All File Changes

v297_preview to v297_preview2 (2014-03-03 to 2014-03-10) v297

• src/hg/encode/hgEncodeApi/hgEncodeApi.c
  • lines changed 3, context: html, text, full: html, text
    Avoid displaying deaccessioned experiments in ENCODE Experiment Matrix. Prompted by deaccessioning of Mouse 3324. refs #10465
• src/hg/encode3/encodeDataWarehouse/oneShot/edwFakeEncode2Submit/edwFakeEncode2Submit.c
  • lines changed 184, context: html, text, full: html, text
    Second cut of edwFakeEncode2Submit.c for Stanford issue 1079,because the requirements had been changed, so the git diff will
    produce a huge delta. Most verbose statements will be eventually
    removed from the source.
    
  • lines changed 4, context: html, text, full: html, text
    Remove duplicate creation of edwSubmit rows statements
• src/hg/hgBlat/hgBlat.c
  • lines changed 1, context: html, text, full: html, text
    now converting hgsid and hguid to strings. when the hgsid cart var or hguid cookie is not found it returns NULL instead of 0.
  • lines changed 13, context: html, text, full: html, text
    fixing hgBlat not working in browserbox if hg19.2bit does not exist,refs #11957
    
• src/hg/hgCustom/hgCustom.c
  • lines changed 2, context: html, text, full: html, text
    Adding possibility to paste URLs of bam/bigWig/bigbed, without acustom track header line, into the hgCustom upload box (refs #12813)
    
• src/hg/hgFileUi/hgFileUi.c
  • lines changed 1, context: html, text, full: html, text
    now converting hgsid and hguid to strings. when the hgsid cart var or hguid cookie is not found it returns NULL instead of 0.
• src/hg/hgGateway/hgGateway.c
  • lines changed 8, context: html, text, full: html, text
    Adding better handling of auto-upgrade for the situation where simultaneous CGIs would try to all upgrade at once. It uses an advisory lock to make sure only one process is trying to upgrade at a time, and it checks again that the field does not exist already before adding the new sessionkey field, it writes the result of success or failure with the error message to a TRASH file so that other CGIs may access it. To prevent them all from repeatedly trying to do the same upgrade with every CGI execution, it checks the time-stamp on the AUTOUPGRADE trash file, and if it is older than 3 minutes, then it will try again to see if the admins have given it the permissions needed - which will then re-write the trash file with the results and its time will be updated. If an error occurs during sql upgrade, it traps the error instead of errAborting and the message is saved to be included in the trash file, and the system proceeds for now without the new sessionKey field.
  • lines changed 1, context: html, text, full: html, text
    Fixing compiler warning for stricter format checkers (don't use variable in place of format argument).
• src/hg/hgGene/hgGeneData/Human/hg38/links.ra
  • lines changed 25, context: html, text, full: html, text
    gene page stuff for hgGene on hg38
• src/hg/hgGene/hgGeneData/Human/hg38/otherOrgs.ra
  • lines changed 17, context: html, text, full: html, text
    gene page stuff for hgGene on hg38
• src/hg/hgGene/hgGeneData/Human/hg38/section.ra
  • lines changed 9, context: html, text, full: html, text
    gene page stuff for hgGene on hg38
• src/hg/hgGene/rnaStructure.c
  • lines changed 26, context: html, text, full: html, text
    Fixing RNAplot problem with newer versions, refs #11957, note 178 andrefs #6382
    
• src/hg/hgMirror/hgMirror
  • lines changed 12, context: html, text, full: html, text
    adding basic security of CGI parameters to hgMirror
• src/hg/hgSession/hgSession.c
  • lines changed 1, context: html, text, full: html, text
    Last little compile failures from changing hgsid to char * for new secure web ids. The problem was hidden because hgSession had makefile with HGWARN turned off. Angie will fix that.
• src/hg/hgSession/makefile
  • lines changed 2, context: html, text, full: html, text
    hgSession/makefile had an override of HG_WARN that prevented compilewarning from halting the build -- oops!
    
• src/hg/hgTables/bam.c
  • lines changed 2, context: html, text, full: html, text
    Adding support for plain VCF custom tracks (as opposed to VCF+tabix),since users seem to want to upload VCF, and as long as the file is
    not too big it will work OK. This means adding a new track type
    vcf (as opposed to vcfTabix) and supporting it in hgTracks, hgTrackUi,
    hgc, hgTables and hgVai. (and others I've forgotten?)
    refs #12416
    
• src/hg/hgTables/bedList.c
  • lines changed 4, context: html, text, full: html, text
    Adding support for plain VCF custom tracks (as opposed to VCF+tabix),since users seem to want to upload VCF, and as long as the file is
    not too big it will work OK. This means adding a new track type
    vcf (as opposed to vcfTabix) and supporting it in hgTracks, hgTrackUi,
    hgc, hgTables and hgVai. (and others I've forgotten?)
    refs #12416
    
• src/hg/hgTables/filterFields.c
  • lines changed 12, context: html, text, full: html, text
    Adding support for plain VCF custom tracks (as opposed to VCF+tabix),since users seem to want to upload VCF, and as long as the file is
    not too big it will work OK. This means adding a new track type
    vcf (as opposed to vcfTabix) and supporting it in hgTracks, hgTrackUi,
    hgc, hgTables and hgVai. (and others I've forgotten?)
    refs #12416
    
