All File Changes
v267_preview to v267_preview2 (2012-05-01 to 2012-05-08) v267
- python/lib/ucscgenomics/mkChangeNotes.py
- python/lib/ucscgenomics/qa.py
- lines changed 17, context: html, text, full: html, text
Added getTrackType(), which uses tdbQuery to determine the track type for a table, if there is one.
- python/lib/ucscgenomics/qa/__init__.py
- lines changed 0, context: html, text, full: html, text
Start of qa package for analyzing tables.
- python/lib/ucscgenomics/qa/encode/tableCheck.py
- lines changed 316, context: html, text, full: html, text
Merge branch 'master' into rhead-pydev
- lines changed 18, context: html, text, full: html, text
Merge branch 'master' into rhead-pydev
- python/lib/ucscgenomics/qa/qaUtils.py
- lines changed 37, context: html, text, full: html, text
Added some new functions: getTrackType, tableExists, checkTablesExist, runCommand.
- lines changed 1, context: html, text, full: html, text
Removed colon from runCommand output. There is no error when using wait instead of communicate.
- lines changed 7, context: html, text, full: html, text
Made runCommand() use subprocess communicate(), and changed it to return stdout and stderr.
- python/lib/ucscgenomics/qa/tables/__init__.py
- lines changed 0, context: html, text, full: html, text
Start of qa package for analyzing tables.
- python/lib/ucscgenomics/qa/tables/factory.py
- lines changed 41, context: html, text, full: html, text
Start of qa package for analyzing tables.
- lines changed 13, context: html, text, full: html, text
Added import statements, fixed many indentation and syntax errors.
- lines changed 9, context: html, text, full: html, text
Made Reporter class for writing results of tests to a file. Wrote genePredCheck, pslCheck and tableDescriptionCheck funcitons using new class.
- lines changed 6, context: html, text, full: html, text
Added summary module for making tab-separated summary output for table QA. Also made qaGbTracks make 3 different files. The .chrom output is just using the tableCheck countPerChrom function for now.
- lines changed 3, context: html, text, full: html, text
Added several track types that are not documented in trackDb/README.
- python/lib/ucscgenomics/qa/tables/genePredQa.py
- lines changed 12, context: html, text, full: html, text
Start of qa package for analyzing tables.
- lines changed 4, context: html, text, full: html, text
Added import statements, fixed many indentation and syntax errors.
- lines changed 12, context: html, text, full: html, text
Made Reporter class for writing results of tests to a file. Wrote genePredCheck, pslCheck and tableDescriptionCheck funcitons using new class.
- lines changed 12, context: html, text, full: html, text
Got the validate methods mostly working. For calls to command-line programs, output is sent to the error log file and 'pass' or 'ERROR' is printed, depending on the return code. Still need to keep track of whether or not errors occurred for summary file.
- lines changed 6, context: html, text, full: html, text
Fixed calls to private parent class method.
- lines changed 1, context: html, text, full: html, text
Added rowCount(), checkLabelLengths(), and featureBits() methods, and changed name of writePossOrFail() to recordPassOrError() and moved it from PositionalQa to TableQa class.
- python/lib/ucscgenomics/qa/tables/pointerQa.py
- lines changed 8, context: html, text, full: html, text
Start of qa package for analyzing tables.
- lines changed 3, context: html, text, full: html, text
Added import statements, fixed many indentation and syntax errors.
- lines changed 1, context: html, text, full: html, text
Got the validate methods mostly working. For calls to command-line programs, output is sent to the error log file and 'pass' or 'ERROR' is printed, depending on the return code. Still need to keep track of whether or not errors occurred for summary file.
- python/lib/ucscgenomics/qa/tables/positionalQa.py
- lines changed 21, context: html, text, full: html, text
Start of qa package for analyzing tables.
- lines changed 3, context: html, text, full: html, text
Added import statements, fixed many indentation and syntax errors.
- lines changed 6, context: html, text, full: html, text
Added featureBits and statistics skeleton methods.
- lines changed 2, context: html, text, full: html, text
Made Reporter class for writing results of tests to a file. Wrote genePredCheck, pslCheck and tableDescriptionCheck funcitons using new class.
- lines changed 30, context: html, text, full: html, text
Got the validate methods mostly working. For calls to command-line programs, output is sent to the error log file and 'pass' or 'ERROR' is printed, depending on the return code. Still need to keep track of whether or not errors occurred for summary file.
- lines changed 5, context: html, text, full: html, text
Added summary module for making tab-separated summary output for table QA. Also made qaGbTracks make 3 different files. The .chrom output is just using the tableCheck countPerChrom function for now.
- lines changed 47, context: html, text, full: html, text
Added rowCount(), checkLabelLengths(), and featureBits() methods, and changed name of writePossOrFail() to recordPassOrError() and moved it from PositionalQa to TableQa class.
- python/lib/ucscgenomics/qa/tables/pslQa.py
- lines changed 12, context: html, text, full: html, text
Start of qa package for analyzing tables.
- lines changed 4, context: html, text, full: html, text
Added import statements, fixed many indentation and syntax errors.
- lines changed 12, context: html, text, full: html, text
Made Reporter class for writing results of tests to a file. Wrote genePredCheck, pslCheck and tableDescriptionCheck funcitons using new class.
- lines changed 12, context: html, text, full: html, text
Got the validate methods mostly working. For calls to command-line programs, output is sent to the error log file and 'pass' or 'ERROR' is printed, depending on the return code. Still need to keep track of whether or not errors occurred for summary file.
- lines changed 6, context: html, text, full: html, text
Fixed calls to private parent class method.
- lines changed 1, context: html, text, full: html, text
Added rowCount(), checkLabelLengths(), and featureBits() methods, and changed name of writePossOrFail() to recordPassOrError() and moved it from PositionalQa to TableQa class.
- python/lib/ucscgenomics/qa/tables/reporter.py
- lines changed 67, context: html, text, full: html, text
Made Reporter class for writing results of tests to a file. Wrote genePredCheck, pslCheck and tableDescriptionCheck funcitons using new class.
- lines changed 4, context: html, text, full: html, text
Got the validate methods mostly working. For calls to command-line programs, output is sent to the error log file and 'pass' or 'ERROR' is printed, depending on the return code. Still need to keep track of whether or not errors occurred for summary file.
