All File Changes
v271_preview to v271_preview2 (2012-07-24 to 2012-07-31) v271
- src/hg/encode/DAFs/3.0/hg19/wgEncodeGisRnaPet.daf
- lines changed 3, context: html, text, full: html, text
Adding the bedClusters fix for Gis Rna Pet
- src/hg/encode/DAFs/3.0/mm9/wgEncodeCshlLongRnaSeq.daf
- src/hg/encode/getTrackReferences/getTrackReferences
- lines changed 2, context: html, text, full: html, text
removed prog= so default behavior happens
- src/hg/encode/validateFiles/validateFiles.c
- lines changed 1, context: html, text, full: html, text
fix bug where buffer is known to be too small, but its growth may still not be enough
- src/hg/hgBlat/hgBlat.c
- lines changed 1, context: html, text, full: html, text
remove hBackgroundImage and hgColOutside
- src/hg/hgFileSearch/hgFileSearch.c
- lines changed 13, context: html, text, full: html, text
resolve merge conflict with master
- lines changed 7, context: html, text, full: html, text
resolve merge conflict with master
- src/hg/hgFileUi/hgFileUi.c
- lines changed 2, context: html, text, full: html, text
resolve merge conflict with master
- src/hg/hgGateway/hgGateway.c
- lines changed 22, context: html, text, full: html, text
integrate suggest into the position box
- lines changed 64, context: html, text, full: html, text
resolve merge conflict with master
- lines changed 8, context: html, text, full: html, text
tweak tables to accomodate new layout
- lines changed 1, context: html, text, full: html, text
make watermark more concise to address width problem in hgGateway
- src/hg/hgGene/hgGeneData/Mouse/mm10/otherOrgs.ra
- lines changed 9, context: html, text, full: html, text
use rn5 refGene for mm10 UCSC genes... maybe we should be using rn4 RGD gene?
- src/hg/hgGenome/browseRegions.c
- src/hg/hgLogin/hgLogin.c
- lines changed 17, context: html, text, full: html, text
Fixed redmine Bug #8341: To retrieve username, if user enter an email address that is not associated with any account, no mail should send out to the address.
- src/hg/hgPcr/hgPcr.c
- src/hg/hgSuggest/hgSuggest.c
- lines changed 17, context: html, text, full: html, text
Include description in gene suggest list to accomodate ambiguous entries (#5962)
- src/hg/hgTables/bedList.c
- lines changed 3, context: html, text, full: html, text
Making final pass through tree of checkins as dictated by Jim. None of these changes should affect executables in any way. This pass is due to expanding fingerprint caused by kompare.
- src/hg/hgTables/hgTables.c
- src/hg/hgTables/mainPage.c
- lines changed 2, context: html, text, full: html, text
Making final pass through tree of checkins as dictated by Jim. None of these changes should affect executables in any way. This pass is due to expanding fingerprint caused by kompare.
- src/hg/hgTables/schema.c
- lines changed 6, context: html, text, full: html, text
Making final pass through tree of checkins as dictated by Jim. None of these changes should affect executables in any way. This pass is due to expanding fingerprint caused by kompare.
- src/hg/hgTrackUi/hgTrackUi.c
- lines changed 1, context: html, text, full: html, text
remove hBackgroundImage and hgColOutside
- lines changed 0, context: html, text, full: html, text
Making final pass through tree of checkins as dictated by Jim. None of these changes should affect executables in any way. This pass is due to expanding fingerprint caused by kompare.
- lines changed 63, context: html, text, full: html, text
Feature #8551 (Sequence Ontology terms for predicted functional effects on SNP details pages):at Ensembl's request, instead of displaying dbSNP's predicted function terms, instead show
terms from the Sequence Ontology (SO). Where possible, terms from Ensembl's list at
http://staging.ensembl.org/info/docs/variation/predicted_data.html are used.
- src/hg/hgTracks/chromGraphTrack.c
- lines changed 0, context: html, text, full: html, text
Making final pass through tree of checkins as dictated by Jim. None of these changes should affect executables in any way. This pass is due to expanding fingerprint caused by kompare.
- src/hg/hgTracks/expRatioTracks.c
- lines changed 4, context: html, text, full: html, text
Making final pass through tree of checkins as dictated by Jim. None of these changes should affect executables in any way. This pass is due to expanding fingerprint caused by kompare.
- src/hg/hgTracks/gencodeTracks.c
- lines changed 507, context: html, text, full: html, text
highlighting by attribute functionality for GENCODE
- src/hg/hgTracks/gencodeTracks.h
- lines changed 9, context: html, text, full: html, text
highlighting by attribute functionality for GENCODE
- src/hg/hgTracks/hgTracks.c
- lines changed 3, context: html, text, full: html, text
enable MERGE_GENE_SUGGEST; remove jumpButtonOnClick from submit button b/c it is no longer needed with merged suggest; change 1em to 0.3em spacing to save some real estate
- lines changed 101, context: html, text, full: html, text
resolve merge conflict with master
- lines changed 14, context: html, text, full: html, text
Making final pass through tree of checkins as dictated by Jim. None of these changes should affect executables in any way. This pass is due to expanding fingerprint caused by kompare.
- src/hg/hgTracks/hgTracks.h
- lines changed 7, context: html, text, full: html, text
highlighting by attribute functionality for GENCODE
- src/hg/hgTracks/imageV2.c
- lines changed 4, context: html, text, full: html, text
remove explicit background for imgTbl (will be done in style file)
- lines changed 70, context: html, text, full: html, text
resolve merge conflict with master
- lines changed 4, context: html, text, full: html, text
Making final pass through tree of checkins as dictated by Jim. None of these changes should affect executables in any way. This pass is due to expanding fingerprint caused by kompare.
- src/hg/hgTracks/mainMain.c
- lines changed 1, context: html, text, full: html, text
remove hBackgroundImage and hgColOutside
- lines changed 1, context: html, text, full: html, text
add hgTracks class to HEAD so we can special-case hgTracks background
- lines changed 1, context: html, text, full: html, text
always add CGI name to the body class (enables special casing in style files)
- lines changed 2, context: html, text, full: html, text
Making final pass through tree of checkins as dictated by Jim. None of these changes should affect executables in any way. This pass is due to expanding fingerprint caused by kompare.
- src/hg/hgTracks/makefile
- lines changed 1, context: html, text, full: html, text
highlighting by attribute functionality for GENCODE
- src/hg/hgTracks/menu.c
- lines changed 5, context: html, text, full: html, text
remove odd/even classes for view menu
- src/hg/hgTracks/searchTracks.c
- lines changed 0, context: html, text, full: html, text
Making final pass through tree of checkins as dictated by Jim. None of these changes should affect executables in any way. This pass is due to expanding fingerprint caused by kompare.
- src/hg/hgTracks/simpleTracks.c
- lines changed 4, context: html, text, full: html, text
Track #8360 (snp137): registering track handlers (late!).
- lines changed 234, context: html, text, full: html, text
highlighting by attribute functionality for GENCODE
- lines changed 13, context: html, text, full: html, text
Making final pass through tree of checkins as dictated by Jim. None of these changes should affect executables in any way. This pass is due to expanding fingerprint caused by kompare.
- src/hg/hgTracks/variation.c
- lines changed 10, context: html, text, full: html, text
Feature #8551 (Sequence Ontology terms for predicted functional effects on SNP details pages):at Ensembl's request, instead of displaying dbSNP's predicted function terms, instead show
terms from the Sequence Ontology (SO). Where possible, terms from Ensembl's list at
http://staging.ensembl.org/info/docs/variation/predicted_data.html are used.
- src/hg/hgTracks/wigTrack.c
- lines changed 0, context: html, text, full: html, text
Making final pass through tree of checkins as dictated by Jim. None of these changes should affect executables in any way. This pass is due to expanding fingerprint caused by kompare.
- src/hg/hgc/gencodeClick.c
- lines changed 20, context: html, text, full: html, text
highlighting by attribute functionality for GENCODE
- src/hg/hgc/hgc.c
- lines changed 10, context: html, text, full: html, text
getDNA2 is close to a plain text dump and needs special handling
- lines changed 20, context: html, text, full: html, text
Making final pass through tree of checkins as dictated by Jim. None of these changes should affect executables in any way. This pass is due to expanding fingerprint caused by kompare.
- lines changed 72, context: html, text, full: html, text
Feature #8551 (Sequence Ontology terms for predicted functional effects on SNP details pages):at Ensembl's request, instead of displaying dbSNP's predicted function terms, instead show
terms from the Sequence Ontology (SO). Where possible, terms from Ensembl's list at
http://staging.ensembl.org/info/docs/variation/predicted_data.html are used.
- src/hg/hgc/lowelab.c
- lines changed 26, context: html, text, full: html, text
Making final pass through tree of checkins as dictated by Jim. None of these changes should affect executables in any way. This pass is due to expanding fingerprint caused by kompare.
- src/hg/hgc/mafClick.c
- lines changed 15, context: html, text, full: html, text
Making final pass through tree of checkins as dictated by Jim. None of these changes should affect executables in any way. This pass is due to expanding fingerprint caused by kompare.