• src/hg/hgTables/galaxy.c
  • lines changed 8, context: html, text, full: html, text
    now converting hgsid and hguid to strings. when the hgsid cart var or hguid cookie is not found it returns NULL instead of 0.
• src/hg/hgTables/great.c
  • lines changed 3, context: html, text, full: html, text
    now converting hgsid and hguid to strings. when the hgsid cart var or hguid cookie is not found it returns NULL instead of 0.
• src/hg/hgTables/hgTables.c
  • lines changed 11, context: html, text, full: html, text
    Adding support for plain VCF custom tracks (as opposed to VCF+tabix),since users seem to want to upload VCF, and as long as the file is
    not too big it will work OK. This means adding a new track type
    vcf (as opposed to vcfTabix) and supporting it in hgTracks, hgTrackUi,
    hgc, hgTables and hgVai. (and others I've forgotten?)
    refs #12416
    
• src/hg/hgTables/hgTables.h
  • lines changed 12, context: html, text, full: html, text
    Adding support for plain VCF custom tracks (as opposed to VCF+tabix),since users seem to want to upload VCF, and as long as the file is
    not too big it will work OK. This means adding a new track type
    vcf (as opposed to vcfTabix) and supporting it in hgTracks, hgTrackUi,
    hgc, hgTables and hgVai. (and others I've forgotten?)
    refs #12416
    
• src/hg/hgTables/identifiers.c
  • lines changed 4, context: html, text, full: html, text
    Adding support for plain VCF custom tracks (as opposed to VCF+tabix),since users seem to want to upload VCF, and as long as the file is
    not too big it will work OK. This means adding a new track type
    vcf (as opposed to vcfTabix) and supporting it in hgTracks, hgTrackUi,
    hgc, hgTables and hgVai. (and others I've forgotten?)
    refs #12416
    
• src/hg/hgTables/intersect.c
  • lines changed 1, context: html, text, full: html, text
    Adding support for plain VCF custom tracks (as opposed to VCF+tabix),since users seem to want to upload VCF, and as long as the file is
    not too big it will work OK. This means adding a new track type
    vcf (as opposed to vcfTabix) and supporting it in hgTracks, hgTrackUi,
    hgc, hgTables and hgVai. (and others I've forgotten?)
    refs #12416
    
• src/hg/hgTables/joining.c
  • lines changed 3, context: html, text, full: html, text
    Adding support for plain VCF custom tracks (as opposed to VCF+tabix),since users seem to want to upload VCF, and as long as the file is
    not too big it will work OK. This means adding a new track type
    vcf (as opposed to vcfTabix) and supporting it in hgTracks, hgTrackUi,
    hgc, hgTables and hgVai. (and others I've forgotten?)
    refs #12416
    
• src/hg/hgTables/mainPage.c
  • lines changed 1, context: html, text, full: html, text
    Adding support for plain VCF custom tracks (as opposed to VCF+tabix),since users seem to want to upload VCF, and as long as the file is
    not too big it will work OK. This means adding a new track type
    vcf (as opposed to vcfTabix) and supporting it in hgTracks, hgTrackUi,
    hgc, hgTables and hgVai. (and others I've forgotten?)
    refs #12416
    
• src/hg/hgTables/schema.c
  • lines changed 4, context: html, text, full: html, text
    Adding support for plain VCF custom tracks (as opposed to VCF+tabix),since users seem to want to upload VCF, and as long as the file is
    not too big it will work OK. This means adding a new track type
    vcf (as opposed to vcfTabix) and supporting it in hgTracks, hgTrackUi,
    hgc, hgTables and hgVai. (and others I've forgotten?)
    refs #12416
    
• src/hg/hgTables/vcf.c
  • lines changed 67, context: html, text, full: html, text
    Adding support for plain VCF custom tracks (as opposed to VCF+tabix),since users seem to want to upload VCF, and as long as the file is
    not too big it will work OK. This means adding a new track type
    vcf (as opposed to vcfTabix) and supporting it in hgTracks, hgTrackUi,
    hgc, hgTables and hgVai. (and others I've forgotten?)
    refs #12416
    
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 7, context: html, text, full: html, text
    now converting hgsid and hguid to strings. when the hgsid cart var or hguid cookie is not found it returns NULL instead of 0.
• src/hg/hgTracks/config.c
  • lines changed 3, context: html, text, full: html, text
    now converting hgsid and hguid to strings. when the hgsid cart var or hguid cookie is not found it returns NULL instead of 0.
• src/hg/hgTracks/hgTracks.c
  • lines changed 8, context: html, text, full: html, text
    now converting hgsid and hguid to strings. when the hgsid cart var or hguid cookie is not found it returns NULL instead of 0.
  • lines changed 7, context: html, text, full: html, text
    Adding support for plain VCF custom tracks (as opposed to VCF+tabix),since users seem to want to upload VCF, and as long as the file is
    not too big it will work OK. This means adding a new track type
    vcf (as opposed to vcfTabix) and supporting it in hgTracks, hgTrackUi,
    hgc, hgTables and hgVai. (and others I've forgotten?)
    refs #12416
    
• src/hg/hgTracks/hgTracks.h
  • lines changed 3, context: html, text, full: html, text
    Adding support for plain VCF custom tracks (as opposed to VCF+tabix),since users seem to want to upload VCF, and as long as the file is
    not too big it will work OK. This means adding a new track type
    vcf (as opposed to vcfTabix) and supporting it in hgTracks, hgTrackUi,
    hgc, hgTables and hgVai. (and others I've forgotten?)
    refs #12416
    