- lines changed 1, context: html, text, full: html, text
Took extra information out of writeStepInfo().
- python/lib/ucscgenomics/qa/tables/summary.py
- lines changed 32, context: html, text, full: html, text
Added summary module for making tab-separated summary output for table QA. Also made qaGbTracks make 3 different files. The .chrom output is just using the tableCheck countPerChrom function for now.
- lines changed 19, context: html, text, full: html, text
Gave tableType and featureBits columns default values, added column for featureBits gap output, changed column headers.
- python/lib/ucscgenomics/qa/tables/tableQa.py
- lines changed 30, context: html, text, full: html, text
Start of qa package for analyzing tables.
- lines changed 2, context: html, text, full: html, text
Added import statements, fixed many indentation and syntax errors.
- lines changed 15, context: html, text, full: html, text
Made Reporter class for writing results of tests to a file. Wrote genePredCheck, pslCheck and tableDescriptionCheck funcitons using new class.
- lines changed 19, context: html, text, full: html, text
Got the validate methods mostly working. For calls to command-line programs, output is sent to the error log file and 'pass' or 'ERROR' is printed, depending on the return code. Still need to keep track of whether or not errors occurred for summary file.
- lines changed 7, context: html, text, full: html, text
Added summary module for making tab-separated summary output for table QA. Also made qaGbTracks make 3 different files. The .chrom output is just using the tableCheck countPerChrom function for now.
- lines changed 26, context: html, text, full: html, text
Added rowCount(), checkLabelLengths(), and featureBits() methods, and changed name of writePossOrFail() to recordPassOrError() and moved it from PositionalQa to TableQa class.
- python/users/kent/django/mysite/cvDb/admin.py
- lines changed 19, context: html, text, full: html, text
Polishing up a few things in preparation for meeting w/ Stanford.
- lines changed 4, context: html, text, full: html, text
Making result.experiment do raw_id in admin to prevent crash when Python trying to make selection box with 1000 items.
- python/users/kent/django/mysite/cvDb/models.py
- lines changed 134, context: html, text, full: html, text
Polishing up a few things in preparation for meeting w/ Stanford.
- lines changed 17, context: html, text, full: html, text
Improving comments, mostly by adding line breaks.
- python/users/kent/django/mysite/djBook/__init__.py
- lines changed 0, context: html, text, full: html, text
Another tutorial to follow
- python/users/kent/django/mysite/djBook/makefile
- lines changed 2, context: html, text, full: html, text
Another tutorial to follow
- python/users/kent/django/mysite/djBook/models.py
- lines changed 3, context: html, text, full: html, text
Another tutorial to follow
- python/users/kent/django/mysite/djBook/tests.py
- lines changed 16, context: html, text, full: html, text
Another tutorial to follow
- python/users/kent/django/mysite/djBook/urls.py
- lines changed 10, context: html, text, full: html, text
Another tutorial to follow
- python/users/kent/django/mysite/djBook/views.py
- lines changed 13, context: html, text, full: html, text
Another tutorial to follow
- python/users/kent/django/mysite/settings.py
- lines changed 1, context: html, text, full: html, text
Another tutorial to follow
- python/users/kent/django/mysite/urls.py
- lines changed 1, context: html, text, full: html, text
Another tutorial to follow
- src/TAGS
- lines changed 18929, context: html, text, full: html, text
No need to have deep level TAGS
- src/hg/encode/DAFs/3.0/hg19/wgEncodeGisRnaPet.daf
- lines changed 1, context: html, text, full: html, text
added sql line to gisRnaPet daf
- src/hg/encode/DAFs/3.0/mm9/wgEncodeSydhHist.daf
- lines changed 3, context: html, text, full: html, text
Fixed lab designations for mouse to be Stanford-m or Yale-m.
- src/hg/encode/DAFs/3.0/mm9/wgEncodeSydhRnaSeq.daf
- lines changed 7, context: html, text, full: html, text
Remvoed Strand specific signal.
- lines changed 3, context: html, text, full: html, text
Fixed lab designations for mouse to be Stanford-m or Yale-m.
- src/hg/encode/DAFs/3.0/mm9/wgEncodeSydhTfbs.daf
- lines changed 3, context: html, text, full: html, text
Fixed lab designations for mouse to be Stanford-m or Yale-m.
- src/hg/encode/encodeLoad/doEncodeLoad.pl
- lines changed 1, context: html, text, full: html, text
forgot to remove the explicit path to galts bin and change to cluster one
- src/hg/encode/encodeQaInit/encodeQaInit
- lines changed 2, context: html, text, full: html, text
fixing for new tree structure
- src/hg/gsBig/gsBig.c
- lines changed 10, context: html, text, full: html, text
after all these years, gsBig has been leaving garbage all over the place for no good reason. Fixed this bug
- src/hg/gsBig/makefile
- src/hg/hgCustom/hgCustom.c
- lines changed 1, context: html, text, full: html, text
refactor loadingImg code so it can be reused in hgVarAnnogrator
- src/hg/hgLogin/gbMembers.as
- lines changed 9, context: html, text, full: html, text
Initial work on email password rest function
- lines changed 4, context: html, text, full: html, text
finished gbMembers table expansion to include security tokens.
- src/hg/hgLogin/gbMembers.c
- lines changed 76, context: html, text, full: html, text
Initial work on email password rest function
- lines changed 76, context: html, text, full: html, text
Finished Greg's Login UI.
- lines changed 69, context: html, text, full: html, text
finished gbMembers table expansion to include security tokens.
- src/hg/hgLogin/gbMembers.h
- lines changed 9, context: html, text, full: html, text
Initial work on email password rest function
- lines changed 9, context: html, text, full: html, text
Finished Greg's Login UI.
- lines changed 9, context: html, text, full: html, text
finished gbMembers table expansion to include security tokens.
- src/hg/hgLogin/gbMembers.sql
- lines changed 15, context: html, text, full: html, text
Initial work on email password rest function
- lines changed 15, context: html, text, full: html, text
Finished Greg's Login UI.
- lines changed 15, context: html, text, full: html, text
finished gbMembers table expansion to include security tokens.