- src/hg/htdocs/ENCODE/encodeTools.html
- lines changed 25, context: html, text, full: html, text
Made changes requested by Mike Pazin (redmine #8607)
- lines changed 1, context: html, text, full: html, text
Fixed updated date (redmine #8607)
- src/hg/htdocs/ENCODE/index.html
- lines changed 44, context: html, text, full: html, text
Update news section for July
- lines changed 98, context: html, text, full: html, text
Retire older news to archive page
- src/hg/htdocs/ENCODE/newsarch.html
- lines changed 101, context: html, text, full: html, text
Retire older news to archive page
- lines changed 1, context: html, text, full: html, text
Add year link to ENCODE portal news archive
- src/hg/htdocs/ENCODE/platform_characterization.html
- lines changed 74, context: html, text, full: html, text
Made changes requested by Mike Pazin (redmine #8606)
- lines changed 1, context: html, text, full: html, text
Corrected spelling of 'mappability' (redmine #8606)
- src/hg/htdocs/ENCODE/qualityMetrics.html
- lines changed 41, context: html, text, full: html, text
Made changes requested by Mike Pazin (redmine #8606)
- lines changed 2, context: html, text, full: html, text
Corrected spelling of 'mappability' (redmine #8606)
- src/hg/htdocs/conditions.html
- src/hg/htdocs/goldenPath/help/multiView.html
- lines changed 5, context: html, text, full: html, text
highlighting by attribute functionality for GENCODE
- src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.html
- lines changed 241, context: html, text, full: html, text
Doc #5088 (clean up trackDb/README): added documentation for variationtrack settings, including moving snpNNN into a new type. Technically
it is still bed 6 +, but I plan to make it a proper type so I can stop
hardcoding registerTrackHandler's. Also removed some hardcoded hostnames
in doc HREF's.
- lines changed 1, context: html, text, full: html, text
Typo fix for previous commit (#5088)
- lines changed 2160, context: html, text, full: html, text
Eliminated the no longer used and commented out alphabetical listing. This was replaced by the self-assembled TOC. Also combined all the special case, deprecated, rejected or rarely used settings into a single table.
- src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
- lines changed 220, context: html, text, full: html, text
Doc #5088 (clean up trackDb/README): added documentation for variationtrack settings, including moving snpNNN into a new type. Technically
it is still bed 6 +, but I plan to make it a proper type so I can stop
hardcoding registerTrackHandler's. Also removed some hardcoded hostnames
in doc HREF's.
- src/hg/htdocs/goldenPath/newsarch.html
- lines changed 1, context: html, text, full: html, text
added quotes around attribute value
- src/hg/htdocs/images/Chinchilla_lanigera.jpg
- lines changed 0, context: html, text, full: html, text
from Wikimedia Commons - Guerin Nicolas
- src/hg/htdocs/images/Geospiza_fortis.jpg
- lines changed 0, context: html, text, full: html, text
from Wikimedia Commons - Charlesjsharp
- src/hg/htdocs/images/arrows-ffffff.png
- lines changed 0, context: html, text, full: html, text
Arrows icon sprite needed for dropdown menus.
- src/hg/htdocs/inc/globalNavBar.inc
- lines changed 1, context: html, text, full: html, text
use LOGIN_START/LOGIN_END comments to strip the hgLogin menu item for sites that aren't using hgLogin
- lines changed 4, context: html, text, full: html, text
change geo mirror items to OPTIONAL_GEO_MIRROR_ITEMS
- lines changed 1, context: html, text, full: html, text
add anchor to Source Code link
- lines changed 18, context: html, text, full: html, text
changed some links, formatted html for easier reading.
- lines changed 2, context: html, text, full: html, text
restore context specific help for some CGIs
- lines changed 3, context: html, text, full: html, text
remove Log in/out menu item
- src/hg/htdocs/inc/topbar.html
- lines changed 2, context: html, text, full: html, text
removed invalid html. added needed #.
- src/hg/htdocs/indexNews.html
- lines changed 1, context: html, text, full: html, text
Added quotes around attribute value, per redmine #8578
- src/hg/htdocs/robots.rr.txt
- lines changed 27, context: html, text, full: html, text
Cleaned up file. Removed redundant stuff. Removed complete block from goldenPath which made bots not index our help pages. Told bots not to index certain file types. And added slight crawl delay so they won't overwhelm servers.
- src/hg/htdocs/robots.txt
- lines changed 5, context: html, text, full: html, text
Added comment at top to remind that this version should not be pushed to the RR.
- src/hg/htdocs/staff.html
- src/hg/htdocs/style/HGStyle.css
- lines changed 7, context: html, text, full: html, text
changed css so only hgTracks would get new background color but all cgis would get prepped with no margin/padding for new menu bar.
- lines changed 1, context: html, text, full: html, text
add default background to body.cgi (used to put in the BODY tag)
- lines changed 3, context: html, text, full: html, text
Added old backgorund color back in for non hgTracks pages.
- lines changed 3, context: html, text, full: html, text
Merge branch 'newMenu' of greg@hgwdev.cse.ucsc.edu:/data/git/kent into newMenu
- lines changed 2, context: html, text, full: html, text
restore definition of .positionDisplay
- lines changed 18, context: html, text, full: html, text
Added styles for older browser look and feel static pages.
- lines changed 1, context: html, text, full: html, text
Set height for top blue nav bar
- lines changed 5, context: html, text, full: html, text
de-emphasize positionInput (work-in-progress)
- lines changed 17, context: html, text, full: html, text
move some stuff into css file
- lines changed 4, context: html, text, full: html, text
highlighting by attribute functionality for GENCODE
- lines changed 6, context: html, text, full: html, text
Reduced padding so that size of box/border matches the input gene search / position input field.
- src/hg/htdocs/style/images/internal_bg1.jpg
- lines changed 0, context: html, text, full: html, text
Background image for new site.
- src/hg/htdocs/style/nice_menu.css
- lines changed 3, context: html, text, full: html, text
Changed font to Arial and changed background color to the Jabico gray.
- lines changed 13, context: html, text, full: html, text
Added new border styles for browser graphics
- lines changed 2, context: html, text, full: html, text
Added styles for the main imgTbl to replace styles removed from the C code.
- lines changed 1, context: html, text, full: html, text
Adjusted start margin of dropdowns to compensate for other adjustments made.
- lines changed 142, context: html, text, full: html, text
Added Superfish styles. Needed for builtin drop down arrow icon. Will end up deleting all styles here that are not sued by us.
- src/hg/inc/hgColors.h
- lines changed 3, context: html, text, full: html, text
remove hBackgroundImage and hgColOutside
- src/hg/inc/hui.h
- lines changed 3, context: html, text, full: html, text
remove hBackgroundImage and hgColOutside
- lines changed 10, context: html, text, full: html, text
highlighting by attribute functionality for GENCODE
- lines changed 10, context: html, text, full: html, text
Making final pass through tree of checkins as dictated by Jim. None of these changes should affect executables in any way. This pass is due to expanding fingerprint caused by kompare.
- src/hg/inc/mafGene.h
- lines changed 1, context: html, text, full: html, text
Changed variable name to one that better describes its function.
- src/hg/inc/snp125CodingCoordless.h
- lines changed 1, context: html, text, full: html, text
Track #8360 (snp137): regenerated snp137CodingDbSnp after finding that itwas omitting func code 43 (stop-loss) and many rows with 45 (cds-indel) that
also had NULL frame... although that may be a red flag for the cds-indel's.
I am waiting to hear back from dbSNP about some possible misuses of cds-indel.
- src/hg/inc/snp125Ui.h
- lines changed 5, context: html, text, full: html, text
Feature #8551 (Sequence Ontology terms for predicted functional effects on SNP details pages):at Ensembl's request, instead of displaying dbSNP's predicted function terms, instead show
terms from the Sequence Ontology (SO). Where possible, terms from Ensembl's list at
http://staging.ensembl.org/info/docs/variation/predicted_data.html are used.
- src/hg/inc/trackDb.h
- lines changed 0, context: html, text, full: html, text
Making final pass through tree of checkins as dictated by Jim. None of these changes should affect executables in any way. This pass is due to expanding fingerprint caused by kompare.