• src/hg/hgTracks/menu.c
  • lines changed 2, context: html, text, full: html, text
    now converting hgsid and hguid to strings. when the hgsid cart var or hguid cookie is not found it returns NULL instead of 0.
• src/hg/hgTracks/simpleTracks.c
  • lines changed 1, context: html, text, full: html, text
    now converting hgsid and hguid to strings. when the hgsid cart var or hguid cookie is not found it returns NULL instead of 0.
  • lines changed 6, context: html, text, full: html, text
    Adding support for plain VCF custom tracks (as opposed to VCF+tabix),since users seem to want to upload VCF, and as long as the file is
    not too big it will work OK. This means adding a new track type
    vcf (as opposed to vcfTabix) and supporting it in hgTracks, hgTrackUi,
    hgc, hgTables and hgVai. (and others I've forgotten?)
    refs #12416
    
  • lines changed 2, context: html, text, full: html, text
    RM 12824 fix display of names in GENCODE 2-way pseudogenes
• src/hg/hgTracks/variation.c
  • lines changed 4, context: html, text, full: html, text
    now converting hgsid and hguid to strings. when the hgsid cart var or hguid cookie is not found it returns NULL instead of 0.
  • lines changed 1, context: html, text, full: html, text
    Fixed a typo that caused hgTracks to ignore settings for coloringSNPs by exceptions. Thanks Brian L!
    fixes #12793
    
• src/hg/hgTracks/vcfTrack.c
  • lines changed 95, context: html, text, full: html, text
    Adding support for plain VCF custom tracks (as opposed to VCF+tabix),since users seem to want to upload VCF, and as long as the file is
    not too big it will work OK. This means adding a new track type
    vcf (as opposed to vcfTabix) and supporting it in hgTracks, hgTrackUi,
    hgc, hgTables and hgVai. (and others I've forgotten?)
    refs #12416
    
  • lines changed 12, context: html, text, full: html, text
    In addition to trimming the left padding base from VCF indels,now we trim identical bases on the right of all alleles, if there
    are any. I've seen multiple cases of user VCF with indels that
    have inflated size due to including right flanking bases; when
    trying to determine functional consequences, it's misleading to
    have an indel sized larger than it has to be.
    
• src/hg/hgVai/hgVai.c
  • lines changed 4, context: html, text, full: html, text
    Adding support for plain VCF custom tracks (as opposed to VCF+tabix),since users seem to want to upload VCF, and as long as the file is
    not too big it will work OK. This means adding a new track type
    vcf (as opposed to vcfTabix) and supporting it in hgTracks, hgTrackUi,
    hgc, hgTables and hgVai. (and others I've forgotten?)
    refs #12416
    
• src/hg/hgVai/libifyMe.c
  • lines changed 5, context: html, text, full: html, text
    Adding support for plain VCF custom tracks (as opposed to VCF+tabix),since users seem to want to upload VCF, and as long as the file is
    not too big it will work OK. This means adding a new track type
    vcf (as opposed to vcfTabix) and supporting it in hgTracks, hgTrackUi,
    hgc, hgTables and hgVai. (and others I've forgotten?)
    refs #12416
    
• src/hg/hgc/hgc.c
  • lines changed 6, context: html, text, full: html, text
    now converting hgsid and hguid to strings. when the hgsid cart var or hguid cookie is not found it returns NULL instead of 0.
  • lines changed 4, context: html, text, full: html, text
    Adding support for plain VCF custom tracks (as opposed to VCF+tabix),since users seem to want to upload VCF, and as long as the file is
    not too big it will work OK. This means adding a new track type
    vcf (as opposed to vcfTabix) and supporting it in hgTracks, hgTrackUi,
    hgc, hgTables and hgVai. (and others I've forgotten?)
    refs #12416
    
  • lines changed 2, context: html, text, full: html, text
    were not correctly identifying on name2 in ensGene table refs #12796
• src/hg/hgc/hgc.h
  • lines changed 3, context: html, text, full: html, text
    Adding support for plain VCF custom tracks (as opposed to VCF+tabix),since users seem to want to upload VCF, and as long as the file is
    not too big it will work OK. This means adding a new track type
    vcf (as opposed to vcfTabix) and supporting it in hgTracks, hgTrackUi,
    hgc, hgTables and hgVai. (and others I've forgotten?)
    refs #12416
    
• src/hg/hgc/pubs.c
  • lines changed 1, context: html, text, full: html, text
    now converting hgsid and hguid to strings. when the hgsid cart var or hguid cookie is not found it returns NULL instead of 0.
• src/hg/hgc/vcfClick.c
  • lines changed 59, context: html, text, full: html, text
    Adding support for plain VCF custom tracks (as opposed to VCF+tabix),since users seem to want to upload VCF, and as long as the file is
    not too big it will work OK. This means adding a new track type
    vcf (as opposed to vcfTabix) and supporting it in hgTracks, hgTrackUi,
    hgc, hgTables and hgVai. (and others I've forgotten?)
    refs #12416
    
  • lines changed 1, context: html, text, full: html, text
    In addition to trimming the left padding base from VCF indels,now we trim identical bases on the right of all alleles, if there
    are any. I've seen multiple cases of user VCF with indels that
    have inflated size due to including right flanking bases; when
    trying to determine functional consequences, it's misleading to
    have an indel sized larger than it has to be.
    