- src/hg/hgLogin/hgLogin.c
- lines changed 98, context: html, text, full: html, text
Finished ser/reset Cookies
- lines changed 13, context: html, text, full: html, text
Finish cancel button to go back to previous page.
- lines changed 64, context: html, text, full: html, text
Finished MD5 hashing pare as mediawiki does.
- lines changed 44, context: html, text, full: html, text
Finished password decrypt.
- lines changed 41, context: html, text, full: html, text
Initial work on email password rest function
- lines changed 3, context: html, text, full: html, text
Finished generate userAccount.css in HEAD and class='userAccount' attributes in BODY.
- lines changed 47, context: html, text, full: html, text
Finished Greg's Login UI.
- lines changed 234, context: html, text, full: html, text
Finished new Login and Signup UI from Greg.
- lines changed 109, context: html, text, full: html, text
Finished new Login and Signup UI.
- lines changed 103, context: html, text, full: html, text
Finished Account Help UI.
- lines changed 97, context: html, text, full: html, text
Finish initial mail out function with accountHelp form.
- lines changed 59, context: html, text, full: html, text
Finish confirmationScreen.
- lines changed 71, context: html, text, full: html, text
Finished email forgotten username(s).
- lines changed 83, context: html, text, full: html, text
finished gbMembers table expansion to include security tokens.
- lines changed 51, context: html, text, full: html, text
Check current password before reset password.
- lines changed 29, context: html, text, full: html, text
Finished require user id before send new password.
- lines changed 38, context: html, text, full: html, text
Finished the idea UI for account Help
- lines changed 51, context: html, text, full: html, text
Finished init part of send new password
- lines changed 4, context: html, text, full: html, text
Reuse the wiki cookies so that the existing session user can stay logged in and do not need to login to the new hgLogin system after the switch over.
- lines changed 10, context: html, text, full: html, text
Minor fix for hgLoginLink to wikiLink transition.
- lines changed 36, context: html, text, full: html, text
Honored the returnto request.
- lines changed 3, context: html, text, full: html, text
finished returnto URL testing.
- lines changed 92, context: html, text, full: html, text
Initial generate new password function.
- lines changed 51, context: html, text, full: html, text
Finished forcing user to change password.
- lines changed 83, context: html, text, full: html, text
Send activation mail to user
- lines changed 21, context: html, text, full: html, text
Fixed the force password change function problem.
- lines changed 21, context: html, text, full: html, text
Fixed the activation code.
- src/hg/hgLogin/hgLogin.h
- lines changed 5, context: html, text, full: html, text
Finished ser/reset Cookies
- lines changed 3, context: html, text, full: html, text
Finished new Login and Signup UI.
- lines changed 33, context: html, text, full: html, text
Initial generate new password function.
- lines changed 3, context: html, text, full: html, text
Finished forcing user to change password.
- lines changed 5, context: html, text, full: html, text
Send activation mail to user
- lines changed 6, context: html, text, full: html, text
Fixed the activation code.
- src/hg/hgLogin/makefile
- lines changed 22, context: html, text, full: html, text
Finished ser/reset Cookies
- src/hg/hgSession/hgSession.c
- lines changed 107, context: html, text, full: html, text
Reuse the wiki cookies so that the existing session user can stay logged in and do not need to login to the new hgLogin system after the switch over.
- src/hg/hgTracks/chromGraphTrack.c
- lines changed 2, context: html, text, full: html, text
Fixing missing c=chromName in a lot of links. A bug Tim put in 2009 from what I can tell that manifests with an empty cart on IE.
- src/hg/hgTracks/config.c
- lines changed 36, context: html, text, full: html, text
added one missing file to theme commit (config option dialog)
- lines changed 3, context: html, text, full: html, text
UI themes for hgc/hgGene and some fixes for hgTracks
- src/hg/hgTracks/expRatioTracks.c
- lines changed 5, context: html, text, full: html, text
Fixing missing c=chromName in a lot of links. A bug Tim put in 2009 from what I can tell that manifests with an empty cart on IE.
- src/hg/hgTracks/hgTracks.c
- lines changed 436, context: html, text, full: html, text
refactor menu bar code into a new file to get ready for new menu bar design (#5245)
- src/hg/hgTracks/hgTracks.h
- lines changed 12, context: html, text, full: html, text
refactor menu bar code into a new file to get ready for new menu bar design (#5245)
- src/hg/hgTracks/makefile
- lines changed 1, context: html, text, full: html, text
refactor menu bar code into a new file to get ready for new menu bar design (#5245)
- src/hg/hgTracks/menu.c
- lines changed 457, context: html, text, full: html, text
refactor menu bar code into a new file to get ready for new menu bar design (#5245)
- src/hg/hgTracks/simpleTracks.c
- lines changed 4, context: html, text, full: html, text
Fixing missing c=chromName in a lot of links. A bug Tim put in 2009 from what I can tell that manifests with an empty cart on IE.
- lines changed 25, context: html, text, full: html, text
remove pubsLoadMarkerItem code which was unnecessarily calling loadSimpleBedAsLinkedFeaturesPerBase (and thus making the pubsMarkerBand track quite slow); move itemName call in genericDrawItem so it's only done when needed
- src/hg/hgVarAnnogrator/hgVarAnnogrator.c
- lines changed 301, context: html, text, full: html, text
hgVarAnnogrator now stores querySpec in the cart, and uses the cart'squerySpec (if exists) to draw the page. It also does a reload when the
user hits the back button, because the web browser forgets all AJAX
updates and the cart has the latest state. It does synchronous AJAX
to lookup the position before executing a query; that causes failure
of ajax.js's setCartVars async GET, so in order to avoid a warning
about network error, we ignore errors for setCartVars. (#6152)
- lines changed 2, context: html, text, full: html, text
Use lastPosition cart variable (when present) when a position lookup fails. (#6152)
- src/hg/hgc/hgc.c
- lines changed 1, context: html, text, full: html, text
Adding missing closing body and html tags on mrna details page.
