All File Changes
v262_preview to v262_preview2 (2012-01-10 to 2012-01-17) v262
- python/lib/ucscgenomics/ra.py
- lines changed 5, context: html, text, full: html, text
fixed a bug handling comments internal to stanzas
- lines changed 4, context: html, text, full: html, text
indent on wrong level, and added continue statements for some minor speed gains
- lines changed 3, context: html, text, full: html, text
wrong method used to add stanzas into raFile object
- lines changed 25, context: html, text, full: html, text
rewrote some of updatediff to take out the metaDb special case, it now does it ra-type agnostically
- lines changed 7, context: html, text, full: html, text
added comments and made variable names better
- lines changed 47, context: html, text, full: html, text
added in willy's ra->trackDb print option
- python/lib/ucscgenomics/ucscUtils.py
- lines changed 2, context: html, text, full: html, text
doesn't skip empty lines now
- src/hg/encode/DAFs/3.0/hg19/wgEncodeCshlShortRnaSeq.daf
- lines changed 17, context: html, text, full: html, text
Adding protocol doc to the DAF and protocols expVar
- src/hg/encode/encodeMkFilesList/encodeMkFilesList
- lines changed 5, context: html, text, full: html, text
widened the filemask and fixed a weird edge case bug
- src/hg/encode/encodeQaPrepareRelease/encodeQaPrepareRelease
- lines changed 107, context: html, text, full: html, text
refactored code to be more python like
- lines changed 4, context: html, text, full: html, text
missed an indent on refactor
- src/hg/encode/encodeValidate/doEncodeValidate.pl
- lines changed 4, context: html, text, full: html, text
added switch for mm9's different dataVersion, right now it's the same as hg19's though
- src/hg/encode/hgEncodeVocab/hgEncodeVocab.c
- lines changed 1, context: html, text, full: html, text
Objectified sortTable and filterTable but no functional change is here.
- src/hg/encode/qaUpdateMetadata/qaUpdateMetadata
- src/hg/encode/raMerge/raMerge
- lines changed 2, context: html, text, full: html, text
structure of merged object changed, compensating
- lines changed 4, context: html, text, full: html, text
modifications for trackDb
- src/hg/hgCustom/hgCustom.c
- lines changed 1, context: html, text, full: html, text
redmine Doc #6507 Need to redirect references to various sections of customTrack.html.
- src/hg/hgFileSearch/hgFileSearch.c
- lines changed 6, context: html, text, full: html, text
Getting rid of the last vestiges of NEW_JQUERY ifdef.
- lines changed 7, context: html, text, full: html, text
Merge branch 'master' into tdreszer-subCfg
- src/hg/hgGateway/hgGateway.c
- lines changed 11, context: html, text, full: html, text
Getting rid of the last vestiges of NEW_JQUERY ifdef.
- src/hg/hgHubConnect/hgHubConnect.c
- lines changed 2, context: html, text, full: html, text
check syntax of urls in "add hubs" tab
- src/hg/hgTables/schema.c
- lines changed 1, context: html, text, full: html, text
redmine Doc #6507 Need to redirect references to various sections of customTrack.html.
- src/hg/hgTables/vcf.c
- lines changed 5, context: html, text, full: html, text
Bug #6529 (VCF internal rep doesn't do missing data): add flags for missingdata values to vcfInfoElement, so we know the difference between "0" and ".".
This applies to both INFO column values and genotype (FORMAT) values.
Also, vcfGenotype's hapIxA and hapIxB are now signed, with negative values
indicating missing data.
User reported bug in MLQ #6462.
- src/hg/hgTrackUi/hgTrackUi.c
- lines changed 5, context: html, text, full: html, text
Initial check-in of not yet comple subtrack configuration module.
- lines changed 23, context: html, text, full: html, text
Merge branch 'master' into tdreszer-subCfg
- lines changed 6, context: html, text, full: html, text
Big load of changes for subCfg.
- lines changed 122, context: html, text, full: html, text
Changes to fix redmine 4892 composite/view/subtrack inconsistency.
- lines changed 104, context: html, text, full: html, text
Further fixes to the cfgByType consistency logic, prompted by side by side comparisons on hg18 tracks.
- lines changed 2, context: html, text, full: html, text
More tightening of screws. Several special cases solved. Altererd which right-click menu items for cfg appear and regularized this with subCfg availability.
- lines changed 52, context: html, text, full: html, text
Major work on bedFilt, psl and wigMaf to make them properly composite ready.
- lines changed 8, context: html, text, full: html, text
Added cancel button for composite configuration.
- lines changed 10, context: html, text, full: html, text
More plus/minus button stylings
- lines changed 6, context: html, text, full: html, text
More touches on BUTTONS_BY_CSS
- lines changed 4, context: html, text, full: html, text
Some older composites have packable children which are seen in rightClick as unpackable. The mixed case that gives rise to this should not be allowed now, but we can support it for those older composites. The rule is, if any single subtrack is packable, then the whole tree is.
- src/hg/hgTracks/bamTrack.c
- lines changed 5, context: html, text, full: html, text
Just a changed name tree wide. The 'compositeLevel' paramter to closestToHome cart functions was confusing. What it means is the request is for a setting one step above the tdb passed in. It is used for view level controls where the model tdb is a subtrack. This checkin has NO functional affect.
- src/hg/hgTracks/bedTrack.c
- lines changed 7, context: html, text, full: html, text
Major work on bedFilt, psl and wigMaf to make them properly composite ready.
- src/hg/hgTracks/config.c
- lines changed 5, context: html, text, full: html, text
More touches on BUTTONS_BY_CSS
- lines changed 1, context: html, text, full: html, text
Some older composites have packable children which are seen in rightClick as unpackable. The mixed case that gives rise to this should not be allowed now, but we can support it for those older composites. The rule is, if any single subtrack is packable, then the whole tree is.
- lines changed 110, context: html, text, full: html, text
Removed old ifdefs. No functional change here.
- src/hg/hgTracks/hgTracks.c
- lines changed 1, context: html, text, full: html, text
Getting rid of the last vestiges of NEW_JQUERY ifdef.
- lines changed 5, context: html, text, full: html, text
More touches on BUTTONS_BY_CSS
- lines changed 1, context: html, text, full: html, text
Some older composites have packable children which are seen in rightClick as unpackable. The mixed case that gives rise to this should not be allowed now, but we can support it for those older composites. The rule is, if any single subtrack is packable, then the whole tree is.
- lines changed 19, context: html, text, full: html, text
Removed old ifdefs. No functional change here.
- src/hg/hgTracks/hgTracks.h
- lines changed 5, context: html, text, full: html, text
Removed old ifdefs. No functional change here.
- src/hg/hgTracks/imageV2.c
- lines changed 6, context: html, text, full: html, text
More tightening of screws. Several special cases solved. Altererd which right-click menu items for cfg appear and regularized this with subCfg availability.
- lines changed 3, context: html, text, full: html, text
Another set of fixes propted by going through all of hg19 again and another 7 assemblies from different species and clades.
- lines changed 3, context: html, text, full: html, text
With subCfg, when only one subtrack, highlevel shouuld show subtrack controls, so that rightClick and subCfg work together.
- lines changed 1, context: html, text, full: html, text
Some older composites have packable children which are seen in rightClick as unpackable. The mixed case that gives rise to this should not be allowed now, but we can support it for those older composites. The rule is, if any single subtrack is packable, then the whole tree is.
- lines changed 12, context: html, text, full: html, text
Removed old ifdefs. No functional change here.
- src/hg/hgTracks/imageV2.h
- lines changed 3, context: html, text, full: html, text
More incremental work on subCfg
- lines changed 5, context: html, text, full: html, text
Merge branches 'master' and 'master' into tdreszer-subCfg
- lines changed 7, context: html, text, full: html, text
Removed old ifdefs. No functional change here.
- src/hg/hgTracks/netTrack.c
- lines changed 4, context: html, text, full: html, text
Removed old ifdefs. No functional change here.
- src/hg/hgTracks/pslTrack.c
- lines changed 5, context: html, text, full: html, text
Major work on bedFilt, psl and wigMaf to make them properly composite ready.
- src/hg/hgTracks/searchTracks.c
- lines changed 6, context: html, text, full: html, text
Getting rid of the last vestiges of NEW_JQUERY ifdef.
- lines changed 10, context: html, text, full: html, text
More plus/minus button stylings
- lines changed 8, context: html, text, full: html, text
More touches on BUTTONS_BY_CSS
- lines changed 7, context: html, text, full: html, text
Removed old ifdefs. No functional change here.