- src/hg/inc/web.h
- lines changed 3, context: html, text, full: html, text
use new menus everywhere in hgNear
- lines changed 8, context: html, text, full: html, text
resolve merge conflict with master
- src/hg/js/autocomplete.js
- lines changed 64, context: html, text, full: html, text
refactor suggestBox code into autocomplete.js so it can be re-used in hgGateway
- lines changed 3, context: html, text, full: html, text
change selectCallback so callback has more info
- lines changed 22, context: html, text, full: html, text
set hgFind.matches to highlight items choosen by users (#6330)
- lines changed 33, context: html, text, full: html, text
code cleanup (get rid of suggestCache global)
- lines changed 2, context: html, text, full: html, text
make watermark more concise to address width problem in hgGateway
- lines changed 1, context: html, text, full: html, text
reset positionInput watermark when user zooms
- src/hg/js/hgGateway.js
- lines changed 3, context: html, text, full: html, text
change selectCallback so callback has more info
- lines changed 9, context: html, text, full: html, text
simplify suggestTrack code
- src/hg/js/hgTracks.js
- lines changed 74, context: html, text, full: html, text
refactor suggestBox code into autocomplete.js so it can be re-used in hgGateway
- lines changed 4, context: html, text, full: html, text
move comment back to the right place
- lines changed 5, context: html, text, full: html, text
handle situations where positionInput doesn't exist (e.g. PDF Output page)
- lines changed 9, context: html, text, full: html, text
change selectCallback so callback has more info
- lines changed 5, context: html, text, full: html, text
set hgFind.matches to highlight items choosen by users (#6330)
- lines changed 9, context: html, text, full: html, text
add hgFind.matches only if last thing user did was to choose from suggest
- lines changed 41, context: html, text, full: html, text
reset positionInput watermark when user zooms
- lines changed 1, context: html, text, full: html, text
fix vis.makeTrackVisible code
- src/hg/js/utils.js
- lines changed 4, context: html, text, full: html, text
move some stuff into css file
- src/hg/lib/cart.c
- lines changed 46, context: html, text, full: html, text
resolve merge conflict with master
- lines changed 1, context: html, text, full: html, text
Making final pass through tree of checkins as dictated by Jim. None of these changes should affect executables in any way. This pass is due to expanding fingerprint caused by kompare.
- src/hg/lib/chainCart.c
- lines changed 2, context: html, text, full: html, text
Making final pass through tree of checkins as dictated by Jim. None of these changes should affect executables in any way. This pass is due to expanding fingerprint caused by kompare.
- src/hg/lib/chromGraphFactory.c
- lines changed 7, context: html, text, full: html, text
adding more snp999 tables to list.
- src/hg/lib/fileUi.c
- lines changed 0, context: html, text, full: html, text
Making final pass through tree of checkins as dictated by Jim. None of these changes should affect executables in any way. This pass is due to expanding fingerprint caused by kompare.
- src/hg/lib/genePredReader.c
- lines changed 34, context: html, text, full: html, text
highlighting by attribute functionality for GENCODE
- src/hg/lib/hgColors.c
- src/hg/lib/hgFind.c
- lines changed 10, context: html, text, full: html, text
move some stuff into css file
- src/hg/lib/hui.c
- lines changed 9, context: html, text, full: html, text
resolve merge conflict with master
- lines changed 89, context: html, text, full: html, text
highlighting by attribute functionality for GENCODE
- lines changed 2, context: html, text, full: html, text
Making final pass through tree of checkins as dictated by Jim. None of these changes should affect executables in any way. This pass is due to expanding fingerprint caused by kompare.
- src/hg/lib/mafGene.c
- lines changed 5, context: html, text, full: html, text
Changed variable name to one that better describes its function.
- src/hg/lib/mdb.c
- lines changed 7, context: html, text, full: html, text
Making final pass through tree of checkins as dictated by Jim. None of these changes should affect executables in any way. This pass is due to expanding fingerprint caused by kompare.
- src/hg/lib/search.c
- lines changed 1, context: html, text, full: html, text
Making final pass through tree of checkins as dictated by Jim. None of these changes should affect executables in any way. This pass is due to expanding fingerprint caused by kompare.
- src/hg/lib/snp125Coding.sql
- lines changed 1, context: html, text, full: html, text
Track #8360 (snp137): regenerated snp137CodingDbSnp after finding that itwas omitting func code 43 (stop-loss) and many rows with 45 (cds-indel) that
also had NULL frame... although that may be a red flag for the cds-indel's.
I am waiting to hear back from dbSNP about some possible misuses of cds-indel.
- src/hg/lib/snp125CodingCoordless.c
- lines changed 1, context: html, text, full: html, text
Track #8360 (snp137): regenerated snp137CodingDbSnp after finding that itwas omitting func code 43 (stop-loss) and many rows with 45 (cds-indel) that
also had NULL frame... although that may be a red flag for the cds-indel's.
I am waiting to hear back from dbSNP about some possible misuses of cds-indel.
- src/hg/lib/snp125CodingCoordless.sql
- lines changed 1, context: html, text, full: html, text
Track #8360 (snp137): regenerated snp137CodingDbSnp after finding that itwas omitting func code 43 (stop-loss) and many rows with 45 (cds-indel) that
also had NULL frame... although that may be a red flag for the cds-indel's.
I am waiting to hear back from dbSNP about some possible misuses of cds-indel.
- src/hg/lib/snp125Ui.c
- lines changed 91, context: html, text, full: html, text
Feature #8551 (Sequence Ontology terms for predicted functional effects on SNP details pages):at Ensembl's request, instead of displaying dbSNP's predicted function terms, instead show
terms from the Sequence Ontology (SO). Where possible, terms from Ensembl's list at
http://staging.ensembl.org/info/docs/variation/predicted_data.html are used.
- src/hg/lib/trackDbCustom.c
- lines changed 6, context: html, text, full: html, text
Making final pass through tree of checkins as dictated by Jim. None of these changes should affect executables in any way. This pass is due to expanding fingerprint caused by kompare.
- src/hg/lib/trashDir.c
- lines changed 1, context: html, text, full: html, text
Making final pass through tree of checkins as dictated by Jim. None of these changes should affect executables in any way. This pass is due to expanding fingerprint caused by kompare.
- src/hg/lib/web.c
- lines changed 2, context: html, text, full: html, text
refactor BODY code; add class='cgi' so we can special case dynamic code
- lines changed 5, context: html, text, full: html, text
use LOGIN_START/LOGIN_END comments to strip the hgLogin menu item for sites that aren't using hgLogin
- lines changed 54, context: html, text, full: html, text
restore context specific help for some CGIs
- lines changed 7, context: html, text, full: html, text
add context-sensitive help for hgCustom
- lines changed 40, context: html, text, full: html, text
use new menus everywhere in hgNear
- lines changed 180, context: html, text, full: html, text
resolve merge conflict with master
- lines changed 4, context: html, text, full: html, text
use cloneString in setContextSpecificHelp
- lines changed 8, context: html, text, full: html, text
Making final pass through tree of checkins as dictated by Jim. None of these changes should affect executables in any way. This pass is due to expanding fingerprint caused by kompare.
- src/hg/makeDb/doc/calJac3.txt
- lines changed 21, context: html, text, full: html, text
Finished chain/net LASTZ of rheMac3 vs monDom5, panTro4 and calJac3.
- src/hg/makeDb/doc/chiLan1.txt
- lines changed 366, context: html, text, full: html, text
running repeat masker and window masker
- lines changed 87, context: html, text, full: html, text
done with masking and cpgIslands and genscan running genbank
- src/hg/makeDb/doc/encodeDccHg19/gencodeV12.txt
- lines changed 3, context: html, text, full: html, text
highlighting by attribute functionality for GENCODE
- src/hg/makeDb/doc/encodeDccHg19/wgEncodeCshlLongRnaSeq.release2.notes
- lines changed 6, context: html, text, full: html, text
Revert "updating notes file"
This reverts commit 2d35026eff77e39f04dc072b74cfce019585778d.
- src/hg/makeDb/doc/encodeDccHg19/wgEncodeFsuRepliChip.release2.notes
- src/hg/makeDb/doc/encodeDccHg19/wgEncodeRikenCage.release4.notes
- lines changed 2170, context: html, text, full: html, text
Adding release notes, needed to use loose option because of Morgan changes for the rawdata see ticket #7771
- src/hg/makeDb/doc/encodeDccHg19/wgEncodeUwAffyExonArray.release4.notes
- lines changed 468, context: html, text, full: html, text
Preparing Uw Affy Exon Release 4, changing long labels, updating the origAssembly to only be there if needed, fixing differentiation.
- src/hg/makeDb/doc/galGal4.txt
- lines changed 57, context: html, text, full: html, text
working on lastz to geoFor1
- src/hg/makeDb/doc/geoFor1.txt
- lines changed 152, context: html, text, full: html, text
running repeat masker, window masker, simple repeats, all gaps are marked
- lines changed 235, context: html, text, full: html, text
done with masking, starting genbank, cpgIslands and genscan
- lines changed 32, context: html, text, full: html, text
done with minimal set of tracks
- lines changed 121, context: html, text, full: html, text
default RHO position set, downloads and pushQ done, lastz swaps for melUnd1 hg19 mm10 and melGal1
- src/hg/makeDb/doc/hetGla1.txt
- lines changed 14, context: html, text, full: html, text
hetGla2 done and in the pushQ
- lines changed 1, context: html, text, full: html, text
done with liftover to hetGla2
- src/hg/makeDb/doc/hetGla2.txt
- lines changed 19, context: html, text, full: html, text
hetGla2 done and in the pushQ
- src/hg/makeDb/doc/hg19.txt
- lines changed 64, context: html, text, full: html, text
completed lastz to geoFor1
- lines changed 15, context: html, text, full: html, text
Track #8360 (snp137): regenerated snp137CodingDbSnp after finding that itwas omitting func code 43 (stop-loss) and many rows with 45 (cds-indel) that
also had NULL frame... although that may be a red flag for the cds-indel's.