- src/hg/hgc/pubs.c
- lines changed 10, context: html, text, full: html, text
code review kate changes: whitespace corrections and changes of comments
- lines changed 1, context: html, text, full: html, text
lowering limit for hgc pubs track, redmine #7836
- src/hg/htdocs/ENCODE/analysisTools.html
- lines changed 20, context: html, text, full: html, text
Added table of contents to encodeTools.html and bulleted items per Katrina's suggestions (redmine #7701)
- lines changed 1, context: html, text, full: html, text
Made some corrections suggested by Katrina (redmine #7701)
- src/hg/htdocs/ENCODE/dataSummary.html
- lines changed 6, context: html, text, full: html, text
Update summary pages as of April 1, 2012
- src/hg/htdocs/ENCODE/dataSummaryMouse.html
- lines changed 5, context: html, text, full: html, text
Update summary pages as of April 1, 2012
- src/hg/htdocs/ENCODE/encodeTools.html
- lines changed 95, context: html, text, full: html, text
Added table of contents to encodeTools.html and bulleted items per Katrina's suggestions (redmine #7701)
- lines changed 7, context: html, text, full: html, text
Made some corrections suggested by Katrina (redmine #7701)
- src/hg/htdocs/ENCODE/search.html
- lines changed 94, context: html, text, full: html, text
making the ENCODE search page into the new styling; first step in #6846
- src/hg/htdocs/ENCODE/softwareTools.html
- lines changed 1, context: html, text, full: html, text
Added table of contents to encodeTools.html and bulleted items per Katrina's suggestions (redmine #7701)
- lines changed 2, context: html, text, full: html, text
Put journal title in italics (redmine #7701)
- src/hg/htdocs/FAQ/FAQformat.html
- lines changed 6, context: html, text, full: html, text
clarifying psl format in faq based on user feedback
- src/hg/htdocs/admin/mirror.html
- lines changed 2, context: html, text, full: html, text
two suggestions from Steve during code review
- src/hg/htdocs/goldenPath/help/query.html
- lines changed 46, context: html, text, full: html, text
Renamed sampleQueries.html as query.html (redmine #7751)
- src/hg/htdocs/goldenPath/help/sampleQueries.html
- lines changed 45, context: html, text, full: html, text
Created new sample query page (redmine #7751)
- lines changed 12, context: html, text, full: html, text
Checking in with new file permissions so the menu bar will be visible (redmine #7751)
- lines changed 46, context: html, text, full: html, text
Renamed sampleQueries.html as query.html (redmine #7751)
- src/hg/htdocs/goldenPath/newsarch.html
- lines changed 39, context: html, text, full: html, text
Added news announcement about OH tutorials.
- src/hg/htdocs/images/floretPreview.jpg
- lines changed 0, context: html, text, full: html, text
Got greg to help make a floret for the preview machine that is easier on the eyes. Redmine #3834.
- src/hg/htdocs/indexNews.html
- lines changed 56, context: html, text, full: html, text
Added news announcement about OH tutorials.
- src/hg/inc/hgConfig.h
- lines changed 3, context: html, text, full: html, text
adding themes to browser: config option and background image overwrite
- src/hg/inc/hgLoginLink.h
- src/hg/inc/trackLayout.h
- lines changed 1, context: html, text, full: html, text
adding themes to browser: config option and background image overwrite
- src/hg/inc/wikiLink.h
- lines changed 9, context: html, text, full: html, text
Reuse the wiki cookies so that the existing session user can stay logged in and do not need to login to the new hgLogin system after the switch over.
- src/hg/js/ajax.js
- lines changed 5, context: html, text, full: html, text
hgVarAnnogrator now stores querySpec in the cart, and uses the cart'squerySpec (if exists) to draw the page. It also does a reload when the
user hits the back button, because the web browser forgets all AJAX
updates and the cart has the latest state. It does synchronous AJAX
to lookup the position before executing a query; that causes failure
of ajax.js's setCartVars async GET, so in order to avoid a warning
about network error, we ignore errors for setCartVars. (#6152)
- lines changed 4, context: html, text, full: html, text
Make setCartVars optionally synchronous too -- page reload was interruptingsetCartVars in some cases. (#6152)
- lines changed 44, context: html, text, full: html, text
refactor loadingImg code so it can be reused in hgVarAnnogrator
- src/hg/js/hgCustom.js
- lines changed 24, context: html, text, full: html, text
refactor loadingImg code so it can be reused in hgVarAnnogrator
- src/hg/js/hgVarAnnogrator.js
- lines changed 35, context: html, text, full: html, text
hgVarAnnogrator now stores querySpec in the cart, and uses the cart'squerySpec (if exists) to draw the page. It also does a reload when the
user hits the back button, because the web browser forgets all AJAX
updates and the cart has the latest state. It does synchronous AJAX
to lookup the position before executing a query; that causes failure
of ajax.js's setCartVars async GET, so in order to avoid a warning
about network error, we ignore errors for setCartVars. (#6152)
- lines changed 1, context: html, text, full: html, text
Make setCartVars optionally synchronous too -- page reload was interruptingsetCartVars in some cases. (#6152)
- src/hg/lib/annoStreamDb.c
- lines changed 41, context: html, text, full: html, text
annoStreamDb now uses mysql server-side sorting in a couple of caseswhere table data may come out unsorted: 1) When a table e.g. knownGene
has an index on txEnd, sometimes the mysql query optimizer uses that
index and then rows come out not sorted by txStart.
2) GenBank tables get ongoing updates, so although they are mostly
sorted from initial load, they are not 100% sorted. (#6152)
- lines changed 12, context: html, text, full: html, text
Turns out that snp135 yields unsorted output for 'where chrom="...' --for now, just sort all queries that have a where clause. (#6152)
- src/hg/lib/cart.c
- lines changed 21, context: html, text, full: html, text
adding themes to browser: config option and background image overwrite
- lines changed 137, context: html, text, full: html, text
UI themes for hgc/hgGene and some fixes for hgTracks
- src/hg/lib/hgConfig.c
- lines changed 16, context: html, text, full: html, text
adding themes to browser: config option and background image overwrite
- src/hg/lib/hgLoginLink.c
- lines changed 3, context: html, text, full: html, text
Finished ser/reset Cookies
- src/hg/lib/hui.c
- lines changed 1, context: html, text, full: html, text
adding themes to browser: config option and background image overwrite
- src/hg/lib/makefile
- lines changed 2, context: html, text, full: html, text
Merge branch 'master' into chinhli-hgLogin
- lines changed 1, context: html, text, full: html, text
Dicomission hgLoginLink.c and .h .