- src/hg/hgTracks/simpleTracks.c
- lines changed 2, context: html, text, full: html, text
More screw tightening. Encode peaks are not configurable unless there are additional trackDb settings that say so.
- lines changed 4, context: html, text, full: html, text
Eliminated a couple more vars from cart and FINALY got rid of funky comp.view.vis cart name. All vis is not standardized to trackName since view is a track.
- lines changed 4, context: html, text, full: html, text
Removed old ifdefs. No functional change here.
- lines changed 2, context: html, text, full: html, text
fixed breakage of labels in gencode V4 caused by changes for V10
- src/hg/hgTracks/vcfTrack.c
- lines changed 17, context: html, text, full: html, text
Bug #6529 (VCF internal rep doesn't do missing data): add flags for missingdata values to vcfInfoElement, so we know the difference between "0" and ".".
This applies to both INFO column values and genotype (FORMAT) values.
Also, vcfGenotype's hapIxA and hapIxB are now signed, with negative values
indicating missing data.
User reported bug in MLQ #6462.
- src/hg/hgTracks/wigMafTrack.c
- lines changed 80, context: html, text, full: html, text
Major work on bedFilt, psl and wigMaf to make them properly composite ready.
- lines changed 2, context: html, text, full: html, text
Slight adjustment to one API
- src/hg/hgc/gencodeClick.c
- lines changed 24, context: html, text, full: html, text
added transcript support levels for version 10, correct some html doc
- lines changed 4, context: html, text, full: html, text
added documentation on GENCODE TSL
- src/hg/hgc/mafClick.c
- lines changed 15, context: html, text, full: html, text
Major work on bedFilt, psl and wigMaf to make them properly composite ready.
- lines changed 7, context: html, text, full: html, text
Slight adjustment to one API
- src/hg/hgc/vcfClick.c
- lines changed 15, context: html, text, full: html, text
Bug #6529 (VCF internal rep doesn't do missing data): add flags for missingdata values to vcfInfoElement, so we know the difference between "0" and ".".
This applies to both INFO column values and genotype (FORMAT) values.
Also, vcfGenotype's hapIxA and hapIxB are now signed, with negative values
indicating missing data.
User reported bug in MLQ #6462.
- src/hg/htdocs/ENCODE/contacts.html
- lines changed 14, context: html, text, full: html, text
Add Ruihua (w/o email for now). Lower visibility of encode@ucsc email)
- lines changed 42, context: html, text, full: html, text
added Ruihua's sanitized email address. Sanitized the encode email address, removed people not on the project and removed project specifics in consultation with Cricket, reorganized and changed the wording of the contact information which still has to be reviewed by Kate. Redmine# 6568
- src/hg/htdocs/ENCODE/index.html
- lines changed 64, context: html, text, full: html, text
Add news items from Nov-Dec 2011
- src/hg/htdocs/ENCODE/newsarch.html
- lines changed 54, context: html, text, full: html, text
Add news items from Nov-Dec 2011
- src/hg/htdocs/FAQ/FAQlink.html
- lines changed 74, context: html, text, full: html, text
Added section about creating a custom URL to view specific tracks
- lines changed 19, context: html, text, full: html, text
Added a line telling users how to find the table name of their track. Made some minor corrections.
- src/hg/htdocs/goldenPath/help/customTrackText.html
- lines changed 7, context: html, text, full: html, text
Changed links for BED, PSL, GFF, GTF and microarray to point to FAQformat.html
- src/hg/htdocs/goldenPath/help/multiView.html
- lines changed 34, context: html, text, full: html, text
Update multiView help to include a short section on subtrack configuration.
- src/hg/htdocs/indexNews.html
- lines changed 2, context: html, text, full: html, text
removed extra 'the' and made hyperlink changes, per redmine #6537
- src/hg/htdocs/makefile
- lines changed 45, context: html, text, full: html, text
redmine track #6406 - tRNA track for several (44) assemblies.
- src/hg/htdocs/style/HGStyle.css
- lines changed 2, context: html, text, full: html, text
Clickable class should get a hand.
- lines changed 2, context: html, text, full: html, text
Support (in progress) for subtrack vis as separate control.
- lines changed 3, context: html, text, full: html, text
More subCfg work. Need to check in to switch branches cleanly.
- lines changed 3, context: html, text, full: html, text
Another load of subCfg module (scm). Heavy work getting subCbs, matCbs and views all playing nice.
- lines changed 2, context: html, text, full: html, text
Turned on matrix squeezing.
- lines changed 5, context: html, text, full: html, text
Exclude IE <9 from particilating in matrixSqueeze
- lines changed 4, context: html, text, full: html, text
IE 9 text rotation conflicts with IE<9 rotation. Removing IE<9 support.
- lines changed 5, context: html, text, full: html, text
More plus/minus button stylings
- lines changed 2, context: html, text, full: html, text
More touches on BUTTONS_BY_CSS
- src/hg/inc/cart.h
- lines changed 12, context: html, text, full: html, text
Just a changed name tree wide. The 'compositeLevel' paramter to closestToHome cart functions was confusing. What it means is the request is for a setting one step above the tdb passed in. It is used for view level controls where the model tdb is a subtrack. This checkin has NO functional affect.
- src/hg/inc/chainCart.h
- lines changed 1, context: html, text, full: html, text
Just a changed name tree wide. The 'compositeLevel' paramter to closestToHome cart functions was confusing. What it means is the request is for a setting one step above the tdb passed in. It is used for view level controls where the model tdb is a subtrack. This checkin has NO functional affect.
- src/hg/inc/encode/wgEncodeGencodeTranscriptionSupportLevel.h
- lines changed 62, context: html, text, full: html, text
added transcript support levels for version 10, correct some html doc
- src/hg/inc/hgMaf.h
- lines changed 2, context: html, text, full: html, text
Major work on bedFilt, psl and wigMaf to make them properly composite ready.
- lines changed 2, context: html, text, full: html, text
Slight adjustment to one API
- src/hg/inc/hui.h
- lines changed 2, context: html, text, full: html, text
A couple were missed in the big first checkin of subtrack cfg.
- lines changed 3, context: html, text, full: html, text
Further fixes to the cfgByType consistency logic, prompted by side by side comparisons on hg18 tracks.
- lines changed 5, context: html, text, full: html, text
More screw tightening. Encode peaks are not configurable unless there are additional trackDb settings that say so.
- lines changed 3, context: html, text, full: html, text
More tightening of screws. Several special cases solved. Altererd which right-click menu items for cfg appear and regularized this with subCfg availability.
- lines changed 9, context: html, text, full: html, text
Major work on bedFilt, psl and wigMaf to make them properly composite ready.
- lines changed 3, context: html, text, full: html, text
Eliminated a couple more vars from cart and FINALY got rid of funky comp.view.vis cart name. All vis is not standardized to trackName since view is a track.
- lines changed 3, context: html, text, full: html, text
Just a changed name tree wide. The 'compositeLevel' paramter to closestToHome cart functions was confusing. What it means is the request is for a setting one step above the tdb passed in. It is used for view level controls where the model tdb is a subtrack. This checkin has NO functional affect.
- src/hg/inc/jsHelper.h
- lines changed 7, context: html, text, full: html, text
Big load of changes for subCfg.
- lines changed 2, context: html, text, full: html, text
Getting rid of the last vestiges of NEW_JQUERY ifdef.
- lines changed 3, context: html, text, full: html, text
More touches on BUTTONS_BY_CSS
- lines changed 3, context: html, text, full: html, text
Katrina does not want buttons by CSS yet.
- src/hg/inc/netCart.h
- lines changed 2, context: html, text, full: html, text
Just a changed name tree wide. The 'compositeLevel' paramter to closestToHome cart functions was confusing. What it means is the request is for a setting one step above the tdb passed in. It is used for view level controls where the model tdb is a subtrack. This checkin has NO functional affect.
- src/hg/inc/trackDb.h
- lines changed 13, context: html, text, full: html, text
Changes to fix redmine 4892 composite/view/subtrack inconsistency.
- lines changed 4, context: html, text, full: html, text
More tightening of screws. Several special cases solved. Altererd which right-click menu items for cfg appear and regularized this with subCfg availability.
- lines changed 3, context: html, text, full: html, text
With subCfg, when only one subtrack, highlevel shouuld show subtrack controls, so that rightClick and subCfg work together.
- lines changed 3, context: html, text, full: html, text
Some older composites have packable children which are seen in rightClick as unpackable. The mixed case that gives rise to this should not be allowed now, but we can support it for those older composites. The rule is, if any single subtrack is packable, then the whole tree is.