I am waiting to hear back from dbSNP about some possible misuses of cds-indel.
- src/hg/makeDb/doc/latCha1.txt
- src/hg/makeDb/doc/melGal1.txt
- lines changed 57, context: html, text, full: html, text
done with lastz to geoFor1
- src/hg/makeDb/doc/melUnd1.txt
- lines changed 19, context: html, text, full: html, text
done and in the pushQ Redmine 6759
- lines changed 58, context: html, text, full: html, text
done with lastz to geoFor1
- src/hg/makeDb/doc/micMur1.txt
- lines changed 17, context: html, text, full: html, text
done and in the pushQ, redmine 7675
- src/hg/makeDb/doc/mm10.txt
- lines changed 61, context: html, text, full: html, text
done with lastz to geoFor1
- src/hg/makeDb/doc/monDom5.txt
- lines changed 23, context: html, text, full: html, text
Finished chain/net LASTZ of rheMac3 vs monDom5, panTro4 and calJac3.
- src/hg/makeDb/doc/nomLeu2.txt
- lines changed 17, context: html, text, full: html, text
done and in the pushQ, redmine 7676
- src/hg/makeDb/doc/ochPri2.txt
- lines changed 17, context: html, text, full: html, text
done and in the pushQ, redmine 7677
- src/hg/makeDb/doc/oreNil2.txt
- lines changed 17, context: html, text, full: html, text
done and in the pushQ, redmine 7678
- src/hg/makeDb/doc/otoGar3.txt
- lines changed 24, context: html, text, full: html, text
default position set at RHO and pushQ entry done
- src/hg/makeDb/doc/panTro3.txt
- lines changed 14, context: html, text, full: html, text
constructed liftOver to panTro4
- src/hg/makeDb/doc/panTro4.txt
- lines changed 62, context: html, text, full: html, text
Finished chain/net LASTZ of rheMac3 vs monDom5, panTro4 and calJac3.
- lines changed 24, context: html, text, full: html, text
done and in the pushQ, redmine 6356
- src/hg/makeDb/doc/papHam1.txt
- lines changed 24, context: html, text, full: html, text
done and in the pushQ, redmine 7669
- src/hg/makeDb/doc/proCap1.txt
- lines changed 24, context: html, text, full: html, text
done and in the pushQ, redmine 7680
- src/hg/makeDb/doc/pteVam1.txt
- lines changed 24, context: html, text, full: html, text
done and in the pushQ, redmine 7681
- src/hg/makeDb/doc/rheMac2.txt
- lines changed 24, context: html, text, full: html, text
liftOver constructed to rheMac3
- src/hg/makeDb/doc/rheMac3.txt
- lines changed 151, context: html, text, full: html, text
Finished chain/net LASTZ of rheMac3 vs monDom5, panTro4 and calJac3.
- lines changed 27, context: html, text, full: html, text
in the pushQ but maybe not ready to go ?
- src/hg/makeDb/doc/rn4.txt
- lines changed 15, context: html, text, full: html, text
liftOver to Rn5 constructed
- src/hg/makeDb/doc/saiBol1.txt
- lines changed 24, context: html, text, full: html, text
done and in the pushQ, redmine 6350
- src/hg/makeDb/doc/sorAra1.txt
- lines changed 24, context: html, text, full: html, text
done and in the pushQ, redmine 7682
- src/hg/makeDb/doc/speTri2.txt
- lines changed 24, context: html, text, full: html, text
done and in the pushQ, redmine 7319
- src/hg/makeDb/doc/susScr2.txt
- lines changed 14, context: html, text, full: html, text
liftOver to susScr3 done
- src/hg/makeDb/doc/susScr3.txt
- lines changed 24, context: html, text, full: html, text
done and in the pushQ, redmine 4015
- src/hg/makeDb/doc/taeGut1.txt
- lines changed 57, context: html, text, full: html, text
working on lastz to geoFor1
- src/hg/makeDb/doc/tarSyr1.txt
- lines changed 24, context: html, text, full: html, text
done and in the pushQ, redmine 7683
- src/hg/makeDb/doc/triMan1.txt
- lines changed 24, context: html, text, full: html, text
done and in the pushQ, redmine 7684
- src/hg/makeDb/doc/tupBel1.txt
- lines changed 24, context: html, text, full: html, text
done and in the pushQ, redmine 7684
- src/hg/makeDb/doc/turTru2.txt
- lines changed 25, context: html, text, full: html, text
done and in the pushQ, redmine 7686
- src/hg/makeDb/doc/ucscGenes/mm10.ucscGenes13.csh
- lines changed 124, context: html, text, full: html, text
ongoing work on mm10 UCSC genes. Fixed KEGG tables, rn5 blastp tables, and technique to lift genes from old assembly. Also added some comments to document the size of some of the tables for future reference.
- src/hg/makeDb/doc/vicPac1.txt
- lines changed 24, context: html, text, full: html, text
setting default track visibilities
- src/hg/makeDb/genbank/etc/align.dbs
- src/hg/makeDb/genbank/etc/genbank.conf
- lines changed 17, context: html, text, full: html, text
adding geoFor1 medium ground finch
- lines changed 17, context: html, text, full: html, text
adding chiLan1 Chinchilla
- src/hg/makeDb/genbank/etc/hgwbeta.dbs
- lines changed 1, context: html, text, full: html, text
We are reinstating danRer4 on the RR. Turning on genbank updates on both hgwbeta and the RR. The tables were synced from hgwdev first.
- src/hg/makeDb/genbank/etc/hgwdev.dbs
- src/hg/makeDb/genbank/etc/rr.dbs
- lines changed 1, context: html, text, full: html, text
We are reinstating danRer4 on the RR. Turning on genbank updates on both hgwbeta and the RR. The tables were synced from hgwdev first.
- src/hg/makeDb/genbank/src/lib/gbGenome.c
- lines changed 2, context: html, text, full: html, text
adding definition for geoForNames
- lines changed 2, context: html, text, full: html, text
adding definition for chiLanNames
- src/hg/makeDb/hgTrackDb/hgTrackDb.c
- lines changed 38, context: html, text, full: html, text
Checking in warnings when subgroup tags do not follow rules. Redmine 6813.
- lines changed 1, context: html, text, full: html, text
Changing some more white space after merging with previous commit
- lines changed 1, context: html, text, full: html, text
Fixing typo that broke compile.
- src/hg/makeDb/schema/all.joiner
- lines changed 10, context: html, text, full: html, text
Added appropriate entries for GRC Patch 9 track (redmine #7195)
- lines changed 2, context: html, text, full: html, text
adding geoFor1 Medium Ground Finch rules
- lines changed 1, context: html, text, full: html, text
adding geoFor1 to the chain/net list
- src/hg/makeDb/trackDb/alpaca/vicPac1/trackDb.ra
- lines changed 15, context: html, text, full: html, text
setting default track visibilities
- src/hg/makeDb/trackDb/baboon/papHam1/trackDb.ra
- lines changed 15, context: html, text, full: html, text
setting default visibilities
- src/hg/makeDb/trackDb/birds/geoFor1/description.html
- lines changed 62, context: html, text, full: html, text
initial contents from makeGenomeDb.pl
- src/hg/makeDb/trackDb/birds/geoFor1/gap.html
- lines changed 30, context: html, text, full: html, text
initial contents from makeGenomeDb.pl
- src/hg/makeDb/trackDb/birds/geoFor1/gold.html
- lines changed 33, context: html, text, full: html, text
initial contents from makeGenomeDb.pl
- src/hg/makeDb/trackDb/birds/geoFor1/trackDb.ra
- lines changed 8, context: html, text, full: html, text
initial contents from makeGenomeDb.pl
- src/hg/makeDb/trackDb/birds/melUnd1/trackDb.ra
- lines changed 9, context: html, text, full: html, text
setting default visibilities
- src/hg/makeDb/trackDb/bushbaby/otoGar3/trackDb.ra
- lines changed 9, context: html, text, full: html, text
setting default visibilities
- src/hg/makeDb/trackDb/chinchilla/chiLan1/description.html
- lines changed 62, context: html, text, full: html, text
initial contents from makeGenomeDb.pl
- src/hg/makeDb/trackDb/chinchilla/chiLan1/gap.html
- lines changed 30, context: html, text, full: html, text
initial contents from makeGenomeDb.pl
- src/hg/makeDb/trackDb/chinchilla/chiLan1/gold.html
- lines changed 33, context: html, text, full: html, text
initial contents from makeGenomeDb.pl
- src/hg/makeDb/trackDb/chinchilla/chiLan1/trackDb.ra
- lines changed 8, context: html, text, full: html, text
initial contents from makeGenomeDb.pl
- src/hg/makeDb/trackDb/cv/alpha/cv.ra
- lines changed 2, context: html, text, full: html, text
Fixed 2 tag's that were not all uper case.
- lines changed 85, context: html, text, full: html, text
Added 5 cell line registrations for UW.
- lines changed 6, context: html, text, full: html, text
Added mouse strain for UW.