• src/hg/htdocs/ENCODE/pubsOther.html
  • lines changed 849, context: html, text, full: html, text
    Adding ENCODE pubs to pubsOther.html from Mike Pazin request, more to come
  • lines changed 1154, context: html, text, full: html, text
    Adding more publications to ENCODE community per Mike Pazin, and cleaning format
• src/hg/htdocs/FAQ/FAQreleases.html
  • lines changed 2, context: html, text, full: html, text
    Added hg38 to release list.
• src/hg/htdocs/goldenPath/credits.html
  • lines changed 2, context: html, text, full: html, text
    Added hg38 to human credits section (redmine #11681)
• src/hg/htdocs/goldenPath/help/customTrackText.html
  • lines changed 8, context: html, text, full: html, text
    changing documentation to reflect previous code commit
• src/hg/htdocs/goldenPath/help/gbib.html
  • lines changed 16, context: html, text, full: html, text
    better gbib help file, refs #11957
• src/hg/htdocs/goldenPath/help/hgTracksHelp.html
  • lines changed 1, context: html, text, full: html, text
    added html anchor to highlighting region section
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 31, context: html, text, full: html, text
    added announcement for new highlight feature, moved item to archives section
  • lines changed 108, context: html, text, full: html, text
    Added hg38 announcement.
• src/hg/htdocs/images/highlight_screenshot.png
  • lines changed 0, context: html, text, full: html, text
    adding highlight screenshot for news announcement
• src/hg/htdocs/inc/globalNavBar.inc
  • lines changed 24, context: html, text, full: html, text
    moving About Us link to the end of the top bluebar. Refs #12121
• src/hg/htdocs/indexNews.html
  • lines changed 69, context: html, text, full: html, text
    added announcement for new highlight feature, moved item to archives section
  • lines changed 161, context: html, text, full: html, text
    Added hg38 announcement.
  • lines changed 6, context: html, text, full: html, text
    Modified info about Karen Miga's work, per input from Karen + Jim.
• src/hg/htdocs/style/nice_menu.css
  • lines changed 1, context: html, text, full: html, text
    Simplest, most transparent fix for Redmine #12122.
• src/hg/inc/cart.h
  • lines changed 6, context: html, text, full: html, text
    now converting hgsid and hguid to strings. when the hgsid cart var or hguid cookie is not found it returns NULL instead of 0.
• src/hg/inc/cartDb.h
  • lines changed 7, context: html, text, full: html, text
    initial work on creating a random session key for greater securiy of cart data
  • lines changed 6, context: html, text, full: html, text
    now converting hgsid and hguid to strings. when the hgsid cart var or hguid cookie is not found it returns NULL instead of 0.
  • lines changed 3, context: html, text, full: html, text
    adding random sessionKey generation
• src/hg/inc/cgiApoptosis.h
  • lines changed 19, context: html, text, full: html, text
    moving the phoneHome business into cgiApoptosis.c/.h to make it callablefrom cart.c. We need to call it from cart.c as otherwise
    cgiApoptosisSetup (originally: phoneHome) will be called after mysql
    connections are opened. This leads to "mysql server has gone away" if
    any CGI is not faster than the child process forked here. The child will
    close all mysql connections of the parent process. With the new setup,
    the childi is forked before any mysql connections are opened. Ideally
    this would be all done in cheapcgi, but cheapcgi is not in the hg/lib
    part of the code.
    
• src/hg/inc/customPp.h
  • lines changed 5, context: html, text, full: html, text
    Adding support for plain VCF custom tracks (as opposed to VCF+tabix),since users seem to want to upload VCF, and as long as the file is
    not too big it will work OK. This means adding a new track type
    vcf (as opposed to vcfTabix) and supporting it in hgTracks, hgTrackUi,
    hgc, hgTables and hgVai. (and others I've forgotten?)
    refs #12416
    
• src/hg/inc/customTrack.h
  • lines changed 8, context: html, text, full: html, text
    Adding possibility to paste URLs of bam/bigWig/bigbed, without acustom track header line, into the hgCustom upload box (refs #12813)
    
• src/hg/inc/encode/encodeExp.h
  • lines changed 3, context: html, text, full: html, text
    Avoid displaying deaccessioned experiments in ENCODE Experiment Matrix. Prompted by deaccessioning of Mouse 3324. refs #10465
• src/hg/inc/hdb.h
  • lines changed 3, context: html, text, full: html, text
    moving the phoneHome business into cgiApoptosis.c/.h to make it callablefrom cart.c. We need to call it from cart.c as otherwise
    cgiApoptosisSetup (originally: phoneHome) will be called after mysql
    connections are opened. This leads to "mysql server has gone away" if
    any CGI is not faster than the child process forked here. The child will
    close all mysql connections of the parent process. With the new setup,
    the childi is forked before any mysql connections are opened. Ideally
    this would be all done in cheapcgi, but cheapcgi is not in the hg/lib
    part of the code.
    