- src/hg/inc/vcfUi.h
- lines changed 1, context: html, text, full: html, text
Just a changed name tree wide. The 'compositeLevel' paramter to closestToHome cart functions was confusing. What it means is the request is for a setting one step above the tdb passed in. It is used for view level controls where the model tdb is a subtrack. This checkin has NO functional affect.
- src/hg/js/ajax.js
- lines changed 47, context: html, text, full: html, text
Initial check-in of not yet comple subtrack configuration module.
- src/hg/js/autocomplete.js
- lines changed 2, context: html, text, full: html, text
Cleaned up old 'newJQuery' dependencies. We are always running as newJQuery now.
- src/hg/js/ddcl.js
- lines changed 19, context: html, text, full: html, text
Initial check-in of not yet comple subtrack configuration module.
- lines changed 2, context: html, text, full: html, text
Merge branch 'master' into tdreszer-subCfg
- lines changed 4, context: html, text, full: html, text
Merge branch 'master' into tdreszer-subCfg
- lines changed 5, context: html, text, full: html, text
Cleaned up old 'newJQuery' dependencies. We are always running as newJQuery now.
- lines changed 2, context: html, text, full: html, text
Merge branch 'master' into tdreszer-subCfg
- lines changed 4, context: html, text, full: html, text
Fixed bug where track search advanced ddcl's were being duplicated.
- lines changed 369, context: html, text, full: html, text
Objectified sortTable and filterTable but no functional change is here.
- src/hg/js/hgGateway.js
- lines changed 19, context: html, text, full: html, text
Cleaned up old 'newJQuery' dependencies. We are always running as newJQuery now.
- src/hg/js/hgTracks.js
- lines changed 26, context: html, text, full: html, text
Cleaned up old 'newJQuery' dependencies. We are always running as newJQuery now.
- lines changed 32, context: html, text, full: html, text
More tightening of screws. Several special cases solved. Altererd which right-click menu items for cfg appear and regularized this with subCfg availability.
- lines changed 2, context: html, text, full: html, text
More touches on BUTTONS_BY_CSS
- lines changed 3, context: html, text, full: html, text
Minor cleanup to hui.c Fix edge case bug in hgTracks.js where right click is lost.
- src/hg/js/hui.js
- lines changed 797, context: html, text, full: html, text
Initial check-in of not yet comple subtrack configuration module.
- lines changed 55, context: html, text, full: html, text
Support (in progress) for subtrack vis as separate control.
- lines changed 62, context: html, text, full: html, text
More subCfg work. Need to check in to switch branches cleanly.
- lines changed 11, context: html, text, full: html, text
Only a tiny incremental change beofre I must return to the master branch.
- lines changed 98, context: html, text, full: html, text
More incremental changes before i most switch back to the master brqanch
- lines changed 131, context: html, text, full: html, text
More incremental work on subCfg
- lines changed 384, context: html, text, full: html, text
Big load of changes for subCfg.
- lines changed 1020, context: html, text, full: html, text
Another load of subCfg module (scm). Heavy work getting subCbs, matCbs and views all playing nice.
- lines changed 61, context: html, text, full: html, text
Tightened a few more screws on subCfg
- lines changed 17, context: html, text, full: html, text
Major rework of subCfg module to no longer rely upon removing name at initialization.
- lines changed 11, context: html, text, full: html, text
A few nice bug catches due to walking through code in firebug.
- lines changed 1, context: html, text, full: html, text
Another set of fixes propted by going through all of hg19 again and another 7 assemblies from different species and clades.
- lines changed 13, context: html, text, full: html, text
With subCfg, when only one subtrack, highlevel shouuld show subtrack controls, so that rightClick and subCfg work together.
- lines changed 2, context: html, text, full: html, text
knocked off another couple of minor bugs in js.
- lines changed 21, context: html, text, full: html, text
Eliminated a couple more vars from cart and FINALY got rid of funky comp.view.vis cart name. All vis is not standardized to trackName since view is a track.
- lines changed 11, context: html, text, full: html, text
Turned on matrix squeezing.
- lines changed 4, context: html, text, full: html, text
matrix side labels don't need too tips.
- lines changed 33, context: html, text, full: html, text
Took care of some of the matrix hilite ghosting. Is it enough?
- lines changed 3, context: html, text, full: html, text
subCfg was not getting initialized if there were no subCfgs. But subVis should also kick this off.
- lines changed 3, context: html, text, full: html, text
Objectified sortTable and filterTable but no functional change is here.
- src/hg/js/makefile
- lines changed 1, context: html, text, full: html, text
Another load of subCfg module (scm). Heavy work getting subCbs, matCbs and views all playing nice.
- lines changed 2, context: html, text, full: html, text
Merge branch 'master' into tdreszer-subCfg
- lines changed 2, context: html, text, full: html, text
Merge branch 'master' into tdreszer-subCfg
- src/hg/js/subCfg.js
- lines changed 953, context: html, text, full: html, text
Another load of subCfg module (scm). Heavy work getting subCbs, matCbs and views all playing nice.
- lines changed 15, context: html, text, full: html, text
Tightened a few more screws on subCfg
- lines changed 302, context: html, text, full: html, text
Major rework of subCfg module to no longer rely upon removing name at initialization.
- lines changed 27, context: html, text, full: html, text
A few nice bug catches due to walking through code in firebug.
- lines changed 22, context: html, text, full: html, text
More tightening of screws. Several special cases solved. Altererd which right-click menu items for cfg appear and regularized this with subCfg availability.
- lines changed 6, context: html, text, full: html, text
Another set of fixes propted by going through all of hg19 again and another 7 assemblies from different species and clades.
- lines changed 3, context: html, text, full: html, text
With subCfg, when only one subtrack, highlevel shouuld show subtrack controls, so that rightClick and subCfg work together.
- lines changed 28, context: html, text, full: html, text
knocked off another couple of minor bugs in js.
- lines changed 41, context: html, text, full: html, text
Eliminated a couple more vars from cart and FINALY got rid of funky comp.view.vis cart name. All vis is not standardized to trackName since view is a track.
- lines changed 1, context: html, text, full: html, text
subCfg was not getting initialized if there were no subCfgs. But subVis should also kick this off.
- lines changed 4, context: html, text, full: html, text
Turns out at least on browser (linux/FF) sends unnamed inputs to the cart. Therefore, unchanged controls are no 'disabled' before submit.
- lines changed 54, context: html, text, full: html, text
Adding an ectra column to subtrack list so that drag and drop works with subVis. 4665
- src/hg/js/utils.js
- lines changed 12, context: html, text, full: html, text
Initial check-in of not yet comple subtrack configuration module.
- lines changed 15, context: html, text, full: html, text
More incremental work on subCfg
- lines changed 75, context: html, text, full: html, text
Big load of changes for subCfg.
- lines changed 15, context: html, text, full: html, text
Another load of subCfg module (scm). Heavy work getting subCbs, matCbs and views all playing nice.
- lines changed 41, context: html, text, full: html, text
Tightened a few more screws on subCfg
- lines changed 6, context: html, text, full: html, text
Major rework of subCfg module to no longer rely upon removing name at initialization.
- lines changed 59, context: html, text, full: html, text
More tightening of screws. Several special cases solved. Altererd which right-click menu items for cfg appear and regularized this with subCfg availability.
- lines changed 13, context: html, text, full: html, text
With subCfg, when only one subtrack, highlevel shouuld show subtrack controls, so that rightClick and subCfg work together.
- lines changed 5, context: html, text, full: html, text
knocked off another couple of minor bugs in js.
- lines changed 6, context: html, text, full: html, text
Eliminated a couple more vars from cart and FINALY got rid of funky comp.view.vis cart name. All vis is not standardized to trackName since view is a track.
- lines changed 4, context: html, text, full: html, text
Fixed one timy bug using 'use strict'
- lines changed 2, context: html, text, full: html, text
Fixed bug where track search advanced ddcl's were being duplicated.
- lines changed 29, context: html, text, full: html, text
More touches on BUTTONS_BY_CSS
- lines changed 46, context: html, text, full: html, text
Extend new buttons to search rows. Fixed some current bugs in the search tab [-][+] buttons
- lines changed 7, context: html, text, full: html, text
IE8 triggers a second onchange event. Add protection when a function is launched with a waitmask.
- lines changed 7, context: html, text, full: html, text
Fixed subtrack sort loosing user setting in drop downs and fixed IE9 subVisDD being unclickable.