- lines changed 1, context: html, text, full: html, text
Changing the defintion of dccInternalNotes to specify a use for it. It looks like we may be reloading a lot of files
- lines changed 113, context: html, text, full: html, text
Adding new antibodies to CV
- lines changed 4, context: html, text, full: html, text
add genome to label for combined genome and gencode database search
- lines changed 9, context: html, text, full: html, text
Adding protocol to CD4 cells
- lines changed 1, context: html, text, full: html, text
Updated the protocol to missing since the protocol existing is actually a generic ChIP-Seq protocol. Redmine #7437.
- lines changed 30, context: html, text, full: html, text
Removed 2 terms that were deprecated:rank, labProtocolId. Level,Annotation and Uniqness were left as they are only on 1 track. Redmine #8286.
- lines changed 5, context: html, text, full: html, text
Added labels to many cell lines that used tissue with lower case. Redmine #7771, note @25.
- lines changed 1, context: html, text, full: html, text
Added some comments about the Cage label
- lines changed 12, context: html, text, full: html, text
restoring labProtocolId, as Cshl uses it for their submissions. This was causing mass failures.
- lines changed 1, context: html, text, full: html, text
Fixed tag to be uppercase for diffProtD_3h.
- lines changed 9, context: html, text, full: html, text
Adding Th1 Th2 protocols to CV
- lines changed 5, context: html, text, full: html, text
Updated labels for Estradiol treatment.
- src/hg/makeDb/trackDb/cv/public/cv.ra
- lines changed 182, context: html, text, full: html, text
Approved all changes and moved from public/cv.ra to beta/cv.ra. Redmine #8576.
- src/hg/makeDb/trackDb/dolphin/turTru2/trackDb.ra
- lines changed 9, context: html, text, full: html, text
setting default track visibilities
- src/hg/makeDb/trackDb/gibbon/nomLeu2/trackDb.ra
- lines changed 5, context: html, text, full: html, text
setting default track visibilities
- src/hg/makeDb/trackDb/human/altSeqComposite.html
- lines changed 1, context: html, text, full: html, text
Staging GRC Patch 9 on beta (redmine #7195)
- lines changed 164, context: html, text, full: html, text
Made necessary corrections to the description page (redmine #7195)
- lines changed 1, context: html, text, full: html, text
Made one more minor correction (redmine #7195)
- src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
- lines changed 2, context: html, text, full: html, text
adding trackDb changes or affy rna chip
- src/hg/makeDb/trackDb/human/hg18/wgEncodeAffyRnaChip.patch.ra
- lines changed 1000, context: html, text, full: html, text
splitting affyrna into patch.ra and normal.ra
- src/hg/makeDb/trackDb/human/hg18/wgEncodeAffyRnaChip.ra
- lines changed 105, context: html, text, full: html, text
fixed the tags in affyRnaChip, comming in branch and testing hte shared branch thing
- lines changed 108, context: html, text, full: html, text
correcting cell tier tags
- lines changed 108, context: html, text, full: html, text
splitting affyrna into patch.ra and normal.ra
- src/hg/makeDb/trackDb/human/hg18/wgEncodeBroadHmm.ra
- lines changed 10, context: html, text, full: html, text
fixed metadata and dates
- lines changed 10, context: html, text, full: html, text
Revert "fixed metadata and dates"
This reverts commit fdd11ddb9f8b6e749175a07e86843ad18e0976fb.
- lines changed 0, context: html, text, full: html, text
correcting spacing and indentation
- lines changed 0, context: html, text, full: html, text
correcting cell tier tags
- src/hg/makeDb/trackDb/human/hg18/wgEncodeCaltechRnaSeq.ra
- lines changed 139, context: html, text, full: html, text
fixed metadata and dates
- lines changed 139, context: html, text, full: html, text
Revert "fixed metadata and dates"
This reverts commit fdd11ddb9f8b6e749175a07e86843ad18e0976fb.
- lines changed 139, context: html, text, full: html, text
fixing the rest of the tags
- lines changed 141, context: html, text, full: html, text
correcting cell tier tags
- src/hg/makeDb/trackDb/human/hg18/wgEncodeCshlLongRnaSeq.ra
- lines changed 49, context: html, text, full: html, text
fixed metadata and dates
- lines changed 49, context: html, text, full: html, text
Revert "fixed metadata and dates"
This reverts commit fdd11ddb9f8b6e749175a07e86843ad18e0976fb.
- lines changed 21, context: html, text, full: html, text
fixing the rest of the tags
- lines changed 22, context: html, text, full: html, text
correcting cell tier tags
- lines changed 49, context: html, text, full: html, text
more qa fixes for hg18 tag correction, this time correctin view tag errors
- src/hg/makeDb/trackDb/human/hg18/wgEncodeCshlShortRnaSeq.ra
- lines changed 98, context: html, text, full: html, text
fixed metadata and dates
- lines changed 98, context: html, text, full: html, text
Revert "fixed metadata and dates"
This reverts commit fdd11ddb9f8b6e749175a07e86843ad18e0976fb.
- lines changed 48, context: html, text, full: html, text
fizing tags for cshl short rna seq
- lines changed 48, context: html, text, full: html, text
Revert "fizing tags for cshl short rna seq"
This reverts commit 3e65bac5c9b15997f7e1ab0a5649596de840d738.
- lines changed 46, context: html, text, full: html, text
fixing the rest of the tags
- lines changed 46, context: html, text, full: html, text
correcting cell tier tags
- lines changed 98, context: html, text, full: html, text
more qa fixes for hg18 tag correction, this time correctin view tag errors
- src/hg/makeDb/trackDb/human/hg18/wgEncodeGisDnaPet.ra
- lines changed 7, context: html, text, full: html, text
Revert "fixed metadata and dates"
This reverts commit fdd11ddb9f8b6e749175a07e86843ad18e0976fb.
- lines changed 8, context: html, text, full: html, text
fixing the rest of the tags
- lines changed 7, context: html, text, full: html, text
correcting cell tier tags
- src/hg/makeDb/trackDb/human/hg18/wgEncodeGisPet.ra
- lines changed 170, context: html, text, full: html, text
fixed metadata and dates
- lines changed 170, context: html, text, full: html, text
Revert "fixed metadata and dates"
This reverts commit fdd11ddb9f8b6e749175a07e86843ad18e0976fb.
- lines changed 87, context: html, text, full: html, text
fixed tag errors for gis pet hg18
- lines changed 87, context: html, text, full: html, text
Revert "fixed tag errors for gis pet hg18"
This reverts commit ad65cd56e8afaae71d73ed6deda9fdd6dee9857b.
- lines changed 82, context: html, text, full: html, text
fixing the rest of the tags
- lines changed 85, context: html, text, full: html, text
correcting cell tier tags
- lines changed 170, context: html, text, full: html, text
more qa fixes for hg18 tag correction, this time correctin view tag errors
- src/hg/makeDb/trackDb/human/hg18/wgEncodeGisRnaSeq.ra
- lines changed 47, context: html, text, full: html, text
fixed metadata and dates
- lines changed 47, context: html, text, full: html, text
Revert "fixed metadata and dates"
This reverts commit fdd11ddb9f8b6e749175a07e86843ad18e0976fb.
- lines changed 20, context: html, text, full: html, text
Revert "fixed gisrna seq tags"
This reverts commit 4066509926bc9530018d96135126dc8c7a214554.
- lines changed 19, context: html, text, full: html, text
fixing the rest of the tags
- lines changed 20, context: html, text, full: html, text
correcting cell tier tags
- lines changed 48, context: html, text, full: html, text
more qa fixes for hg18 tag correction, this time correctin view tag errors
- src/hg/makeDb/trackDb/human/hg18/wgEncodeRikenCage.ra
- lines changed 122, context: html, text, full: html, text
fixed metadata and dates
- lines changed 122, context: html, text, full: html, text
Revert "fixed metadata and dates"
This reverts commit fdd11ddb9f8b6e749175a07e86843ad18e0976fb.
- lines changed 62, context: html, text, full: html, text
fixing tags for riken cage
- lines changed 62, context: html, text, full: html, text
Revert "fixing tags for riken cage"
This reverts commit 2a44d0254c171c351833b144781630eea5dda7b5.
- lines changed 59, context: html, text, full: html, text
fixing the rest of the tags
- lines changed 60, context: html, text, full: html, text
correcting cell tier tags
- lines changed 122, context: html, text, full: html, text
more qa fixes for hg18 tag correction, this time correctin view tag errors
- src/hg/makeDb/trackDb/human/hg18/wgEncodeUwChIPSeq.ra
- lines changed 300, context: html, text, full: html, text
fixed metadata and dates
- lines changed 300, context: html, text, full: html, text
Revert "fixed metadata and dates"
This reverts commit fdd11ddb9f8b6e749175a07e86843ad18e0976fb.
- lines changed 300, context: html, text, full: html, text
fixing the rest of the tags
- lines changed 294, context: html, text, full: html, text
correcting cell tier tags
- src/hg/makeDb/trackDb/human/hg18/wgEncodeUwDnaseSeq.ra
- lines changed 230, context: html, text, full: html, text
fixed metadata and dates
- lines changed 230, context: html, text, full: html, text
Revert "fixed metadata and dates"
This reverts commit fdd11ddb9f8b6e749175a07e86843ad18e0976fb.