  • lines changed 3, context: html, text, full: html, text
    Allow special value HTTPHOST for central.domain and wiki.host, so aserver can be reached under multiple names. Might be a good default
    value for our example hg.conf? refs #11957
    
• src/hg/inc/trackDb.h
  • lines changed 1, context: html, text, full: html, text
    Adding support for plain VCF custom tracks (as opposed to VCF+tabix),since users seem to want to upload VCF, and as long as the file is
    not too big it will work OK. This means adding a new track type
    vcf (as opposed to vcfTabix) and supporting it in hgTracks, hgTrackUi,
    hgc, hgTables and hgVai. (and others I've forgotten?)
    refs #12416
    
• src/hg/inc/wikiLink.h
  • lines changed 4, context: html, text, full: html, text
    Last little compile failures from changing hgsid to char * for new secure web ids. The problem was hidden because hgSession had makefile with HGWARN turned off. Angie will fix that.
• src/hg/js/hgTracks.js
  • lines changed 17, context: html, text, full: html, text
    Adding hgsid back into the visible (shortened URL). Occassoinally this URL is used automatically by the browser/history plugin to refresh the page. The result was multiplying cart sessions. Redmine #12819. Also in this check-in, changes by Ted Goldstein to replace regex pattern mapping with standard js calls. This should have no functional effect on our browser, othere than allowing redirections from MedBook to work.
  • lines changed 5, context: html, text, full: html, text
    Fixed bug in Ted's changes that did not set the classes correctly. Redmine #12829.
• src/hg/lib/annoGratorGpVar.c
  • lines changed 17, context: html, text, full: html, text
    In addition to trimming the left padding base from VCF indels,now we trim identical bases on the right of all alleles, if there
    are any. I've seen multiple cases of user VCF with indels that
    have inflated size due to including right flanking bases; when
    trying to determine functional consequences, it's misleading to
    have an indel sized larger than it has to be.
    
• src/hg/lib/cart.c
  • lines changed 3, context: html, text, full: html, text
    initial work on creating a random session key for greater securiy of cart data
  • lines changed 96, context: html, text, full: html, text
    now converting hgsid and hguid to strings. when the hgsid cart var or hguid cookie is not found it returns NULL instead of 0.
  • lines changed 16, context: html, text, full: html, text
    adding random sessionKey generation
  • lines changed 2, context: html, text, full: html, text
    moving the phoneHome business into cgiApoptosis.c/.h to make it callablefrom cart.c. We need to call it from cart.c as otherwise
    cgiApoptosisSetup (originally: phoneHome) will be called after mysql
    connections are opened. This leads to "mysql server has gone away" if
    any CGI is not faster than the child process forked here. The child will
    close all mysql connections of the parent process. With the new setup,
    the childi is forked before any mysql connections are opened. Ideally
    this would be all done in cheapcgi, but cheapcgi is not in the hg/lib
    part of the code.
    
  • lines changed 12, context: html, text, full: html, text
    Allow special value HTTPHOST for central.domain and wiki.host, so aserver can be reached under multiple names. Might be a good default
    value for our example hg.conf? refs #11957
    
  • lines changed 4, context: html, text, full: html, text
    woke up at night and suddenly remembered that url string should be on the stack,not on the heap.
    
  • lines changed 6, context: html, text, full: html, text
    updateOne needs to use sessionKey; writeCookie needs to use the secureId instead of plain id
  • lines changed 38, context: html, text, full: html, text
    Resolved merge conflict
• src/hg/lib/cartDb.as
  • lines changed 1, context: html, text, full: html, text
    Adding better handling of auto-upgrade for the situation where simultaneous CGIs would try to all upgrade at once. It uses an advisory lock to make sure only one process is trying to upgrade at a time, and it checks again that the field does not exist already before adding the new sessionkey field, it writes the result of success or failure with the error message to a TRASH file so that other CGIs may access it. To prevent them all from repeatedly trying to do the same upgrade with every CGI execution, it checks the time-stamp on the AUTOUPGRADE trash file, and if it is older than 3 minutes, then it will try again to see if the admins have given it the permissions needed - which will then re-write the trash file with the results and its time will be updated. If an error occurs during sql upgrade, it traps the error instead of errAborting and the message is saved to be included in the trash file, and the system proceeds for now without the new sessionKey field.
• src/hg/lib/cartDb.c
  • lines changed 72, context: html, text, full: html, text
    initial work on creating a random session key for greater securiy of cart data
  • lines changed 47, context: html, text, full: html, text
    now converting hgsid and hguid to strings. when the hgsid cart var or hguid cookie is not found it returns NULL instead of 0.
  • lines changed 19, context: html, text, full: html, text
    adding random sessionKey generation
  • lines changed 30, context: html, text, full: html, text
    adding support for auto-upgrade of userDb and sessionDb tables when sessionKey field is missing
  • lines changed 153, context: html, text, full: html, text
    Adding better handling of auto-upgrade for the situation where simultaneous CGIs would try to all upgrade at once. It uses an advisory lock to make sure only one process is trying to upgrade at a time, and it checks again that the field does not exist already before adding the new sessionkey field, it writes the result of success or failure with the error message to a TRASH file so that other CGIs may access it. To prevent them all from repeatedly trying to do the same upgrade with every CGI execution, it checks the time-stamp on the AUTOUPGRADE trash file, and if it is older than 3 minutes, then it will try again to see if the admins have given it the permissions needed - which will then re-write the trash file with the results and its time will be updated. If an error occurs during sql upgrade, it traps the error instead of errAborting and the message is saved to be included in the trash file, and the system proceeds for now without the new sessionKey field.
• src/hg/lib/cartDb.sql
  • lines changed 2, context: html, text, full: html, text
    Adding better handling of auto-upgrade for the situation where simultaneous CGIs would try to all upgrade at once. It uses an advisory lock to make sure only one process is trying to upgrade at a time, and it checks again that the field does not exist already before adding the new sessionkey field, it writes the result of success or failure with the error message to a TRASH file so that other CGIs may access it. To prevent them all from repeatedly trying to do the same upgrade with every CGI execution, it checks the time-stamp on the AUTOUPGRADE trash file, and if it is older than 3 minutes, then it will try again to see if the admins have given it the permissions needed - which will then re-write the trash file with the results and its time will be updated. If an error occurs during sql upgrade, it traps the error instead of errAborting and the message is saved to be included in the trash file, and the system proceeds for now without the new sessionKey field.
• src/hg/lib/cgapAlias.sql
  • lines changed 1, context: html, text, full: html, text
    more UCSC genes changes.
• src/hg/lib/cgapBiocDesc.sql
  • lines changed 1, context: html, text, full: html, text
    more UCSC genes changes.
• src/hg/lib/cgapBiocPathway.sql
  • lines changed 1, context: html, text, full: html, text
    more UCSC genes changes.
• src/hg/lib/cgiApoptosis.c
  • lines changed 130, context: html, text, full: html, text
    moving the phoneHome business into cgiApoptosis.c/.h to make it callablefrom cart.c. We need to call it from cart.c as otherwise
    cgiApoptosisSetup (originally: phoneHome) will be called after mysql
    connections are opened. This leads to "mysql server has gone away" if
    any CGI is not faster than the child process forked here. The child will
    close all mysql connections of the parent process. With the new setup,
    the childi is forked before any mysql connections are opened. Ideally
    this would be all done in cheapcgi, but cheapcgi is not in the hg/lib
    part of the code.
    
