm Feature #161 (New): Include scaffolds on genome snapshot
- Would be nice to view scaffolds and unassigned chromosome fragments (in danRer7 referred to as "NA###") in the "genom...
- 03:27 pm Bug #160 (Closed): Custom PE BAM files unstable
- BAM tracks of paired-end alignments appear unstable on the browser. Relocating or zooming in/out causes reads to "mov...
- 03:20 pm Bug #159 (Closed): Session not saving
- Was trying to save a session to send you another bug ... but sessions not working on danRer7!
- 03:18 pm Feature #158 (New): wrapping for tooltip read information
- Would be nice if information in tooltip would automatically wrap to display all information. For example, I want to v...
02/11/2014
- 10:52 pm Bug #123 (Closed): embedded browser cannot handle hidden tracks
- 10:52 pm Feature #145 (Closed): loose format requirement for coordinates format
- * yes, it works great!
- 10:52 pm Bug #152 (Closed): clicking "zoom in" button makes browser unresponsive
- 10:51 pm Bug #148 (Closed): add geneset to genome snapshot error
- 10:50 pm Bug #157 (New): refSeq gene position didn't keep in session
- * move refSeq gene to top of canvas
* same session, load, the refSeq gene goes to bottom
02/07/2014
- 11:45 pm washugb v32 release
- * We have released v32 of WashU EpiGenome Browser.
h2. Updates
* shared metadata, for details please see: http:... - 11:32 pm Complete Epigenome Browser Bug #156 (New): WUGB popup link get blocked
- * the popup being blocked seems are default behavior of most modern browsers
- 04:11 pm Bug #155 (Rejected): browser url parameter for coordinate not working
- Xin,
If you go to my Feb. 2014 wiki and on Feb. 6-7, I have a table of regions and in the last column there are brow...
02/06/2014
- 02:11 pm Bug #154 (Resolved): Cannot search for gene in embedded browser
- Fixed in v32.0.7.
See this example: http://cgs.wustl.edu/~xzhou/embed/1.html - 02:04 pm Bug #154 (Closed): Cannot search for gene in embedded browser
- If the embedded browser only imports "base.js" it can't search and jump to a gene, this error will be given:
Objec...
02/05/2014
- 12:31 pm Bug #153 (Closed): track information display error
- * same a session, load it with the link generated
* right click a track, choose Information, you will see some infor... - 10:32 am Bug #152 (Resolved): clicking "zoom in" button makes browser unresponsive
- Fixed in v32.0.3 on public browser
The bug is still there on test server for you to check out. - 10:31 am Bug #152 (Closed): clicking "zoom in" button makes browser unresponsive
- CLick the "+" (zoom in) button multiple times until getting this message:
At finest level, cannot zoom in
And t...
02/01/2014
- 08:35 am Feature #145 (Resolved): loose format requirement for coordinates format
- Fixed in v32.0.1. Try these coordinates with multiple spaces separating fields:
chr7 55418829 55419003
chr7...
01/31/2014
- 08:41 am Bug #119 (Closed): fixedscale and track height probem in json hub
- 08:40 am Bug #144 (Closed): mouse over event for meta data header ( in track table ) disappear
- 08:40 am Bug #150 (Closed): js error and clickable 'None yet'
- 08:31 am Bug #150 (Resolved): js error and clickable 'None yet'
- Fixed, thanks for finding out this tricky problem!
- 12:19 am Bug #150 (Closed): js error and clickable 'None yet'
- * the js errors in the console seems happened when open 2nd panel, while no crash happens
* the 'None yet' in 'custo...
01/30/2014
- 06:50 am Bug #149 (Rejected): possible coordinate issue
- 06:50 am Bug #149: possible coordinate issue
- Thanks for reporting this. This is because our browser's coordinates are 0-offset, they all start from 0. But in UCSC...
- 01:09 am Bug #149 (Rejected): possible coordinate issue
- I was looking at a SNP (chr16:89986117-89986117) which is a C shown on UCSC browser (see attached image) but it's a G...
01/28/2014
- 07:20 am Bug #148 (Resolved): add geneset to genome snapshot error
- Fixed, thanks!
01/27/2014
- 05:22 pm Bug #148 (Closed): add geneset to genome snapshot error
- * submit a list of coordinates to gene set
* looks like browser didn't give a default name for the list, when you cl... - 03:11 pm Bug #147 (Closed): crash when track file not exist in json hub
- * I found if I renamed a file in my hub, loading the hub without updating it, browser will throw 'Json syntax error'
01/24/2014
- 05:21 pm Support #136 (Closed): Collecting new Hi-C data sets
- 05:07 pm Support #136: Collecting new Hi-C data sets
- * processed the data, but found the data was already in our browser....
01/23/2014
- 11:58 am Bug #140 (Resolved): error with tracks of same file URL
- Fixed in v31.0.8
Load a hub with duplicated track URLs:
http://epigenomegateway.wustl.edu/browser/?genome=hg19&... - 11:57 am Bug #144 (Resolved): mouse over event for meta data header ( in track table ) disappear
- Fixed in v31.0.8
- 11:56 am Feature #139 (Resolved): metadata heatmap compatibility between data hubs
- A mechanism for sharing metadata vocabulary among hubs is now available in v31.0.8
Example: a pair of hubs sharing... - 08:35 am Bug #144: mouse over event for meta data header ( in track table ) disappear
- I will put it back then!
- 08:33 am Bug #144: mouse over event for meta data header ( in track table ) disappear
- ok...at least Bo and I think it's pretty useful and convenient...
- 08:32 am Feature #145: loose format requirement for coordinates format
- how about not limit to 1 space delimited? People usually view DMRs copied from terminal may have multiple space betw...
- 07:37 am Bug #146 (New): Session cannot save more than 1 custom metadata vocabularies
- If 2 or more custom metadata vocabularies are loaded, only 1st one can be saved in session.
- 07:08 am Feature #145: loose format requirement for coordinates format
- what other formats do you suggest?
- 07:06 am Bug #144: mouse over event for meta data header ( in track table ) disappear
- No I removed this feature.
Also available in: Atom