- lines changed 230, context: html, text, full: html, text
fixed tags in uw dnase seq
- lines changed 230, context: html, text, full: html, text
Revert "fixed tags in uw dnase seq"
This reverts commit 2154fc5e2abf17b785892cc4c2b7bb599efc1abf.
- lines changed 230, context: html, text, full: html, text
fixing the rest of the tags
- src/hg/makeDb/trackDb/human/hg19/altSeqComposite9.ra
- lines changed 1, context: html, text, full: html, text
Changed the short label so it was under 17 characters (redmine #7195)
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeBroadHistone.ra
- lines changed 2045, context: html, text, full: html, text
loaded a lot of broad histone tracks
- lines changed 3338, context: html, text, full: html, text
added in new broad tracks
- lines changed 696, context: html, text, full: html, text
addedi in lat of Broad histone tracks
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeBuOrchid.ra
- lines changed 2, context: html, text, full: html, text
removed reserved accession from BuOrchid, since it will not be submitted to GEO
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCaltechRnaSeq.ra
- lines changed 991, context: html, text, full: html, text
Adding in 4 replacement fastqs and dropping useless lines like treatment None
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra
- lines changed 928, context: html, text, full: html, text
loaded protocols and transcipt denovos for cshl long
- lines changed 97, context: html, text, full: html, text
removed tableNames from transcipt denovos cshl long
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeFsuRepliChip.ra
- lines changed 237, context: html, text, full: html, text
Adding new stanzas from submission 7727
- lines changed 39, context: html, text, full: html, text
Adding md5sums, expIds, accsssions, corrected H9ES
- lines changed 11, context: html, text, full: html, text
Adding in dateUnrestricted
- lines changed 3, context: html, text, full: html, text
Updating more dateUnrestricted
- lines changed 19, context: html, text, full: html, text
Chainging more restriction dates
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGencodeV4.ra
- lines changed 3, context: html, text, full: html, text
Correcting an error in expVars
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisChiaPet.ra
- lines changed 62, context: html, text, full: html, text
added accession numbers for recent hg19 submissions
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisRnaPet.ra
- lines changed 69, context: html, text, full: html, text
adding in replacement clusters for gisRnaPet
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra
- lines changed 6007, context: html, text, full: html, text
adding in more haib tfbs tracks
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromChip.ra
- lines changed 881, context: html, text, full: html, text
added in new tracks for open chrom chip
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeRikenCage.ra
- lines changed 28, context: html, text, full: html, text
added new md5s for Riken after fixing double compression issue on dev. Also added 2 stanzas from cricket. 3rd stanza, wgEncodeRikenCageNhekNucleusPapTssHmm still needs to be verified from cricket.
- lines changed 36, context: html, text, full: html, text
Sorting out the V1, V3, V4 issue with NHEK, see ticket #7771
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhHistone.ra
- lines changed 9, context: html, text, full: html, text
added accession numbers for recent hg19 submissions
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUmassDekker5C.ra
- lines changed 46, context: html, text, full: html, text
added accession numbers for recent hg19 submissions
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUw5C.ra
- lines changed 38, context: html, text, full: html, text
added accession numbers for recent hg19 submissions
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwAffyExonArray.ra
- lines changed 321, context: html, text, full: html, text
added in last uw affy exon tracks
- lines changed 154, context: html, text, full: html, text
Preparing Uw Affy Exon Release 4, changing long labels, updating the origAssembly to only be there if needed, fixing differentiation.
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDgf.ra
- lines changed 145, context: html, text, full: html, text
corrected some metaDb errors
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDnase.ra
- lines changed 51, context: html, text, full: html, text
md5s originally created by double compression fix were bad, Ive replaced with good ones for both UwDnase and repli seq
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwRepliSeq.ra
- lines changed 15, context: html, text, full: html, text
md5s originally created by double compression fix were bad, Ive replaced with good ones for both UwDnase and repli seq
- src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeFsuRepliChip.ra
- lines changed 293, context: html, text, full: html, text
Staging on public FSU Replication Timing (Release 2) RM# 7663
- src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeRikenCage.ra
- lines changed 61, context: html, text, full: html, text
added new md5s for Riken after fixing double compression issue on dev. Also added 2 stanzas from cricket. 3rd stanza, wgEncodeRikenCageNhekNucleusPapTssHmm still needs to be verified from cricket.
- lines changed 36, context: html, text, full: html, text
Staging on Beta, RIKEN CAGE loc (Release 4) RM#7771
- src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeUwDnase.ra
- lines changed 51, context: html, text, full: html, text
md5s originally created by double compression fix were bad, Ive replaced with good ones for both UwDnase and repli seq
- src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeUwRepliSeq.ra
- lines changed 15, context: html, text, full: html, text
md5s originally created by double compression fix were bad, Ive replaced with good ones for both UwDnase and repli seq
- src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeHaibMethylRrbs.ra
- lines changed 522, context: html, text, full: html, text
Releasing HAIB RRBS (Release 3) to the RR (redmine #6773)
- src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeRikenCage.ra
- lines changed 96, context: html, text, full: html, text
Staging on public RIKEN CAGE (Release 4) RM#7771
- src/hg/makeDb/trackDb/human/hg19/snp137.shared.html
- lines changed 16, context: html, text, full: html, text
Added quotes around attribute values where missing. Changed bad link text of 'here' to something more descriptive.
- lines changed 110, context: html, text, full: html, text
Feature #8551 (Sequence Ontology terms for predicted functional effects on SNP details pages):at Ensembl's request, instead of displaying dbSNP's predicted function terms, instead show
terms from the Sequence Ontology (SO). Where possible, terms from Ensembl's list at
http://staging.ensembl.org/info/docs/variation/predicted_data.html are used.
- src/hg/makeDb/trackDb/human/hg19/trackDb.ra
- lines changed 1, context: html, text, full: html, text
Modified release tags for GRC Patch Release 5 (redmine #7195)
- lines changed 2, context: html, text, full: html, text
Staging GRC Patch 9 on beta (redmine #7195)
- src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
- lines changed 2, context: html, text, full: html, text
Staging on Beta, RIKEN CAGE loc (Release 4) RM#7771
- lines changed 8, context: html, text, full: html, text
highlighting by attribute functionality for GENCODE
- lines changed 2, context: html, text, full: html, text
Releasing HAIB RRBS (Release 3) to the RR (redmine #6773)
- lines changed 2, context: html, text, full: html, text
Forgot to commit changes to trackDb.wgEncode.ra when staging public for RIKEN CAGE (Release 4) RM7771, making public and pushing now
- lines changed 2, context: html, text, full: html, text
added in last uw affy exon tracks
- lines changed 1, context: html, text, full: html, text
Changing this release 3 to release 4
- lines changed 2, context: html, text, full: html, text
Staging on public FSU Replication Timing (Release 2) RM# 7663
- src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHistone.release3.ra
- lines changed 393, context: html, text, full: html, text
loaded a lot of broad histone tracks
- lines changed 487, context: html, text, full: html, text
added in new broad tracks
- lines changed 90, context: html, text, full: html, text
addedi in lat of Broad histone tracks
- src/hg/makeDb/trackDb/human/hg19/wgEncodeFsuRepliChip.html
- src/hg/makeDb/trackDb/human/hg19/wgEncodeFsuRepliChip.release2.ra
- lines changed 61, context: html, text, full: html, text
Adding new stanzas from submission 7727
- lines changed 2, context: html, text, full: html, text
Adding md5sums, expIds, accsssions, corrected H9ES
- src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV10.release3.ra
- lines changed 227, context: html, text, full: html, text
highlighting by attribute functionality for GENCODE
- src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV11.ra
- lines changed 18, context: html, text, full: html, text
highlighting by attribute functionality for GENCODE
- src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV12.release3.ra
- lines changed 227, context: html, text, full: html, text
highlighting by attribute functionality for GENCODE
- src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV5.ra
- lines changed 151, context: html, text, full: html, text
highlighting by attribute functionality for GENCODE
- src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV6.ra
- lines changed 129, context: html, text, full: html, text
highlighting by attribute functionality for GENCODE
- src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV7.release3.ra
- lines changed 225, context: html, text, full: html, text
highlighting by attribute functionality for GENCODE
- src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV9.ra
- lines changed 68, context: html, text, full: html, text
highlighting by attribute functionality for GENCODE
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethyl450.ra
- lines changed 64, context: html, text, full: html, text
Promoted tier 2.5 cell lines and collapsed the HCT116 line in the matrix to represnt both Stanford and Haib samples
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibRnaSeq.ra
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.release3.ra