- src/hg/lib/wikiLink.c
- lines changed 33, context: html, text, full: html, text
Reuse the wiki cookies so that the existing session user can stay logged in and do not need to login to the new hgLogin system after the switch over.
- src/hg/makeDb/doc/canFam2.txt
- lines changed 28, context: html, text, full: html, text
completed liftOver to canFam3
- src/hg/makeDb/doc/canFam3.txt
- src/hg/makeDb/doc/choHof1.txt
- lines changed 25, context: html, text, full: html, text
done with windowMasker track
- src/hg/makeDb/doc/dipOrd1.txt
- lines changed 84, context: html, text, full: html, text
done with windowMasker and running genbank
- src/hg/makeDb/doc/echTel1.txt
- src/hg/makeDb/doc/encodeDccHg19/wgEncodeCshlLongRnaSeq.release2.notes
- lines changed 333, context: html, text, full: html, text
added in new notes and html changers for cshl long
- src/hg/makeDb/doc/encodeDccHg19/wgEncodeSydhTfbs.release2.notes
- lines changed 4336, context: html, text, full: html, text
Added notes files for Release 2 and made release3 ra file. Redmine #4486, #7510.
- lines changed 32, context: html, text, full: html, text
Fixed the control id for dccAccession: wgEncodeEH000769. Redmine #4486.
- src/hg/makeDb/doc/felCat5.txt
- lines changed 123, context: html, text, full: html, text
completed a tough genscan run
- src/hg/makeDb/doc/micMur1.txt
- src/hg/makeDb/doc/mm6.txt
- lines changed 34, context: html, text, full: html, text
constructing liftOver to Mm10
- src/hg/makeDb/doc/mm8.txt
- lines changed 20, context: html, text, full: html, text
constructing liftOver to Mm10
- src/hg/makeDb/doc/ochPri2.txt
- lines changed 25, context: html, text, full: html, text
completed windowMasker track
- src/hg/makeDb/doc/panTro4.txt
- lines changed 125, context: html, text, full: html, text
completed a difficult gencode run
- lines changed 94, context: html, text, full: html, text
completed genbank operations
- src/hg/makeDb/doc/papHam1.txt
- lines changed 86, context: html, text, full: html, text
completed windowMasker track
- src/hg/makeDb/doc/proCap1.txt
- lines changed 25, context: html, text, full: html, text
completed windowMasker track
- src/hg/makeDb/doc/pteVam1.txt
- src/hg/makeDb/doc/rn5.txt
- lines changed 120, context: html, text, full: html, text
completed a complicated genscan run
- src/hg/makeDb/doc/tarSyr1.txt
- src/hg/makeDb/doc/tupBel1.txt
- lines changed 25, context: html, text, full: html, text
completed windowMasker track
- src/hg/makeDb/doc/vicPac1.txt
- lines changed 21, context: html, text, full: html, text
completed windowMasker track
- src/hg/makeDb/genbank/etc/align.dbs
- src/hg/makeDb/genbank/etc/genbank.conf
- lines changed 17, context: html, text, full: html, text
adding definition for canFam3
- lines changed 1, context: html, text, full: html, text
unplacedChroms should be chrUn_*
- lines changed 1, context: html, text, full: html, text
unplacedChroms means any chrom with non-bridged gaps as marked in the lift file
- lines changed 5, context: html, text, full: html, text
canFam3 is labelled finished
- lines changed 18, context: html, text, full: html, text
adding choHof1 and removing blanks at end of line
- lines changed 17, context: html, text, full: html, text
adding chrPic1 painted turtle
- lines changed 17, context: html, text, full: html, text
adding dasNov3 painted turtle
- lines changed 17, context: html, text, full: html, text
adding dipOrd1 kangaroo rat
- lines changed 2, context: html, text, full: html, text
broken definition for felCat5
- lines changed 1, context: html, text, full: html, text
correct specifications for panTro4
- lines changed 1, context: html, text, full: html, text
correct specifications for susScr3
- lines changed 20, context: html, text, full: html, text
adding hetGla2 painted turtle
- src/hg/makeDb/genbank/etc/hgwbeta.dbs
- lines changed 1, context: html, text, full: html, text
added new naked mole-rat assembly
- src/hg/makeDb/genbank/etc/hgwdev.dbs
- src/hg/makeDb/genbank/src/lib/gbGenome.c
- lines changed 2, context: html, text, full: html, text
adding definition for choHofNames Choloepus hoffmanni
- lines changed 2, context: html, text, full: html, text
adding definition for chrPicNames Chrysemys picta bellii
- lines changed 2, context: html, text, full: html, text
adding definition for dipOrdNames Dipodomys ordii
- lines changed 2, context: html, text, full: html, text
adding definition for otoGarNames Otolemur garnettii
- lines changed 2, context: html, text, full: html, text
adding definition for turTruNames Tursiops truncatus
- src/hg/makeDb/trackDb/cv/alpha/cv.ra
- lines changed 46, context: html, text, full: html, text
Added terms for Mouse FSU track. Redmine #6627.
- lines changed 17, context: html, text, full: html, text
Removing PROVISIONAL tags from CV
- lines changed 1, context: html, text, full: html, text
Fixed description for protocol.
- lines changed 19, context: html, text, full: html, text
ScienCell primary cells are all normal- CV
- lines changed 14, context: html, text, full: html, text
Lonza emailed me their naming schema for diseased cells, so I annotated their normal cell lines in the CV
- lines changed 27, context: html, text, full: html, text
Adding karyotype normal to Coriell GM cell lines in CV
- lines changed 1, context: html, text, full: html, text
Removed ; from listing of many protocols, found in html link check error.
- lines changed 6, context: html, text, full: html, text
Added some protocols for parent registrations and updated tags for protocols to have lab.
- src/hg/makeDb/trackDb/cv/beta/cv.ra
- lines changed 11, context: html, text, full: html, text
Removing PROVISIONAL tags from cv
- src/hg/makeDb/trackDb/cv/public/cv.ra
- lines changed 132, context: html, text, full: html, text
Moved over approved changes to public/cv.ra from beta/cv.ra. Redmine #7800.
- lines changed 1, context: html, text, full: html, text
Removed ; from listing of many protocols, found in html link check error.