- lines changed 2, context: html, text, full: html, text
Fixed the tableSort. insertBefore is effective BUT you shouldn't insert before yourself, at least in IE8.
- lines changed 612, context: html, text, full: html, text
Objectified sortTable and filterTable but no functional change is here.
- lines changed 4, context: html, text, full: html, text
Substantial speed up of long table sort. IE needs every bit of help it can get.
- lines changed 17, context: html, text, full: html, text
Massive sorts on IE9 were still dying, until I replaced using 'sorting' class with 'showLoadingImage()'. The loading image eliminateates redrawing on every little change.
- src/hg/lib/cart.c
- lines changed 2, context: html, text, full: html, text
Another load of subCfg module (scm). Heavy work getting subCbs, matCbs and views all playing nice.
- lines changed 7, context: html, text, full: html, text
Eliminated a couple more vars from cart and FINALY got rid of funky comp.view.vis cart name. All vis is not standardized to trackName since view is a track.
- lines changed 58, context: html, text, full: html, text
Working towards fix in viewVis reshaping.
- lines changed 25, context: html, text, full: html, text
Plugged that viewVis override bug
- lines changed 24, context: html, text, full: html, text
Just a changed name tree wide. The 'compositeLevel' paramter to closestToHome cart functions was confusing. What it means is the request is for a setting one step above the tdb passed in. It is used for view level controls where the model tdb is a subtrack. This checkin has NO functional affect.
- lines changed 38, context: html, text, full: html, text
Removing old ifdefs. No functional changes here.
- src/hg/lib/chainCart.c
- lines changed 2, context: html, text, full: html, text
Just a changed name tree wide. The 'compositeLevel' paramter to closestToHome cart functions was confusing. What it means is the request is for a setting one step above the tdb passed in. It is used for view level controls where the model tdb is a subtrack. This checkin has NO functional affect.
- src/hg/lib/customFactory.c
- lines changed 14, context: html, text, full: html, text
move chrom name normalizing code out of bamFile (we weren't handling stuff like 'IV' and '2L')
- src/hg/lib/encode/wgEncodeGencodeTranscriptionSupportLevel.as
- lines changed 6, context: html, text, full: html, text
added transcript support levels for version 10, correct some html doc
- src/hg/lib/encode/wgEncodeGencodeTranscriptionSupportLevel.c
- lines changed 120, context: html, text, full: html, text
added transcript support levels for version 10, correct some html doc
- src/hg/lib/encode/wgEncodeGencodeTranscriptionSupportLevel.sql
- lines changed 12, context: html, text, full: html, text
added transcript support levels for version 10, correct some html doc
- src/hg/lib/fileUi.c
- lines changed 10, context: html, text, full: html, text
Getting rid of the last vestiges of NEW_JQUERY ifdef.
- lines changed 2, context: html, text, full: html, text
Objectified sortTable and filterTable but no functional change is here.
- lines changed 15, context: html, text, full: html, text
Removing old ifdefs. No functional changes here.
- src/hg/lib/hdb.c
- lines changed 4, context: html, text, full: html, text
Removing old ifdef. No functional change here.
- src/hg/lib/hgMaf.c
- lines changed 2, context: html, text, full: html, text
Major work on bedFilt, psl and wigMaf to make them properly composite ready.
- lines changed 4, context: html, text, full: html, text
Slight adjustment to one API
- src/hg/lib/hui.c
- lines changed 103, context: html, text, full: html, text
Initial check-in of not yet comple subtrack configuration module.
- lines changed 49, context: html, text, full: html, text
Just want to check in ifdefed code while working on 2 possible paths to take.
- lines changed 14, context: html, text, full: html, text
Support (in progress) for subtrack vis as separate control.
- lines changed 72, context: html, text, full: html, text
More subCfg work. Need to check in to switch branches cleanly.
- lines changed 19, context: html, text, full: html, text
More incremental changes before i most switch back to the master brqanch
- lines changed 28, context: html, text, full: html, text
More incremental work on subCfg
- lines changed 66, context: html, text, full: html, text
Big load of changes for subCfg.
- lines changed 45, context: html, text, full: html, text
Another load of subCfg module (scm). Heavy work getting subCbs, matCbs and views all playing nice.
- lines changed 3, context: html, text, full: html, text
Tightened a few more screws on subCfg
- lines changed 6, context: html, text, full: html, text
Major rework of subCfg module to no longer rely upon removing name at initialization.
- lines changed 7, context: html, text, full: html, text
Drag and drop subtracks only on when requested AND not sortable.
- lines changed 53, context: html, text, full: html, text
Further fixes to the cfgByType consistency logic, prompted by side by side comparisons on hg18 tracks.
- lines changed 41, context: html, text, full: html, text
More screw tightening. Encode peaks are not configurable unless there are additional trackDb settings that say so.
- lines changed 43, context: html, text, full: html, text
More tightening of screws. Several special cases solved. Altererd which right-click menu items for cfg appear and regularized this with subCfg availability.
- lines changed 57, context: html, text, full: html, text
Another set of fixes propted by going through all of hg19 again and another 7 assemblies from different species and clades.
- lines changed 3, context: html, text, full: html, text
Minor change to protect variable for SUBTRACK_CONFIG only code.
- lines changed 50, context: html, text, full: html, text
With subCfg, when only one subtrack, highlevel shouuld show subtrack controls, so that rightClick and subCfg work together.
- lines changed 212, context: html, text, full: html, text
Major work on bedFilt, psl and wigMaf to make them properly composite ready.
- lines changed 3, context: html, text, full: html, text
Slight adjustment to one API
- lines changed 9, context: html, text, full: html, text
Eliminated a couple more vars from cart and FINALY got rid of funky comp.view.vis cart name. All vis is not standardized to trackName since view is a track.
- lines changed 3, context: html, text, full: html, text
Little more merge madness
- lines changed 79, context: html, text, full: html, text
Merge up straighten out.
- lines changed 5, context: html, text, full: html, text
Turned on matrix squeezing.
- lines changed 5, context: html, text, full: html, text
Exclude IE <9 from particilating in matrixSqueeze
- lines changed 13, context: html, text, full: html, text
Took care of some of the matrix hilite ghosting. Is it enough?
- lines changed 30, context: html, text, full: html, text
More plus/minus button stylings
- lines changed 30, context: html, text, full: html, text
More touches on BUTTONS_BY_CSS
- lines changed 8, context: html, text, full: html, text
Fixed subtrack sort loosing user setting in drop downs and fixed IE9 subVisDD being unclickable.
- lines changed 4, context: html, text, full: html, text
Chrome also has interference between dragAndDrop and subVisDD.
- lines changed 1, context: html, text, full: html, text
Same problem in safari: drag and drop don't play with subtrack vis dropdown.
- lines changed 62, context: html, text, full: html, text
Make [add][clear] buttons use the same javascript that matrix [+][-] buttons use.
- lines changed 11, context: html, text, full: html, text
Minor cleanup to hui.c Fix edge case bug in hgTracks.js where right click is lost.
- lines changed 56, context: html, text, full: html, text
Just a changed name tree wide. The 'compositeLevel' paramter to closestToHome cart functions was confusing. What it means is the request is for a setting one step above the tdb passed in. It is used for view level controls where the model tdb is a subtrack. This checkin has NO functional affect.
- lines changed 5, context: html, text, full: html, text
Fixed bug where view starts with digit.
- lines changed 110, context: html, text, full: html, text
Removed some old ifdefs. No functional change here.
- lines changed 32, context: html, text, full: html, text
Adding an ectra column to subtrack list so that drag and drop works with subVis. 4665
- lines changed 39, context: html, text, full: html, text
tagEncoding needed to be extended to the ABC dimensions default checked logic.
- src/hg/lib/jsHelper.c
- lines changed 22, context: html, text, full: html, text
Big load of changes for subCfg.
- lines changed 6, context: html, text, full: html, text
More touches on BUTTONS_BY_CSS
- lines changed 3, context: html, text, full: html, text
Merge branch 'master' into tdreszer-subCfg
- src/hg/lib/makefile
- lines changed 2, context: html, text, full: html, text
added transcript support levels for version 10, correct some html doc
- src/hg/lib/netCart.c
- lines changed 4, context: html, text, full: html, text
Just a changed name tree wide. The 'compositeLevel' paramter to closestToHome cart functions was confusing. What it means is the request is for a setting one step above the tdb passed in. It is used for view level controls where the model tdb is a subtrack. This checkin has NO functional affect.