- lines changed 1061, context: html, text, full: html, text
adding in more haib tfbs tracks
- src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromChip.release2.ra
- lines changed 130, context: html, text, full: html, text
added in new tracks for open chrom chip
- src/hg/makeDb/trackDb/human/hg19/wgEncodeProtGenoSuper.html
- src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.release4.html
- src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.release4.ra
- lines changed 21, context: html, text, full: html, text
Sorting out the V1, V3, V4 issue with NHEK, see ticket #7771
- lines changed 5, context: html, text, full: html, text
Changed the rnaExtract to all, changed prostate to Prostate, changed two of the TssHmm files to be on by defualt
- lines changed 29, context: html, text, full: html, text
Making Brians small edits
- src/hg/makeDb/trackDb/human/hg19/wgEncodeRnaSeqSuper.html
- lines changed 13, context: html, text, full: html, text
Updating mapper algorithm details in RNA-seq
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProtGenc.release1.html
- lines changed 11, context: html, text, full: html, text
modify display convention
- lines changed 25, context: html, text, full: html, text
modify display convention
- lines changed 1, context: html, text, full: html, text
update display convention
- lines changed 12, context: html, text, full: html, text
modify display convention
- lines changed 22, context: html, text, full: html, text
modify display convention
- lines changed 20, context: html, text, full: html, text
modify display convention
- lines changed 5, context: html, text, full: html, text
modify display convention
- lines changed 3, context: html, text, full: html, text
fixing blank line, space, change peptide rank to rank
- lines changed 3, context: html, text, full: html, text
modify display conventions
- lines changed 27, context: html, text, full: html, text
changed the field name from the long definition/description back to column name based on the email form John, added subtitle for fields that are common for regular and PTM peptides
- lines changed 27, context: html, text, full: html, text
format italics for column header in the text
- lines changed 41, context: html, text, full: html, text
shorten the length of the text so it's easier to read
- lines changed 7, context: html, text, full: html, text
add display convention entry specific to PTM peptide
- lines changed 16, context: html, text, full: html, text
remove subtitle in display convention, instead added for regular (PTM) peptide only in the end of the description of the field
- lines changed 41, context: html, text, full: html, text
modify methods in 2nd paragraph
- lines changed 2, context: html, text, full: html, text
change underline to bold as underline maybe confused with link
- lines changed 22, context: html, text, full: html, text
updates from John's email
- lines changed 33, context: html, text, full: html, text
some edit for GENCODE version
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProtGenc.release1.ra
- lines changed 12, context: html, text, full: html, text
add column number to bigBed type
- lines changed 1, context: html, text, full: html, text
added and to the view labels
- lines changed 2, context: html, text, full: html, text
add option box for protocol
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwAffyExonArray.patch.html
- lines changed 13, context: html, text, full: html, text
Making changes to methods and release notes for Univ Wash Affy Exxon Array (Release3 patch) as per Code Review RM#8588
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwAffyExonArray.release3.ra
- lines changed 72, context: html, text, full: html, text
added in last uw affy exon tracks
- lines changed 73, context: html, text, full: html, text
moving patch changes in and correcting tags
- lines changed 1531, context: html, text, full: html, text
Changing this release 3 to release 4
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwAffyExonArray.release4.html
- lines changed 96, context: html, text, full: html, text
Starting to clean up long and short labels and adding the new html file
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwAffyExonArray.release4.ra
- lines changed 1531, context: html, text, full: html, text
Changing this release 3 to release 4
- lines changed 33, context: html, text, full: html, text
Starting to clean up long and short labels and adding the new html file
- lines changed 10, context: html, text, full: html, text
Preparing Uw Affy Exon Release 4, changing long labels, updating the origAssembly to only be there if needed, fixing differentiation.
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.release6.ra
- lines changed 7, context: html, text, full: html, text
Removed the 4 from 4OHTAM according to ticket 8408
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwRepliSeq.ra
- lines changed 191, context: html, text, full: html, text
Promoting the tier 2.5 cell lines and fixing the tags for the phase and the views
- src/hg/makeDb/trackDb/latCha/latCha1/trackDb.ra
- lines changed 11, context: html, text, full: html, text
setting default visibilities
- src/hg/makeDb/trackDb/loadTracks
- lines changed 2, context: html, text, full: html, text
Changing some more white space after merging with previous commit
- lines changed 2, context: html, text, full: html, text
loadTracks did not belong in the previous commit, I am undoing it
- src/hg/makeDb/trackDb/makefile
- lines changed 1, context: html, text, full: html, text
adding geoFor1 to the build
- lines changed 1, context: html, text, full: html, text
adding Chinchilla to the build
- src/hg/makeDb/trackDb/manatee/triMan1/trackDb.ra
- lines changed 6, context: html, text, full: html, text
setting default track visibilities
- src/hg/makeDb/trackDb/megabat/pteVam1/trackDb.ra
- lines changed 15, context: html, text, full: html, text
setting default visibilities
- src/hg/makeDb/trackDb/mouse/mm10/trackDb.60way.ra
- lines changed 1, context: html, text, full: html, text
Changed several assemblies in speciesDefaultOff to match the actual assemblies being used.
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/makefile
- lines changed 1, context: html, text, full: html, text
Added in the 2 experiments, with updated labels, md5sum's. Redmine #109.
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra
- lines changed 3894, context: html, text, full: html, text
added in enw cshl mouse long tracks
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeMapability.ra
- lines changed 16, context: html, text, full: html, text
fixed metadata and dates
- lines changed 16, context: html, text, full: html, text
Revert "fixed metadata and dates"
This reverts commit fdd11ddb9f8b6e749175a07e86843ad18e0976fb.
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodePsuDnase.ra
- lines changed 366, context: html, text, full: html, text
Added in the 2 experiments, with updated labels, md5sum's. Redmine #109.
- lines changed 2, context: html, text, full: html, text
Added treatment as an experimental variable. Redmine #109
- lines changed 33, context: html, text, full: html, text
Experimentified track and fixed typo in trackDb. Redmine #109.
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodePsuHistone.ra
- lines changed 2, context: html, text, full: html, text
Added md5sum and updated track description. Redmine #6703.
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodePsuRnaSeq.ra
- lines changed 1870, context: html, text, full: html, text
Added 9 data-sets to track. All data has been loaded and displayed. Redmine #107.
- lines changed 255, context: html, text, full: html, text
Updated metadata for all RNA-seq data to have rnaExtract polyA and localization cell. Redmine #107.
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhRnaSeq.ra
- lines changed 33, context: html, text, full: html, text
Added V2 of Signal data to replaced original submission that contained an empty file. Redmine #8653.
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/wgEncodeLicrRnaSeq.ra
- lines changed 7, context: html, text, full: html, text
Correcting Incorrect Strain Associated in metadata, should be unknown, for MEL cell line. RM#8435)
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/public/wgEncodeLicrRnaSeq.ra
- lines changed 7, context: html, text, full: html, text
Staging on public, Correcting Incorrect Strain Associated in metadata, should be unknown, for MEL cell line. RM#8435)
- src/hg/makeDb/trackDb/mouse/mm9/trackDb.wgEncode.ra
- lines changed 3, context: html, text, full: html, text
Added in the 2 experiments, with updated labels, md5sum's. Redmine #109.
- lines changed 4, context: html, text, full: html, text
Updated include file to include the correct data sets for PSU TFBS and Histone.
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCaltechRnaSeq.release1.ra
- lines changed 11, context: html, text, full: html, text
Updated tags for cell lines, should be no visible change
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCshlLongRnaSeq.release3.ra
- lines changed 304, context: html, text, full: html, text
added in enw cshl mouse long tracks
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuDnase.ra
- lines changed 119, context: html, text, full: html, text
Added in the 2 experiments, with updated labels, md5sum's. Redmine #109.
- lines changed 1, context: html, text, full: html, text
Updated tag for Estradiol treatment. Redmine #109.
- lines changed 17, context: html, text, full: html, text
Updated track labels and View configuration. Redmine #109.
- lines changed 1, context: html, text, full: html, text
Experimentified track and fixed typo in trackDb. Redmine #109.
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuHistone.release2.html
- lines changed 13, context: html, text, full: html, text
Added md5sum and updated track description. Redmine #6703.
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuRnaSeq.html
- lines changed 15, context: html, text, full: html, text
Made a few modifications to track description for better organization and clarity. In addition, add information. Redmine #107.
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuRnaSeq.ra
- lines changed 463, context: html, text, full: html, text
Added 9 data-sets to track. All data has been loaded and displayed. Redmine #107.
- lines changed 188, context: html, text, full: html, text
First pass at short and long labels. Redmine #107.