- src/hg/makeDb/trackDb/human/altSeqComposite.html
- lines changed 39, context: html, text, full: html, text
Added color scheme information to the description section as suggested by Hiram (redmine #7835)
- src/hg/makeDb/trackDb/human/gwasCatalog.html
- lines changed 11, context: html, text, full: html, text
Made minor formatting corrections
- src/hg/makeDb/trackDb/human/hg18/knownGene.html
- lines changed 2, context: html, text, full: html, text
Corrected a spacing error
- src/hg/makeDb/trackDb/human/hg19/knownGene.html
- lines changed 2, context: html, text, full: html, text
Corrected a spacing error
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeBroadHistone.ra
- lines changed 13, context: html, text, full: html, text
added geo accession numbers back into hg19. Everything is now almost completely up to date, although there are a few minor inconsistencies
- lines changed 55, context: html, text, full: html, text
Removed dataUnrestricted for published datasets. Redmine #7515.
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra
- lines changed 90, context: html, text, full: html, text
added geo accession numbers back into hg19. Everything is now almost completely up to date, although there are a few minor inconsistencies
- lines changed 1039, context: html, text, full: html, text
added in expIds and accessions
- lines changed 1285, context: html, text, full: html, text
added in new metadata for cshl long
- lines changed 85, context: html, text, full: html, text
added in expIds and dcc accessions
- lines changed 478, context: html, text, full: html, text
renamed tracks, and added in some new stanzas
- lines changed 506, context: html, text, full: html, text
renaming more stuff to make donor cell lines consistent
- lines changed 429, context: html, text, full: html, text
last of the renamed for donor cell lines
- lines changed 71, context: html, text, full: html, text
added in known expIds and accessions
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlShortRnaSeq.ra
- lines changed 266, context: html, text, full: html, text
added geo accession numbers back into hg19. Everything is now almost completely up to date, although there are a few minor inconsistencies
- lines changed 883, context: html, text, full: html, text
added in new cshl short tracks
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibRnaSeq.ra
- lines changed 129, context: html, text, full: html, text
forgot to add accessions for haib rna seq, so thats in now too
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeRikenCage.ra
- lines changed 312, context: html, text, full: html, text
added geo accession numbers back into hg19. Everything is now almost completely up to date, although there are a few minor inconsistencies
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhHistone.ra
- lines changed 11, context: html, text, full: html, text
added geo accession numbers back into hg19. Everything is now almost completely up to date, although there are a few minor inconsistencies
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhNsome.ra
- lines changed 44, context: html, text, full: html, text
added geo accession numbers back into hg19. Everything is now almost completely up to date, although there are a few minor inconsistencies
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhRnaSeq.ra
- lines changed 9, context: html, text, full: html, text
added geo accession numbers back into hg19. Everything is now almost completely up to date, although there are a few minor inconsistencies
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra
- lines changed 25, context: html, text, full: html, text
added geo accession numbers back into hg19. Everything is now almost completely up to date, although there are a few minor inconsistencies
- lines changed 1336, context: html, text, full: html, text
Updated labels, experimentIds and controlIds.
- lines changed 3, context: html, text, full: html, text
Removed dataVersion ENCODE Freeze.
- lines changed 7, context: html, text, full: html, text
Fixed the control id for dccAccession: wgEncodeEH000769. Redmine #4486.
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDgf.ra
- lines changed 43, context: html, text, full: html, text
added geo accession numbers back into hg19. Everything is now almost completely up to date, although there are a few minor inconsistencies
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwRepliSeq.ra
- lines changed 257, context: html, text, full: html, text
added geo accession numbers back into hg19. Everything is now almost completely up to date, although there are a few minor inconsistencies
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwTfbs.ra
- lines changed 49, context: html, text, full: html, text
added geo accession numbers back into hg19. Everything is now almost completely up to date, although there are a few minor inconsistencies
- src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeRikenCage.ra
- lines changed 312, context: html, text, full: html, text
Morgan added new geoAccession numbers (redmine #6579)
- src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeSydhTfbs.ra
- lines changed 11224, context: html, text, full: html, text
staging SYDH TFBS (Release 2) on beta, redmine# 4486
- src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeRikenCage.ra
- lines changed 10626, context: html, text, full: html, text
Releasing RIKEN CAGE Loc (Release 3) to the RR (redmine #6579)
- src/hg/makeDb/trackDb/human/hg19/trackDb.ra
- lines changed 18, context: html, text, full: html, text
add a track for skunk-works project
- src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
- lines changed 2, context: html, text, full: html, text
Releasing RIKEN CAGE Loc (Release 3) to the RR (redmine #6579)
- lines changed 2, context: html, text, full: html, text
adding in patch release for label change
- lines changed 2, context: html, text, full: html, text
staging SYDH TFBS (Release 2) on beta, redmine# 4486
- src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.release2.html
- lines changed 2, context: html, text, full: html, text
added in new notes and html changers for cshl long
- src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.release2.ra
- lines changed 56, context: html, text, full: html, text
renamed tracks, and added in some new stanzas
- lines changed 18, context: html, text, full: html, text
renaming more stuff to make donor cell lines consistent
- src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.release3.ra
- lines changed 623, context: html, text, full: html, text
removing gunked comment lines
- lines changed 578, context: html, text, full: html, text
removing double newlines
- lines changed 8, context: html, text, full: html, text
removing experiment meant for attic
- lines changed 487, context: html, text, full: html, text
redoing last 2 commits on this file correctly
- lines changed 307, context: html, text, full: html, text
changed labels to reflect that things are raw signals
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibRnaSeq.patch.ra
- lines changed 870, context: html, text, full: html, text
adding in patch release for label change
- lines changed 45, context: html, text, full: html, text
moved signal over to raw signal
- src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromChip.release2.html
- src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.release3.html
- lines changed 4, context: html, text, full: html, text
fixed stuff at qa requests
- src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.release3.ra
- lines changed 11, context: html, text, full: html, text
fixed stuff at qa requests
- src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.release2.html
- lines changed 5, context: html, text, full: html, text
Updated labels, experimentIds and controlIds.
- lines changed 1, context: html, text, full: html, text
Added notes files for Release 2 and made release3 ra file. Redmine #4486, #7510.