- src/hg/lib/pal.c
- lines changed 1, context: html, text, full: html, text
Major work on bedFilt, psl and wigMaf to make them properly composite ready.
- lines changed 11, context: html, text, full: html, text
Merge branch 'master' into tdreszer-subCfg
- src/hg/lib/pgSnp.c
- lines changed 9, context: html, text, full: html, text
Bug #6529 (VCF internal rep doesn't do missing data): add flags for missingdata values to vcfInfoElement, so we know the difference between "0" and ".".
This applies to both INFO column values and genotype (FORMAT) values.
Also, vcfGenotype's hapIxA and hapIxB are now signed, with negative values
indicating missing data.
User reported bug in MLQ #6462.
- src/hg/lib/search.c
- lines changed 5, context: html, text, full: html, text
Extend new buttons to search rows. Fixed some current bugs in the search tab [-][+] buttons
- src/hg/lib/trackDbCustom.c
- lines changed 2, context: html, text, full: html, text
Initial check-in of not yet comple subtrack configuration module.
- lines changed 23, context: html, text, full: html, text
Changes to fix redmine 4892 composite/view/subtrack inconsistency.
- lines changed 4, context: html, text, full: html, text
More screw tightening. Encode peaks are not configurable unless there are additional trackDb settings that say so.
- lines changed 40, context: html, text, full: html, text
More tightening of screws. Several special cases solved. Altererd which right-click menu items for cfg appear and regularized this with subCfg availability.
- lines changed 2, context: html, text, full: html, text
Another set of fixes propted by going through all of hg19 again and another 7 assemblies from different species and clades.
- lines changed 9, context: html, text, full: html, text
With subCfg, when only one subtrack, highlevel shouuld show subtrack controls, so that rightClick and subCfg work together.
- lines changed 1, context: html, text, full: html, text
Major work on bedFilt, psl and wigMaf to make them properly composite ready.
- lines changed 2, context: html, text, full: html, text
Merge branch 'master' into tdreszer-subCfg
- lines changed 34, context: html, text, full: html, text
Some older composites have packable children which are seen in rightClick as unpackable. The mixed case that gives rise to this should not be allowed now, but we can support it for those older composites. The rule is, if any single subtrack is packable, then the whole tree is.
- src/hg/lib/vcfUi.c
- lines changed 29, context: html, text, full: html, text
Just a changed name tree wide. The 'compositeLevel' paramter to closestToHome cart functions was confusing. What it means is the request is for a setting one step above the tdb passed in. It is used for view level controls where the model tdb is a subtrack. This checkin has NO functional affect.
- src/hg/lib/wiggleCart.c
- lines changed 24, context: html, text, full: html, text
Just a changed name tree wide. The 'compositeLevel' paramter to closestToHome cart functions was confusing. What it means is the request is for a setting one step above the tdb passed in. It is used for view level controls where the model tdb is a subtrack. This checkin has NO functional affect.
- src/hg/makeDb/doc/bosTau7.txt
- lines changed 138, context: html, text, full: html, text
Finished genbank and blat server tasks.
- src/hg/makeDb/doc/dm3.txt
- lines changed 2, context: html, text, full: html, text
Added note to multiz section about phylogenetic tree not being correct
- lines changed 3, context: html, text, full: html, text
Removed the note and just inserted the correct tree
- lines changed 3, context: html, text, full: html, text
Reinserted old tree and added a note that the new tree is a correction
- src/hg/makeDb/doc/encodeDccHg19/wgEncodeGencodeV10.release1.notes
- lines changed 83, context: html, text, full: html, text
Generating notes files, including fixing the table name in the metaDb
- src/hg/makeDb/doc/encodeDccHg19/wgEncodeHaibGenotype.release2.notes
- lines changed 359, context: html, text, full: html, text
this is the real notes, last time I forgot the --loose option when saving
- src/hg/makeDb/doc/hetGla1.txt
- lines changed 36, context: html, text, full: html, text
Finished genbank and blat server tasks.
- src/hg/makeDb/doc/latCha1.txt
- src/hg/makeDb/doc/rheMac3.txt
- lines changed 221, context: html, text, full: html, text
Finished genbank and blat server tasks.
- src/hg/makeDb/doc/tRNAsTrack.txt
- lines changed 94, context: html, text, full: html, text
redmine track #6406 - tRNA track for several (44) assemblies.
- src/hg/makeDb/genbank/etc/align.dbs
- lines changed 2, context: html, text, full: html, text
Added bosTau7 Cow and rehMac3 Rhesus
- src/hg/makeDb/genbank/etc/genbank.conf
- lines changed 18, context: html, text, full: html, text
Add rheMac3 to etc/genbank.conf
- lines changed 8, context: html, text, full: html, text
Add bosTau7.upstreamGeneTbl = refGene
- src/hg/makeDb/genbank/etc/hgwbeta.dbs
- src/hg/makeDb/genbank/etc/hgwdev.dbs
- lines changed 2, context: html, text, full: html, text
Added bosTau7 Cow and rehMac3 Rhesus
- src/hg/makeDb/genbank/src/gbSanity/chkMetaDataTbls.c
- lines changed 3, context: html, text, full: html, text
fix up error message to be more useful by include accession number
- src/hg/makeDb/trackDb/cv/alpha/cv.ra
- lines changed 3, context: html, text, full: html, text
Adding the issue with gender to the U87 cell line. Changing gender to unknown.
- lines changed 11, context: html, text, full: html, text
added in some treatments for crawford
- lines changed 4, context: html, text, full: html, text
fixed tag and added labels to serum treatments from crawford lab
- lines changed 1, context: html, text, full: html, text
Shortened tag for WholeBrain from WHOLEBRAIN -> WBRAIN to accomadate longer file names. Renamed objects accordingly and following release policy, kept old objects with Wholebrain that were released in the UwDnase track.
- lines changed 47, context: html, text, full: html, text
added new antibodies NR2F2 (sc-271940) BCL11A (sc-56011) CBX3 (sc-101004)
- lines changed 2, context: html, text, full: html, text
Fixing GR Genecard reference
- lines changed 6, context: html, text, full: html, text
added validation methods, fixed tags, and changed doc targets of new antibodies
- lines changed 2, context: html, text, full: html, text
Fixing Antibody Cat Number Bug
- lines changed 6, context: html, text, full: html, text
removing the datatype cnv entry, conflicts with CNV view
- lines changed 665, context: html, text, full: html, text
Recovered missing parts of the cv that were accidently deleted in commit 80cb7d51f7359d767e174c991f56c2cdd4ccd1a7.
- lines changed 656, context: html, text, full: html, text
my merge broke things, I'm reverting to 0bce6f57b2a869efad314fe3411f83984bae91fa
- lines changed 7, context: html, text, full: html, text
chiapet datatpye got merged wuth ruan lab entry
- lines changed 1, context: html, text, full: html, text
Fixes isssues found in Redmine #4577
1. Updated label of dataType from "Repli-Seq" -> "Repli-seq"
2. Standardized apperance of "Wavelet-smoothed Signal" in track description
3. Added clarification of "six fraction profile" as refereing to "six cell cycle fractions"
4. Update long labels to be "Repli-seq" instead of "Replication Timing"
- lines changed 1, context: html, text, full: html, text
Revert "Fixes isssues found in Redmine #4577"
This reverts commit 2adb93cfa1136c629a53c8cae9e56c6254c14703.
- lines changed 1, context: html, text, full: html, text
Fixes isssues found in Redmine #4577
1. Updated label of dataType from "Repli-Seq" -> "Repli-seq"
2. Standardized apperance of "Wavelet-smoothed Signal" in track description
3. Added clarification of "six fraction profile" as refereing to "six cell cycle fractions"
- lines changed 6, context: html, text, full: html, text
removing Cnv datatype again
- src/hg/makeDb/trackDb/cv/beta/cv.ra
- lines changed 795, context: html, text, full: html, text
Pushing alpha cv to beta
- lines changed 1321, context: html, text, full: html, text
Copying corrected alpha cv without deletions to beta
- lines changed 656, context: html, text, full: html, text
Copying Matts fixed cv from alpha to beta
- lines changed 7, context: html, text, full: html, text
fixed chia-pet's entry in beta cv
- src/hg/makeDb/trackDb/dog/canFam2/multiz4way.html
- lines changed 46, context: html, text, full: html, text
Added line in Credits section referencing the phylogenetic tree. Added citation to References section for phylogenetic tree.
- lines changed 1, context: html, text, full: html, text
Added punctuation for consistency
- src/hg/makeDb/trackDb/drosophila/dm2/multiz15way.html
- lines changed 5, context: html, text, full: html, text
Added a link to PHAST. Added reference to Teri Markow in Credits section.