• src/hg/lib/customFactory.c
  • lines changed 1, context: html, text, full: html, text
    improve error message about chr names refs #12821
  • lines changed 155, context: html, text, full: html, text
    Adding support for plain VCF custom tracks (as opposed to VCF+tabix),since users seem to want to upload VCF, and as long as the file is
    not too big it will work OK. This means adding a new track type
    vcf (as opposed to vcfTabix) and supporting it in hgTracks, hgTrackUi,
    hgc, hgTables and hgVai. (and others I've forgotten?)
    refs #12416
    
  • lines changed 4, context: html, text, full: html, text
    Handle blank line(s) preceding header lines that specify format.
• src/hg/lib/customPp.c
  • lines changed 16, context: html, text, full: html, text
    Adding support for plain VCF custom tracks (as opposed to VCF+tabix),since users seem to want to upload VCF, and as long as the file is
    not too big it will work OK. This means adding a new track type
    vcf (as opposed to vcfTabix) and supporting it in hgTracks, hgTrackUi,
    hgc, hgTables and hgVai. (and others I've forgotten?)
    refs #12416
    
  • lines changed 31, context: html, text, full: html, text
    Adding possibility to paste URLs of bam/bigWig/bigbed, without acustom track header line, into the hgCustom upload box (refs #12813)
    
• src/hg/lib/customTrack.c
  • lines changed 24, context: html, text, full: html, text
    Adding possibility to paste URLs of bam/bigWig/bigbed, without acustom track header line, into the hgCustom upload box (refs #12813)
    
• src/hg/lib/encode/encodeExp.c
  • lines changed 6, context: html, text, full: html, text
    Avoid displaying deaccessioned experiments in ENCODE Experiment Matrix. Prompted by deaccessioning of Mouse 3324. refs #10465
• src/hg/lib/genePred.c
  • lines changed 2, context: html, text, full: html, text
    Fixed bug in GTF to genePred conversion where an assertion was triggered when theGTF had a spliced stop codon where the exon containing the first part of the
    stop codon only consisted of the stop codon bases. For example, a two-base exon where
    with two bases are the first two bases of the stop codon.
    
  • lines changed 2, context: html, text, full: html, text
    commit 5a7542dced0497f6d08a503a95eba87619b23a8aAuthor: Mark Diekhans <markd@soe.ucsc.edu>
    Date: Wed Mar 5 19:35:34 2014 -0800
    
    Fixed bug in GTF to genePred conversion where an assertion was triggered when the
    GTF had a spliced stop codon where the exon containing the first part of the
    stop codon only consisted of the stop codon bases. For example, a two-base exon where
    with two bases are the first two bases of the stop codon. This commit handle negative
    strand case.
    
• src/hg/lib/hdb.c
  • lines changed 8, context: html, text, full: html, text
    moving the phoneHome business into cgiApoptosis.c/.h to make it callablefrom cart.c. We need to call it from cart.c as otherwise
    cgiApoptosisSetup (originally: phoneHome) will be called after mysql
    connections are opened. This leads to "mysql server has gone away" if
    any CGI is not faster than the child process forked here. The child will
    close all mysql connections of the parent process. With the new setup,
    the childi is forked before any mysql connections are opened. Ideally
    this would be all done in cheapcgi, but cheapcgi is not in the hg/lib
    part of the code.
    