- src/hg/makeDb/trackDb/mouseLemur/micMur1/trackDb.ra
- lines changed 25, context: html, text, full: html, text
setting default visibilities
- src/hg/makeDb/trackDb/oreNil/oreNil2/trackDb.ra
- lines changed 12, context: html, text, full: html, text
setting default track visibilities
- src/hg/makeDb/trackDb/pig/susScr3/trackDb.ra
- lines changed 9, context: html, text, full: html, text
seting default track visibilities
- src/hg/makeDb/trackDb/pika/ochPri2/trackDb.ra
- lines changed 9, context: html, text, full: html, text
setting default track visibilities
- src/hg/makeDb/trackDb/rhesus/rheMac3/trackDb.ra
- lines changed 14, context: html, text, full: html, text
setting default visibilities for tracks
- src/hg/makeDb/trackDb/rhesus/trackDb.chainNet.ra
- lines changed 4, context: html, text, full: html, text
adding override for PanTro4
- src/hg/makeDb/trackDb/rockHyrax/proCap1/trackDb.ra
- lines changed 6, context: html, text, full: html, text
set default track visibilities
- src/hg/makeDb/trackDb/saiBol/saiBol1/trackDb.ra
- lines changed 8, context: html, text, full: html, text
setting default track visibilities
- src/hg/makeDb/trackDb/shrew/sorAra1/trackDb.ra
- lines changed 11, context: html, text, full: html, text
setting default track visibilities
- src/hg/makeDb/trackDb/squirrel/speTri2/trackDb.ra
- lines changed 12, context: html, text, full: html, text
setting default track visibilities
- src/hg/makeDb/trackDb/tagTypes.tab
- lines changed 2, context: html, text, full: html, text
highlighting by attribute functionality for GENCODE
- src/hg/makeDb/trackDb/tarsier/tarSyr1/trackDb.ra
- lines changed 15, context: html, text, full: html, text
setting default track visibilities
- src/hg/makeDb/trackDb/tenrec/echTel1/trackDb.ra
- lines changed 1, context: html, text, full: html, text
Changed the visibility setting of the Other RefSeq track
- src/hg/makeDb/trackDb/trackDb.chainNet.ra
- lines changed 50, context: html, text, full: html, text
adding definition for chainNetPanTro4
- lines changed 102, context: html, text, full: html, text
adding melUnd1 and geoFor1
- src/hg/makeDb/trackDb/treeShrew/tupBel1/trackDb.ra
- lines changed 16, context: html, text, full: html, text
setting default track visibilities
- src/hg/makefile
- lines changed 1, context: html, text, full: html, text
add pslToBed to directories to test
- src/hg/near/hgNear/configure.c
- lines changed 2, context: html, text, full: html, text
use new menus everywhere in hgNear
- src/hg/near/hgNear/customColumn.c
- lines changed 10, context: html, text, full: html, text
use new menus everywhere in hgNear
- src/hg/near/hgNear/hgNear.c
- lines changed 9, context: html, text, full: html, text
work in progress to use new menus
- lines changed 4, context: html, text, full: html, text
use new menus everywhere in hgNear
- lines changed 4, context: html, text, full: html, text
Fixing stricter-gcc compiler warning 'format not a string literal and no format arguments' (cartWebStart needs a proper format string).
- src/hg/near/hgNear/order.c
- lines changed 3, context: html, text, full: html, text
use new menus everywhere in hgNear
- src/hg/phyloGif/phyloGif.c
- lines changed 1, context: html, text, full: html, text
remove hBackgroundImage and hgColOutside
- src/hg/protein/pbGlobal/pbGlobal.c
- src/hg/protein/pbTracks/pbTracks.c
- src/hg/pslToBed/makefile
- lines changed 5, context: html, text, full: html, text
add some tests, make the code easier to understand, and fix a problem with no CDS being indicated by thickStart == chromStart && thickEnd == chromEnd, instead of thickStart==thickEnd==0 as should have been the case. Thanks Tim for the code review!!!
- src/hg/pslToBed/pslToBed.c
- lines changed 46, context: html, text, full: html, text
add some tests, make the code easier to understand, and fix a problem with no CDS being indicated by thickStart == chromStart && thickEnd == chromEnd, instead of thickStart==thickEnd==0 as should have been the case. Thanks Tim for the code review!!!
- lines changed 17, context: html, text, full: html, text
oops... wasn't dealing with CDS start and stop correctly on '-' strand
- lines changed 6, context: html, text, full: html, text
round #3. Now genePredToBed matches what comes out of genePredToFakePsl followed by pslToBed if you make thickStart and thickEnd equal 0 when they equal each other. Now cdsEnd points to the base after the last base in CDS, even if that base is not in one of the exons.
- src/hg/pslToBed/tests/expected/doTest1.bed
- lines changed 285, context: html, text, full: html, text
add some tests, make the code easier to understand, and fix a problem with no CDS being indicated by thickStart == chromStart && thickEnd == chromEnd, instead of thickStart==thickEnd==0 as should have been the case. Thanks Tim for the code review!!!
- src/hg/pslToBed/tests/expected/doTest2.bed
- lines changed 55307, context: html, text, full: html, text
add some tests, make the code easier to understand, and fix a problem with no CDS being indicated by thickStart == chromStart && thickEnd == chromEnd, instead of thickStart==thickEnd==0 as should have been the case. Thanks Tim for the code review!!!
- lines changed 20685, context: html, text, full: html, text
oops... wasn't dealing with CDS start and stop correctly on '-' strand
- lines changed 236, context: html, text, full: html, text
round #3. Now genePredToBed matches what comes out of genePredToFakePsl followed by pslToBed if you make thickStart and thickEnd equal 0 when they equal each other. Now cdsEnd points to the base after the last base in CDS, even if that base is not in one of the exons.
- src/hg/pslToBed/tests/input/mm10.chrom.sizes
- lines changed 66, context: html, text, full: html, text
add some tests, make the code easier to understand, and fix a problem with no CDS being indicated by thickStart == chromStart && thickEnd == chromEnd, instead of thickStart==thickEnd==0 as should have been the case. Thanks Tim for the code review!!!
- src/hg/pslToBed/tests/input/test1.psl
- lines changed 285, context: html, text, full: html, text
add some tests, make the code easier to understand, and fix a problem with no CDS being indicated by thickStart == chromStart && thickEnd == chromEnd, instead of thickStart==thickEnd==0 as should have been the case. Thanks Tim for the code review!!!
- src/hg/pslToBed/tests/input/test2.cds
- lines changed 43689, context: html, text, full: html, text
add some tests, make the code easier to understand, and fix a problem with no CDS being indicated by thickStart == chromStart && thickEnd == chromEnd, instead of thickStart==thickEnd==0 as should have been the case. Thanks Tim for the code review!!!
- src/hg/pslToBed/tests/input/test2.psl
- lines changed 55307, context: html, text, full: html, text
add some tests, make the code easier to understand, and fix a problem with no CDS being indicated by thickStart == chromStart && thickEnd == chromEnd, instead of thickStart==thickEnd==0 as should have been the case. Thanks Tim for the code review!!!
- src/hg/pslToBed/tests/makefile
- lines changed 31, context: html, text, full: html, text
add some tests, make the code easier to understand, and fix a problem with no CDS being indicated by thickStart == chromStart && thickEnd == chromEnd, instead of thickStart==thickEnd==0 as should have been the case. Thanks Tim for the code review!!!
- src/hg/ratStuff/mafGene/mafGene.c
- lines changed 29, context: html, text, full: html, text
Removed getPredsFromFile() function as not needed. changed new options to have names that describe their function better.
- lines changed 2, context: html, text, full: html, text
Changed file variable name as it was undeclared.
- src/hg/utils/automation/geoMirrorNode.pl
- lines changed 0, context: html, text, full: html, text
Merge commit 'origin'; branch 'master' into newMenu
- src/hg/utils/automation/makeDownloads.pl
- lines changed 69, context: html, text, full: html, text
adding genbank usage message
- src/hg/utils/phyloTrees/placentals.txt
- lines changed 3, context: html, text, full: html, text
add medium ground finch geoFor1 and Chinchilla lanigera chiLan
- src/hg/utils/phyloTrees/vertebrates.txt
- lines changed 3, context: html, text, full: html, text
add medium ground finch geoFor1 and Chinchilla lanigera chiLan
- src/inc/cheapcgi.h
- lines changed 2, context: html, text, full: html, text
Making final pass through tree of checkins as dictated by Jim. None of these changes should affect executables in any way. This pass is due to expanding fingerprint caused by kompare.
- src/inc/htmshell.h
- lines changed 3, context: html, text, full: html, text
refactor BODY code; add class='cgi' so we can special case dynamic code
- src/lib/common.c
- lines changed 4, context: html, text, full: html, text
Making final pass through tree of checkins as dictated by Jim. None of these changes should affect executables in any way. This pass is due to expanding fingerprint caused by kompare.
- src/lib/htmshell.c
- lines changed 27, context: html, text, full: html, text
refactor BODY code; add class='cgi' so we can special case dynamic code
- lines changed 14, context: html, text, full: html, text
always add CGI name to the body class (enables special casing in style files)
- lines changed 14, context: html, text, full: html, text
Merge commit 'origin'; branch 'master' into newMenu
- lines changed 4, context: html, text, full: html, text
move some stuff into css file
- src/lib/ra.c
- lines changed 0, context: html, text, full: html, text
Making final pass through tree of checkins as dictated by Jim. None of these changes should affect executables in any way. This pass is due to expanding fingerprint caused by kompare.
- src/utils/bedToBigBed/bedToBigBed.c
- lines changed 8, context: html, text, full: html, text
keeping res* variables from overflowing integers when averageSpan is large. fixes #8630
- src/utils/qa/weeklybld/buildEnv.csh
- lines changed: 232229
- files changed: 579