- lines changed 1, context: html, text, full: html, text
Corrected spelling of Adam Siepel's name
- src/hg/makeDb/trackDb/drosophila/dm3/multiz15way.html
- lines changed 3, context: html, text, full: html, text
Added reference to Teri Markow in Credits section
- lines changed 1, context: html, text, full: html, text
Corrected spelling of Adam Siepel's name
- src/hg/makeDb/trackDb/human/hg18/trackDb.ra
- lines changed 19, context: html, text, full: html, text
redmine track #6406 Add tRNA track for several assemblies.
- src/hg/makeDb/trackDb/human/hg19/description.html
- lines changed 9, context: html, text, full: html, text
added chromBand and SNP# as search types
- lines changed 2, context: html, text, full: html, text
uncommented link to release notes at NCBI
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlShortRnaSeq.ra
- lines changed 114, context: html, text, full: html, text
Removing all traces of the HUVEC files see ticket 1634, note 37
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGencodeV10.ra
- lines changed 51, context: html, text, full: html, text
Added md5sums, missing file, and corrected file names to not have .gz
- lines changed 35, context: html, text, full: html, text
Zipping up the downloads files
- lines changed 3, context: html, text, full: html, text
Generating notes files, including fixing the table name in the metaDb
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisRnaPet.ra
- lines changed 2, context: html, text, full: html, text
updating object status to replaced for 2 objects
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibGenotype.ra
- lines changed 2, context: html, text, full: html, text
Adding sex F to all U87 cell lines, the actual gender of the cell is in question but these files are mapped to female
- lines changed 1, context: html, text, full: html, text
Removing sex from Genotype because Flo says that the reporting is gender indifferent
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethyl450.ra
- lines changed 2, context: html, text, full: html, text
Adding sex F to all U87 cell lines, the actual gender of the cell is in question but these files are mapped to female
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylRrbs.ra
- lines changed 5, context: html, text, full: html, text
Adding sex F to all U87 cell lines, the actual gender of the cell is in question but these files are mapped to female
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibRnaSeq.ra
- lines changed 9, context: html, text, full: html, text
Adding sex F to all U87 cell lines, the actual gender of the cell is in question but these files are mapped to female
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra
- lines changed 29, context: html, text, full: html, text
Adding sex F to all U87 cell lines, the actual gender of the cell is in question but these files are mapped to female
- lines changed 411, context: html, text, full: html, text
added in new tracks to haib tfbs
- lines changed 927, context: html, text, full: html, text
changed dataVersion date
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeMapability.ra
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromChip.ra
- lines changed 31, context: html, text, full: html, text
changed dataVersion date
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromDnase.ra
- lines changed 91, context: html, text, full: html, text
changed dataVersion date
- lines changed 10, context: html, text, full: html, text
added in bai's for open chrom dnase
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromFaire.ra
- lines changed 15, context: html, text, full: html, text
changed dataVersion date
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromSynth.ra
- lines changed 11, context: html, text, full: html, text
changed dataVersion date
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra
- lines changed 139, context: html, text, full: html, text
Replaced expId=623 with a better experiment using a different control. Redmine #4486.
- lines changed 59, context: html, text, full: html, text
Added md5sum's for files and bai files in fileName var. Also replaced 2 duplicate bam's with updated files. Redmine #4486, #4931.
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDgf.ra
- lines changed 121, context: html, text, full: html, text
changed dataVersion date
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDnase.ra
- lines changed 151, context: html, text, full: html, text
changed dataVersion date
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwHistone.ra
- lines changed 384, context: html, text, full: html, text
changed dataVersion date
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwRepliSeq.ra
- lines changed 2, context: html, text, full: html, text
Added GEO Series number to track. Redmine #4577.
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwTfbs.ra
- lines changed 286, context: html, text, full: html, text
changed dataVersion date
- src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeHaibTfbs.ra
- lines changed 444, context: html, text, full: html, text
staging on beta for tracks that can go ahead and push the dataVersion change, my tracks only
- src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeMapability.ra
- lines changed 5, context: html, text, full: html, text
staging on beta for tracks that can go ahead and push the dataVersion change, my tracks only
- src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeOpenChromDnase.ra
- lines changed 3, context: html, text, full: html, text
staging on beta for tracks that can go ahead and push the dataVersion change, my tracks only
- src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeOpenChromFaire.ra
- lines changed 6, context: html, text, full: html, text
staging on beta for tracks that can go ahead and push the dataVersion change, my tracks only
- src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeUwDnase.ra
- lines changed 61, context: html, text, full: html, text
staging on beta for tracks that can go ahead and push the dataVersion change, my tracks only
- src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeUwHistone.ra
- lines changed 247, context: html, text, full: html, text
staging on beta for tracks that can go ahead and push the dataVersion change, my tracks only
- src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeUwTfbs.ra
- lines changed 10270, context: html, text, full: html, text
staging UW CTCF Binding (Release 2) on beta, redmine # 4461
- src/hg/makeDb/trackDb/human/hg19/pseudoYale60.html
- lines changed 1, context: html, text, full: html, text
added semi-colon to journal citation
- src/hg/makeDb/trackDb/human/hg19/trackDb.ra
- lines changed 2, context: html, text, full: html, text
A couple were missed in the big first checkin of subtrack cfg.
- lines changed 19, context: html, text, full: html, text
redmine track #6406 Add tRNA track for several assemblies.
- src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
- lines changed 1, context: html, text, full: html, text
Removing sex from Genotype because Flo says that the reporting is gender indifferent
- lines changed 2, context: html, text, full: html, text
staging UW CTCF Binding (Release 2) on beta, redmine # 4461
- src/hg/makeDb/trackDb/human/hg19/wgEncodeCaltechRnaSeq.new.html
- lines changed 5, context: html, text, full: html, text
removed hard coded links and made them relative to the server root for Caltech RNA-seq (Release2), redmine# 2019
- src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.release2.html
- lines changed 31, context: html, text, full: html, text
Changing some labels and wording according to ticket 5698 note #8
- src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.release2.ra
- lines changed 3, context: html, text, full: html, text
Changing some labels and wording according to ticket 5698 note #8
- src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.new.ra
- lines changed 2241, context: html, text, full: html, text
Changing to release2.ra from new.ra
- src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.release2.html
- lines changed 1, context: html, text, full: html, text
Removed a $ that caused issues in the mailto
- src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.release2.ra
- lines changed 2241, context: html, text, full: html, text
Changing to release2.ra from new.ra
- lines changed 120, context: html, text, full: html, text
Removing all traces of the HUVEC files see ticket 1634, note 37
- src/hg/makeDb/trackDb/human/hg19/wgEncodeDukeAffyExon.new.ra
- lines changed 2, context: html, text, full: html, text
fixed a score filter thing, and changed type to broadpeak
- src/hg/makeDb/trackDb/human/hg19/wgEncodeGencode.html
- lines changed 1, context: html, text, full: html, text
added transcript support levels for version 10, correct some html doc
- src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV10.html
- lines changed 3, context: html, text, full: html, text
added transcript support levels for version 10, correct some html doc
- lines changed 55, context: html, text, full: html, text
added documentation on GENCODE TSL
- lines changed 1, context: html, text, full: html, text
added missing Yale people
- src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV10.ra
- lines changed 1, context: html, text, full: html, text
added transcript support levels for version 10, correct some html doc
- lines changed 4, context: html, text, full: html, text
fixed breakage of labels in gencode V4 caused by changes for V10
- src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV3.html
- lines changed 1, context: html, text, full: html, text
added transcript support levels for version 10, correct some html doc
- src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV4.html
- lines changed 1, context: html, text, full: html, text
added transcript support levels for version 10, correct some html doc
- lines changed 1, context: html, text, full: html, text
added missing Yale people
- src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV7.html
- lines changed 2, context: html, text, full: html, text
added transcript support levels for version 10, correct some html doc
- lines changed 1, context: html, text, full: html, text
added missing Yale people
- src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV9.html
- lines changed 2, context: html, text, full: html, text
added transcript support levels for version 10, correct some html doc
- lines changed 1, context: html, text, full: html, text
added missing Yale people
- src/hg/makeDb/trackDb/human/hg19/wgEncodeGisChiaPet.html
- src/hg/makeDb/trackDb/human/hg19/wgEncodeGisChiaPet.ra
- lines changed 6, context: html, text, full: html, text
Fixing antibody designation
- lines changed 1, context: html, text, full: html, text
Fixing mispelled title and expanding abbreviation
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibGenotype.release2.html
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibRnaSeq.html
- lines changed 2, context: html, text, full: html, text
Rephrasing Verification section as per ticket 1710
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.release2.ra
- lines changed 73, context: html, text, full: html, text
added in new tracks to haib tfbs
- lines changed 14, context: html, text, full: html, text
removed metadata lines in trackDb
- src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromSynth.release2.html
- lines changed 2, context: html, text, full: html, text
my merge broke things, I'm reverting to 0bce6f57b2a869efad314fe3411f83984bae91fa
- lines changed 2, context: html, text, full: html, text
redoing a change i did, because of a revert
- src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.new.ra
- lines changed 34, context: html, text, full: html, text
Replaced expId=623 with a better experiment using a different control. Redmine #4486.