  • lines changed 16, context: html, text, full: html, text
    Allow special value HTTPHOST for central.domain and wiki.host, so aserver can be reached under multiple names. Might be a good default
    value for our example hg.conf? refs #11957
    
• src/hg/lib/hgFind.c
  • lines changed 1, context: html, text, full: html, text
    now converting hgsid and hguid to strings. when the hgsid cart var or hguid cookie is not found it returns NULL instead of 0.
• src/hg/lib/jksql.c
  • lines changed 165, context: html, text, full: html, text
    browserbox changes: In refs #11957, refs #12524 and refs #12615, it wasnoted that a jksql connection can move from a db that is present only
    remotely to a db that is present again locally (main) and remotely
    (slow). QA found that this happens in the table browser. Moving existing
    code into sqlUnconnectedConn and sqlMustUseFailover. This simplifies
    sqlChangeDb, which has now two clear codepaths browserbox versus normal
    site. Also handling the case that a DB is only remote upon connect. In
    this case do connect, but with a NULL db (mysql accepts that).
    Because we accept remote-only DBs now, not enforcing a table cache anymore.
    
• src/hg/lib/keggMapDesc.sql
  • lines changed 1, context: html, text, full: html, text
    more UCSC genes changes.
• src/hg/lib/keggPathway.sql
  • lines changed 1, context: html, text, full: html, text
    more UCSC genes changes.
• src/hg/lib/knownToKeggEntrez.sql
  • lines changed 1, context: html, text, full: html, text
    more UCSC genes changes.
• src/hg/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    moving the phoneHome business into cgiApoptosis.c/.h to make it callablefrom cart.c. We need to call it from cart.c as otherwise
    cgiApoptosisSetup (originally: phoneHome) will be called after mysql
    connections are opened. This leads to "mysql server has gone away" if
    any CGI is not faster than the child process forked here. The child will
    close all mysql connections of the parent process. With the new setup,
    the childi is forked before any mysql connections are opened. Ideally
    this would be all done in cheapcgi, but cheapcgi is not in the hg/lib
    part of the code.
    
• src/hg/lib/pgSnp.c
  • lines changed 9, context: html, text, full: html, text
    Added a few tests for 0-length (insertion) variants, to avoid errAbortwhen trying to fetch sequence for empty region.
    
• src/hg/lib/scopDesc.sql
  • lines changed 1, context: html, text, full: html, text
    more UCSC genes changes.
• src/hg/lib/spMrna.sql
  • lines changed 1, context: html, text, full: html, text
    more UCSC genes changes.
• src/hg/lib/tests/annoGratorTester.c
  • lines changed 28, context: html, text, full: html, text
    In addition to trimming the left padding base from VCF indels,now we trim identical bases on the right of all alleles, if there
    are any. I've seen multiple cases of user VCF with indels that
    have inflated size due to including right flanking bases; when
    trying to determine functional consequences, it's misleading to
    have an indel sized larger than it has to be.
    
• src/hg/lib/tests/annoGratorTests.mk
  • lines changed 5, context: html, text, full: html, text
    In addition to trimming the left padding base from VCF indels,now we trim identical bases on the right of all alleles, if there
    are any. I've seen multiple cases of user VCF with indels that
    have inflated size due to including right flanking bases; when
    trying to determine functional consequences, it's misleading to
    have an indel sized larger than it has to be.
    
• src/hg/lib/tests/expected/annoGrator/vepOutIndelTrim.txt
  • lines changed 82, context: html, text, full: html, text
    In addition to trimming the left padding base from VCF indels,now we trim identical bases on the right of all alleles, if there
    are any. I've seen multiple cases of user VCF with indels that
    have inflated size due to including right flanking bases; when
    trying to determine functional consequences, it's misleading to
    have an indel sized larger than it has to be.
    
• src/hg/lib/tests/input/annoGrator/indelTrim.vcf
  • lines changed 17, context: html, text, full: html, text
    In addition to trimming the left padding base from VCF indels,now we trim identical bases on the right of all alleles, if there
    are any. I've seen multiple cases of user VCF with indels that
    have inflated size due to including right flanking bases; when
    trying to determine functional consequences, it's misleading to
    have an indel sized larger than it has to be.
    
• src/hg/lib/trackDbCustom.c
  • lines changed 2, context: html, text, full: html, text
    Adding support for plain VCF custom tracks (as opposed to VCF+tabix),since users seem to want to upload VCF, and as long as the file is
    not too big it will work OK. This means adding a new track type
    vcf (as opposed to vcfTabix) and supporting it in hgTracks, hgTrackUi,
    hgc, hgTables and hgVai. (and others I've forgotten?)
    refs #12416
    
• src/hg/lib/ucscScop.sql
  • lines changed 1, context: html, text, full: html, text
    more UCSC genes changes.
• src/hg/lib/vcfUi.c
  • lines changed 15, context: html, text, full: html, text
    Adding support for plain VCF custom tracks (as opposed to VCF+tabix),since users seem to want to upload VCF, and as long as the file is
    not too big it will work OK. This means adding a new track type
    vcf (as opposed to vcfTabix) and supporting it in hgTracks, hgTrackUi,
    hgc, hgTables and hgVai. (and others I've forgotten?)
    refs #12416
    
• src/hg/lib/web.c
  • lines changed 2, context: html, text, full: html, text
    now converting hgsid and hguid to strings. when the hgsid cart var or hguid cookie is not found it returns NULL instead of 0.
  • lines changed 10, context: html, text, full: html, text
    fixing crash at first startup of new mirror by phoneHome, refs #148
  • lines changed 137, context: html, text, full: html, text
    moving the phoneHome business into cgiApoptosis.c/.h to make it callablefrom cart.c. We need to call it from cart.c as otherwise
    cgiApoptosisSetup (originally: phoneHome) will be called after mysql
    connections are opened. This leads to "mysql server has gone away" if
    any CGI is not faster than the child process forked here. The child will
    close all mysql connections of the parent process. With the new setup,
    the childi is forked before any mysql connections are opened. Ideally
    this would be all done in cheapcgi, but cheapcgi is not in the hg/lib
    part of the code.
    