- src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.release2.ra
- lines changed 722, context: html, text, full: html, text
long labels for sydh tfbs
- lines changed 171, context: html, text, full: html, text
fixed short labels for sydh tfbs
- lines changed 76, context: html, text, full: html, text
Updated labels, experimentIds and controlIds.
- src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.release3.ra
- lines changed 6922, context: html, text, full: html, text
Added notes files for Release 2 and made release3 ra file. Redmine #4486, #7510.
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeCaltechHist.ra
- lines changed 47, context: html, text, full: html, text
added geo accession numbers to mm9. As with hg19, its not quite comprehensive but its very close
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeCaltechTfbs.ra
- lines changed 93, context: html, text, full: html, text
added geo accession numbers to mm9. As with hg19, its not quite comprehensive but its very close
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra
- lines changed 171, context: html, text, full: html, text
added geo accession numbers to mm9. As with hg19, its not quite comprehensive but its very close
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrTfbs.ra
- lines changed 222, context: html, text, full: html, text
added geo accession numbers to mm9. As with hg19, its not quite comprehensive but its very close
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodePsuHistone.ra
- lines changed 102, context: html, text, full: html, text
Removed date unrestricted for PSU Experiments referenced from paper in Publications section. Redmine #7515.
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodePsuTfbs.ra
- lines changed 179, context: html, text, full: html, text
added geo accession numbers to mm9. As with hg19, its not quite comprehensive but its very close
- lines changed 96, context: html, text, full: html, text
Removed date unrestricted for PSU Experiments referenced from paper in Publications section. Redmine #7515.
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhTfbs.ra
- lines changed 169, context: html, text, full: html, text
added geo accession numbers to mm9. As with hg19, its not quite comprehensive but its very close
- lines changed 106, context: html, text, full: html, text
correct lab name from Stanford to Stanford-m
- lines changed 106, context: html, text, full: html, text
Revert "correct lab name from Stanford to Stanford-m"mistakenly changed Yale-m to Stanford-m when changing all the Stanford to Stanford-m, trying to revert this change
This reverts commit b12191e5ac5ef581be4e9ce8df8d541654d6d99a.
- lines changed 94, context: html, text, full: html, text
change lab=Stanford to lab=Stanford-m
- lines changed 18, context: html, text, full: html, text
set controlId for their corresponding treatment datasets
- lines changed 358, context: html, text, full: html, text
add controlId to their corresponding treated datasets
- lines changed 376, context: html, text, full: html, text
change controlId from expId to ucsc accession
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeUwDgf.ra
- lines changed 1185, context: html, text, full: html, text
Added 8 submissions for the track. Redmine #3631.
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeUwDnase.ra
- lines changed 132, context: html, text, full: html, text
Renamed original replicate 1 to replicate 2 and laoded new replicate 1. Redmine #4468.
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/wgEncodeLicrRnaSeq.ra
- lines changed 135, context: html, text, full: html, text
staging updated metadata; venkat added readType and GeoSeriesAccession, redmine #6476
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/public/makefile
- lines changed 1, context: html, text, full: html, text
releasing mm9 Caltech RNA-seq, redmine #4156
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/public/wgEncodeCaltechRnaSeq.ra
- lines changed 578, context: html, text, full: html, text
releasing mm9 Caltech RNA-seq, redmine #4156
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/public/wgEncodeLicrRnaSeq.ra
- lines changed 2340, context: html, text, full: html, text
releasing LICR RNA-seq (Release 2), redmine #6476
- src/hg/makeDb/trackDb/mouse/mm9/trackDb.wgEncode.ra
- lines changed 2, context: html, text, full: html, text
releasing LICR RNA-seq (Release 2), redmine #6476
- lines changed 1, context: html, text, full: html, text
releasing mm9 Caltech RNA-seq, redmine #4156
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCaltechRnaSeq.release1.html
- lines changed 4, context: html, text, full: html, text
removing 'All Reads' from Raw Signals and making polishing up 'Unique Reads' clarificaiton for the Signals, redmine #6476
- lines changed 4, context: html, text, full: html, text
changing instances of RNA-Seq to RNA-seq (except in journal titles where the title actually has it that way), redmine #4156
- lines changed 18, context: html, text, full: html, text
remove download file section
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCaltechRnaSeq.release1.ra
- lines changed 17, context: html, text, full: html, text
removing 'All Reads' from Raw Signals and making polishing up 'Unique Reads' clarificaiton for the Signals, redmine #6476
- lines changed 1, context: html, text, full: html, text
adding a setting, off, to the bamColorMode tag in the Alignments view because it was lacking one, redmine #4156
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrRnaSeq.release2.html
- lines changed 1, context: html, text, full: html, text
adding missing period, redmine #6476
- lines changed 3, context: html, text, full: html, text
changing RNA-Seq to RNA-seq, redmine #6476
- lines changed 1, context: html, text, full: html, text
moving period to inside the html tag, redmine #6476
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrRnaSeq.release2.ra
- lines changed 1, context: html, text, full: html, text
added a setting to the bamColorMode tag so that the 'Aditional coloring modes' section of the Alignments configuration box would have a default selection and the alignments wouldn't just be in black as they had been, redmine 6476
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwDgf.ra
- lines changed 357, context: html, text, full: html, text
Added 8 submissions for the track. Redmine #3631.
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwDnase.release2.ra
- lines changed 42, context: html, text, full: html, text
Renamed original replicate 1 to replicate 2 and laoded new replicate 1. Redmine #4468.
- src/hg/makeDb/trackDb/trackDb.ra
- lines changed 3, context: html, text, full: html, text
pubsMarker tracks are in fact bed 5 not bed 4 (I'm also removing redundant bedSize = 5 from the code)
- src/hg/makeDb/trackDb/wallaby/macEug1/description.html
- lines changed 2, context: html, text, full: html, text
fixed bounding box around image to allow full width
- src/hg/makeDb/trackDb/wallaby/macEug2/description.html
- lines changed 1, context: html, text, full: html, text
fixed bounding box around image to allow full width
- src/hg/makefile
- lines changed 4, context: html, text, full: html, text
Merge branch 'master' into chinhli-hgLogin
- src/hg/oneShot/encodeExpToCvDb/doIt
- lines changed 1, context: html, text, full: html, text
Renaming a few files for consistency.