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.patch.ra
- lines changed 559, context: html, text, full: html, text
same dimension fix for patch now
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.release2.ra
- lines changed 559, context: html, text, full: html, text
fixed numeral in dimentionNchecked bug in histone
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.release3.ra
- lines changed 638, context: html, text, full: html, text
fixed dimensionNchecked bug in release 3 of histone
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwRepliSeq.html
- lines changed 5, context: html, text, full: html, text
Added perioed to end of view descriptions. Redmine #4577, Note #42
- lines changed 3, context: html, text, full: html, text
Fixes isssues found in Redmine #4577
1. Updated label of dataType from "Repli-Seq" -> "Repli-seq"
2. Standardized apperance of "Wavelet-smoothed Signal" in track description
3. Added clarification of "six fraction profile" as refereing to "six cell cycle fractions"
4. Update long labels to be "Repli-seq" instead of "Replication Timing"
- lines changed 3, context: html, text, full: html, text
Revert "Fixes isssues found in Redmine #4577"
This reverts commit 2adb93cfa1136c629a53c8cae9e56c6254c14703.
- lines changed 3, context: html, text, full: html, text
Fixes isssues found in Redmine #4577
1. Updated label of dataType from "Repli-Seq" -> "Repli-seq"
2. Standardized apperance of "Wavelet-smoothed Signal" in track description
3. Added clarification of "six fraction profile" as refereing to "six cell cycle fractions"
- lines changed 2, context: html, text, full: html, text
Updated label of dataType from 'Repli-Seq' -> 'Repli-seq', missed in commit 0520f9972ef107cedffcb0653f9f110b8dc9020d. Redmine #4577
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwRepliSeq.ra
- lines changed 161, context: html, text, full: html, text
Fixes isssues found in Redmine #4577
1. Updated label of dataType from "Repli-Seq" -> "Repli-seq"
2. Standardized apperance of "Wavelet-smoothed Signal" in track description
3. Added clarification of "six fraction profile" as refereing to "six cell cycle fractions"
4. Update long labels to be "Repli-seq" instead of "Replication Timing"
- lines changed 161, context: html, text, full: html, text
Revert "Fixes isssues found in Redmine #4577"
This reverts commit 2adb93cfa1136c629a53c8cae9e56c6254c14703.
- lines changed 129, context: html, text, full: html, text
Fixes isssues found in Redmine #4577
1. Updated label of dataType from "Repli-Seq" -> "Repli-seq"
2. Standardized apperance of "Wavelet-smoothed Signal" in track description
3. Added clarification of "six fraction profile" as refereing to "six cell cycle fractions"
- lines changed 1, context: html, text, full: html, text
Updated label of dataType from 'Repli-Seq' -> 'Repli-seq', missed in commit 0520f9972ef107cedffcb0653f9f110b8dc9020d. Redmine #4577
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwTfbs.release2.html
- lines changed 3, context: html, text, full: html, text
added in line about false discovery rates
- lines changed 1, context: html, text, full: html, text
changing date for release 2, redmine #4461
- lines changed 2, context: html, text, full: html, text
changed hypersensitivity to affinity
- lines changed 4, context: html, text, full: html, text
fixing wording, redmine 4461
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwTfbs.release2.ra
- lines changed 2, context: html, text, full: html, text
fixed short labels, qa request
- lines changed 69, context: html, text, full: html, text
removed FDR from the labels
- lines changed 400, context: html, text, full: html, text
cleaned up trackDb stuff, and fixed the problem with the matrix
- src/hg/makeDb/trackDb/human/trackDb.ra
- lines changed 2, context: html, text, full: html, text
A couple were missed in the big first checkin of subtrack cfg.
- src/hg/makeDb/trackDb/lancelet/braFlo1/multiz5way.html
- lines changed 2, context: html, text, full: html, text
Corrected mislabeling of lancelet as petMar1
- src/hg/makeDb/trackDb/latCha/latCha1/description.html
- lines changed 129, context: html, text, full: html, text
initial contents from makeGenomeDb.pl
- src/hg/makeDb/trackDb/latCha/latCha1/gap.html
- lines changed 64, context: html, text, full: html, text
initial contents from makeGenomeDb.pl
- src/hg/makeDb/trackDb/latCha/latCha1/gold.html
- lines changed 23, context: html, text, full: html, text
initial contents from makeGenomeDb.pl
- src/hg/makeDb/trackDb/latCha/latCha1/trackDb.ra
- lines changed 8, context: html, text, full: html, text
initial contents from makeGenomeDb.pl
- src/hg/makeDb/trackDb/makefile
- lines changed 1, context: html, text, full: html, text
adding latCha1 to the build
- lines changed 1, context: html, text, full: html, text
adding saiBol1 Squirrel Monkey to the build
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra
- lines changed 263, context: html, text, full: html, text
Added 1 more submission. Redmine #5986.
- lines changed 6, context: html, text, full: html, text
Added composite level meta-data.
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrHistone.ra
- lines changed 23, context: html, text, full: html, text
Shortened tag for WholeBrain from WHOLEBRAIN -> WBRAIN to accomadate longer file names. Renamed objects accordingly and following release policy, kept old objects with Wholebrain that were released in the UwDnase track.
- lines changed 261, context: html, text, full: html, text
Added 2 more submissions. Redmine #5393.
- lines changed 11, context: html, text, full: html, text
Added md5sum's for new submissions. Redmine #5393.
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrRnaSeq.ra
- lines changed 17, context: html, text, full: html, text
Shortened tag for WholeBrain from WHOLEBRAIN -> WBRAIN to accomadate longer file names. Renamed objects accordingly and following release policy, kept old objects with Wholebrain that were released in the UwDnase track.
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrTfbs.ra
- lines changed 23, context: html, text, full: html, text
Shortened tag for WholeBrain from WHOLEBRAIN -> WBRAIN to accomadate longer file names. Renamed objects accordingly and following release policy, kept old objects with Wholebrain that were released in the UwDnase track.
- lines changed 3, context: html, text, full: html, text
Added objStatus for the replaced files. Redmine #5394.
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodePsuHistone.ra
- lines changed 17, context: html, text, full: html, text
Fixed an error with an experiement where the dateResubmitted replaced dateSubmitted and dateUnrestricted.
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhHist.ra
- lines changed 10, context: html, text, full: html, text
Added index file into fileName field.
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhRnaSeq.ra
- lines changed 4, context: html, text, full: html, text
Added index file into fileName field.
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeUwDgf.ra
- lines changed 33, context: html, text, full: html, text
Shortened tag for WholeBrain from WHOLEBRAIN -> WBRAIN to accomadate longer file names. Renamed objects accordingly and following release policy, kept old objects with Wholebrain that were released in the UwDnase track.
- lines changed 6, context: html, text, full: html, text
Added composite level meta-data.
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeUwDnase.ra
- lines changed 1414, context: html, text, full: html, text
Shortened tag for WholeBrain from WHOLEBRAIN -> WBRAIN to accomadate longer file names. Renamed objects accordingly and following release policy, kept old objects with Wholebrain that were released in the UwDnase track.
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeUwRnaSeq.ra
- lines changed 57, context: html, text, full: html, text
Shortened tag for WholeBrain from WHOLEBRAIN -> WBRAIN to accomadate longer file names. Renamed objects accordingly and following release policy, kept old objects with Wholebrain that were released in the UwDnase track.
- src/hg/makeDb/trackDb/mouse/mm9/pseudoYale60.html
- lines changed 3, context: html, text, full: html, text
Fixed journal citations, per redmine #6537
- src/hg/makeDb/trackDb/mouse/mm9/trackDb.ra
- lines changed 19, context: html, text, full: html, text
redmine track #6406 Add tRNA track for several assemblies.
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCshlLongRnaSeq.ra
- lines changed 27, context: html, text, full: html, text
Added 1 more submission. Redmine #5986.
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrHistone.new.ra
- lines changed 7, context: html, text, full: html, text
Shortened tag for WholeBrain from WHOLEBRAIN -> WBRAIN to accomadate longer file names. Renamed objects accordingly and following release policy, kept old objects with Wholebrain that were released in the UwDnase track.
- lines changed 18, context: html, text, full: html, text
Added 2 more submissions. Redmine #5393.
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrRnaSeq.new.ra
- lines changed 13, context: html, text, full: html, text
Shortened tag for WholeBrain from WHOLEBRAIN -> WBRAIN to accomadate longer file names. Renamed objects accordingly and following release policy, kept old objects with Wholebrain that were released in the UwDnase track.
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrTfbs.new.ra
- lines changed 7, context: html, text, full: html, text
Shortened tag for WholeBrain from WHOLEBRAIN -> WBRAIN to accomadate longer file names. Renamed objects accordingly and following release policy, kept old objects with Wholebrain that were released in the UwDnase track.
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuHistone.ra
- lines changed 146, context: html, text, full: html, text
Updated track short and long labels as well as has experiment specific viewLimits for Signals. Redmine #111
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuTfbs.ra
- lines changed 115, context: html, text, full: html, text
Updated track to short and long labels as well as has experiment specific viewLimits for Signals. Redmine #110.
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwDgf.ra
- lines changed 25, context: html, text, full: html, text
Shortened tag for WholeBrain from WHOLEBRAIN -> WBRAIN to accomadate longer file names. Renamed objects accordingly and following release policy, kept old objects with Wholebrain that were released in the UwDnase track.
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwDnase.new.ra
- lines changed 91, context: html, text, full: html, text
Shortened tag for WholeBrain from WHOLEBRAIN -> WBRAIN to accomadate longer file names. Renamed objects accordingly and following release policy, kept old objects with Wholebrain that were released in the UwDnase track.
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwRnaSeq.ra
- lines changed 49, context: html, text, full: html, text
Shortened tag for WholeBrain from WHOLEBRAIN -> WBRAIN to accomadate longer file names. Renamed objects accordingly and following release policy, kept old objects with Wholebrain that were released in the UwDnase track.
- src/hg/makeDb/trackDb/rat/rn4/trackDb.ra
- lines changed 19, context: html, text, full: html, text
redmine track #6406 Add tRNA track for several assemblies.
- src/hg/makeDb/trackDb/sacCer/sacCer2/multiz7way.html
- lines changed 5, context: html, text, full: html, text
Added line to the Credits section about the source of the phylogenetic tree
- src/hg/makeDb/trackDb/sacCer/sacCer3/multiz7way.html
- lines changed 5, context: html, text, full: html, text
Added line to the Credits section about the source of the phylogenetic tree
- src/hg/makeDb/trackDb/saiBol/saiBol1/description.html
- lines changed 129, context: html, text, full: html, text
initial contents from makeGenomeDb.pl
- src/hg/makeDb/trackDb/saiBol/saiBol1/gap.html
- lines changed 64, context: html, text, full: html, text
initial contents from makeGenomeDb.pl
- src/hg/makeDb/trackDb/saiBol/saiBol1/gold.html
- lines changed 23, context: html, text, full: html, text
initial contents from makeGenomeDb.pl
- src/hg/makeDb/trackDb/saiBol/saiBol1/trackDb.ra
- lines changed 8, context: html, text, full: html, text
initial contents from makeGenomeDb.pl
- src/hg/makeDb/trackDb/tagTypes.tab
- lines changed 1, context: html, text, full: html, text
added transcript support levels for version 10, correct some html doc
- src/hg/makeDb/trackDb/trackDb.ra
- lines changed 20, context: html, text, full: html, text
redmine track #6406 Add tRNA track for several assemblies.
- lines changed 3, context: html, text, full: html, text
add . to t2g tracks to allow right-click configuration
- src/hg/makeDb/trackDb/worm/ce10/cons7way.html
- src/hg/makeDb/trackDb/worm/ce4/multiz5way.html
- lines changed 9, context: html, text, full: html, text
Added line to Credits section about phylogenetic tree. Added citation to References section based on ce6.
- src/hg/makeDb/trackDb/worm/ce6/multiz6way.html
- lines changed 5, context: html, text, full: html, text
Added line about phylogenetic tree to Credits section. Edited citation.
- lines changed 1, context: html, text, full: html, text
Italicized Caenorhabditis in citation
- src/hg/makeDb/trackDb/xenTro/xenTro1/multiz5way.html
- lines changed 52, context: html, text, full: html, text
Added line in Credits section referencing the phylogenetic tree. Added citation to References section for phylogenetic tree.
- src/hg/near/hgMapToGene/hgMapToGene.c
- lines changed 5, context: html, text, full: html, text
Addressing code review feedback from Hiram
- src/hg/txGene/txGeneXref/txGeneXref.c
- lines changed 6, context: html, text, full: html, text
Code change in response to a question from Brooke on Redmine #5290. Now that we're getting Rfam coordinate data from the Rfam consortium, the gene symbols all began Alias= and the descriptions all contained Note= (i.e. we needed to adapt the code to the way Rfam is packaging their data on their track hub). Those tags are now stripped out of the gene symbol and description
- src/hg/utils/automation/Encode.pm
- lines changed 2, context: html, text, full: html, text
updating dataVersion date
- src/inc/bamFile.h
- lines changed 2, context: html, text, full: html, text
move chrom name normalizing code out of bamFile (we weren't handling stuff like 'IV' and '2L')
- src/inc/vcf.h
- lines changed 5, context: html, text, full: html, text
Bug #6529 (VCF internal rep doesn't do missing data): add flags for missingdata values to vcfInfoElement, so we know the difference between "0" and ".".
This applies to both INFO column values and genotype (FORMAT) values.
Also, vcfGenotype's hapIxA and hapIxB are now signed, with negative values
indicating missing data.
User reported bug in MLQ #6462.
- src/lib/bamFile.c
- lines changed 29, context: html, text, full: html, text
move chrom name normalizing code out of bamFile (we weren't handling stuff like 'IV' and '2L')
- src/lib/blackList.c
- lines changed 2, context: html, text, full: html, text
fix up comment from code review #6456
- src/lib/cheapcgi.c
- lines changed 1, context: html, text, full: html, text
Big load of changes for subCfg.
- lines changed 3, context: html, text, full: html, text
Another load of subCfg module (scm). Heavy work getting subCbs, matCbs and views all playing nice.
- lines changed 6, context: html, text, full: html, text
Major rework of subCfg module to no longer rely upon removing name at initialization.
- src/lib/vcf.c
- lines changed 14, context: html, text, full: html, text
Bug #6529 (VCF internal rep doesn't do missing data): add flags for missingdata values to vcfInfoElement, so we know the difference between "0" and ".".
This applies to both INFO column values and genotype (FORMAT) values.
Also, vcfGenotype's hapIxA and hapIxB are now signed, with negative values
indicating missing data.
User reported bug in MLQ #6462.
- src/utils/qa/getField.csh
- lines changed 1, context: html, text, full: html, text
Added &hgta_group=allTables per Angie. We were seeing a problem when this script was run from checkTrackUiLinks.csh that was caused by the url specifying a table but not a group and track. This fix gets around the problem by selecting adding the all tables parameter instead.
- src/utils/qa/weeklybld/buildEnv.csh
- src/utils/qa/weeklybld/doNewBranch.csh
- lines changed 3, context: html, text, full: html, text
added a line to send mail to engineers who want to be notified when to do their code summaries
- lines changed 3, context: html, text, full: html, text
Revert "added a line to send mail to engineers who want to be notified when to do their code summaries"
This reverts commit dcf66b3c55013eea7ed8ade634b64d067286dda9.
- lines changed 5, context: html, text, full: html, text
send out mail to the engineers telling them to send in their summaries
- lines changed 1, context: html, text, full: html, text
fix a typo, thanks Angie!
- lines changed 1, context: html, text, full: html, text
add tim to summaries notification
- src/utils/twoBitDup/makefile
- lines changed 18, context: html, text, full: html, text
a little utility to check to see if a twoBit file has duplicated sequences
- src/utils/twoBitDup/twoBitDup.c
- lines changed 63, context: html, text, full: html, text
a little utility to check to see if a twoBit file has duplicated sequences
- lines changed: 45957
- files changed: 510