- src/hg/oneShot/encodeExpToCvDb/encodeExpToCvDb.c
- lines changed 4, context: html, text, full: html, text
Renaming a few files for consistency.
- src/hg/oneShot/encodeExpToCvDb/exp.sql
- lines changed 36, context: html, text, full: html, text
Renaming a few files for consistency.
- src/hg/oneShot/encodeExpToCvDb/experiment.sql
- lines changed 36, context: html, text, full: html, text
Renaming a few files for consistency.
- src/hg/oneShot/encodeExpToCvDb/go
- lines changed 5, context: html, text, full: html, text
Renaming a few files for consistency.
- src/hg/oneShot/encodeExpToCvDb/result.sql
- lines changed 13, context: html, text, full: html, text
Renaming a few files for consistency.
- src/hg/oneShot/encodeExpToCvDb/results.sql
- lines changed 13, context: html, text, full: html, text
Renaming a few files for consistency.
- src/hg/oneShot/testCvToSql/testCvToSql.c
- lines changed 7, context: html, text, full: html, text
Changed cellLine to cellType in most of output.
- src/hg/utils/automation/doSameSpeciesLiftOver.pl
- lines changed 16, context: html, text, full: html, text
allow /hive/data/genomes/ to satisify the patch to the 2bit files
- src/hg/utils/automation/doWindowMasker.pl
- lines changed 38, context: html, text, full: html, text
adding the bits that used to be done manually after it was finished, cleaning the sequence of gaps
- src/hg/utils/omim/checkOmim.sh
- lines changed 2, context: html, text, full: html, text
add upload to OMIM as part of the otto tasks. #6493
- src/hg/utils/omim/checkOmimUpload.sh
- lines changed 80, context: html, text, full: html, text
add upload to OMIM as part of the otto tasks. #6493
- src/hg/utils/omim/makefile
- lines changed 1, context: html, text, full: html, text
add upload to OMIM as part of the otto tasks. #6493
- src/hg/utils/omim/omimUploadWrapper.sh
- lines changed 9, context: html, text, full: html, text
add upload to OMIM as part of the otto tasks. #6493
- src/inc/common.h
- lines changed 4, context: html, text, full: html, text
Make sqlList.c dynamic arrays thread-safe. Fixes bug in bigBed reported by user #7850.
- src/inc/htmshell.h
- lines changed 7, context: html, text, full: html, text
Finished Greg's Login UI.
- lines changed 4, context: html, text, full: html, text
UI themes for hgc/hgGene and some fixes for hgTracks
- lines changed 12, context: html, text, full: html, text
fixed conflict with chins stylesheet function. A better long-term solution would be to introduce functions like addStylesheet to htmshell and keep a list of stylesheets instead of 3 diff functions
- src/inc/sqlNum.h
- lines changed 36, context: html, text, full: html, text
Make sqlList.c dynamic arrays thread-safe. Fixes bug in bigBed reported by user #7850.
- src/kehayden/alphaChain/alphaChain.c
- lines changed 113, context: html, text, full: html, text
Getting rid of dummy nodes. Output looking more reasonable, but still not 100%.
- lines changed 103, context: html, text, full: html, text
Further work on faux-generation side. Getting close but not quite perfect.
- lines changed 171, context: html, text, full: html, text
Refactoring to get rid of rbTrees, and replace with simple children lists.
- lines changed 95, context: html, text, full: html, text
When we use up our target out count, revert to original input counts when making random choices.
- src/kehayden/alphaChain/doIt
- lines changed 1, context: html, text, full: html, text
Getting rid of dummy nodes. Output looking more reasonable, but still not 100%.
- lines changed 1, context: html, text, full: html, text
Further work on faux-generation side. Getting close but not quite perfect.
- lines changed 1, context: html, text, full: html, text
When we use up our target out count, revert to original input counts when making random choices.
- src/kehayden/alphaChain/sample.txt
- lines changed 10, context: html, text, full: html, text
Further work on faux-generation side. Getting close but not quite perfect.
- src/kehayden/alphaChain/sampleIt
- lines changed 1, context: html, text, full: html, text
Further work on faux-generation side. Getting close but not quite perfect.
- lines changed 1, context: html, text, full: html, text
When we use up our target out count, revert to original input counts when making random choices.
- src/lib/common.c
- lines changed 17, context: html, text, full: html, text
Make sqlList.c dynamic arrays thread-safe. Fixes bug in bigBed reported by user #7850.
- src/lib/htmshell.c
- lines changed 21, context: html, text, full: html, text
Finished generate userAccount.css in HEAD and class='userAccount' attributes in BODY.
- lines changed 4, context: html, text, full: html, text
Finished Greg's Login UI.
- lines changed 12, context: html, text, full: html, text
UI themes for hgc/hgGene and some fixes for hgTracks
- lines changed 33, context: html, text, full: html, text
fixed conflict with chins stylesheet function. A better long-term solution would be to introduce functions like addStylesheet to htmshell and keep a list of stylesheets instead of 3 diff functions
- src/lib/sqlList.c
- lines changed 243, context: html, text, full: html, text
Make sqlList.c dynamic arrays thread-safe. Fixes bug in bigBed reported by user #7850.
- src/lib/sqlNum.c
- lines changed 173, context: html, text, full: html, text
Make sqlList.c dynamic arrays thread-safe. Fixes bug in bigBed reported by user #7850.
- src/utils/qa/makefile
- src/utils/qa/qaGbTracks
- lines changed 76, context: html, text, full: html, text
Started using new classes in ucscgenomics/qa/tables and started putting things into functions.
- lines changed 5, context: html, text, full: html, text
Got the validate methods mostly working. For calls to command-line programs, output is sent to the error log file and 'pass' or 'ERROR' is printed, depending on the return code. Still need to keep track of whether or not errors occurred for summary file.
- lines changed 31, context: html, text, full: html, text
Added summary module for making tab-separated summary output for table QA. Also made qaGbTracks make 3 different files. The .chrom output is just using the tableCheck countPerChrom function for now.
- lines changed 28, context: html, text, full: html, text
Tweaked description, changed outFile variable name, put delimter line in a variable.
- src/utils/qa/weeklybld/buildEnv.csh
- lines changed: 82098
- files changed: 400