• src/hg/lib/wikiLink.c
  • lines changed 8, context: html, text, full: html, text
    Allow special value HTTPHOST for central.domain and wiki.host, so aserver can be reached under multiple names. Might be a good default
    value for our example hg.conf? refs #11957
    
  • lines changed 6, context: html, text, full: html, text
    Last little compile failures from changing hgsid to char * for new secure web ids. The problem was hidden because hgSession had makefile with HGWARN turned off. Angie will fix that.
• src/hg/makeDb/doc/hg19.txt
  • lines changed 9, context: html, text, full: html, text
    document hg38ContigDiff table procedure refs #11681
• src/hg/makeDb/doc/hg38.txt
  • lines changed 5, context: html, text, full: html, text
    corrected hg19 to rn4 rn5 lastz procedure refs #11681
  • lines changed 3, context: html, text, full: html, text
    correct table load altSeqLiftOverPsl for Hg19 Diff track refs #11681
  • lines changed 39, context: html, text, full: html, text
    updated ideogram from NCBI refs #11681
• src/hg/makeDb/doc/quickAssembly.txt
  • lines changed 200, context: html, text, full: html, text
    very quick genome browser build procedure refs #252
  • lines changed 54, context: html, text, full: html, text
    add the dbDb/clade/genomeClade table additions refs #252
• src/hg/makeDb/doc/ucscGenes/hg38.ucscGenes15.csh
  • lines changed 296, context: html, text, full: html, text
    ongoing work on UCSC genes for hg38
  • lines changed 1, context: html, text, full: html, text
    more UCSC genes changes.
• src/hg/makeDb/genbank/etc/hgwbeta.dbs
  • lines changed 1, context: html, text, full: html, text
    Added hg38 (redmine #11681)
• src/hg/makeDb/genbank/etc/rr.dbs
  • lines changed 1, context: html, text, full: html, text
    Added hg38 (redmine #11681)
• src/hg/makeDb/schema/all.joiner
  • lines changed 6, context: html, text, full: html, text
    add altSeqLiftOver check rule refs #11681
  • lines changed 5, context: html, text, full: html, text
    adding hg38ContigDiff identifier for hg19 and hg38 refs #11681
  • lines changed 3, context: html, text, full: html, text
    add altLocations to the ignore list for hg18 refs #11681
  • lines changed 2, context: html, text, full: html, text
    Adding mm10 tablesIgnored entries for 2-way pseudogenes and polyA site tables, refs #12701
  • lines changed 6, context: html, text, full: html, text
    add rules for seqNcbiAltSequence and extNcbiAltSequence tables in hg38 refs #11681
  • lines changed 3, context: html, text, full: html, text
    some fixes to support hg38 knownGene
  • lines changed 13, context: html, text, full: html, text
    better linkage of altSeqLiftOverPsl seqNcbiAltSequence extNcbiAltSequence tables refs #11681
  • lines changed 1, context: html, text, full: html, text
    add kg7ToKg8
• src/hg/makeDb/trackDb/dog/canFam3/trackDb.chainNet.ra
  • lines changed 15, context: html, text, full: html, text
    Made changes so hg19 and hg38 chain/net tracks could co-exist with unique labels (redmine #11681)
• src/hg/makeDb/trackDb/grcIncidentDb.html
  • lines changed 12, context: html, text, full: html, text
    Edited these files.
• src/hg/makeDb/trackDb/human/chainNetEchTel1.ra
  • lines changed 15, context: html, text, full: html, text
    moving chainNetPlacental up one level refs #11681
• src/hg/makeDb/trackDb/human/chainNetEchTel2.ra
  • lines changed 15, context: html, text, full: html, text
    moving chainNetPlacental up one level refs #11681
• src/hg/makeDb/trackDb/human/chainNetFelCat4.ra
  • lines changed 15, context: html, text, full: html, text
    adding felCat5 to the placental composite refs #11681
• src/hg/makeDb/trackDb/human/chainNetFelCat5.ra
  • lines changed 15, context: html, text, full: html, text
    adding felCat5 to the placental composite refs #11681
• src/hg/makeDb/trackDb/human/chainNetFr2.ra
  • lines changed 15, context: html, text, full: html, text
    moving composite chainNetVertebrate up one level to use in hg38 also refs #11681
• src/hg/makeDb/trackDb/human/chainNetFr3.ra
  • lines changed 15, context: html, text, full: html, text
    moving composite chainNetVertebrate up one level to use in hg38 also refs #11681
• src/hg/makeDb/trackDb/human/chainNetGalGal3.ra
  • lines changed 15, context: html, text, full: html, text
    moving composite chainNetVertebrate up one level to use in hg38 also refs #11681
• src/hg/makeDb/trackDb/human/chainNetGalGal4.ra
  • lines changed 15, context: html, text, full: html, text
    moving composite chainNetVertebrate up one level to use in hg38 also refs #11681
• src/hg/makeDb/trackDb/human/chainNetLegacy.ra
  • lines changed 546, context: html, text, full: html, text
    moving chainNetLegacy.ra up refs #11681
  • lines changed 16, context: html, text, full: html, text
    adding felCat5 to the placental composite refs #11681
• src/hg/makeDb/trackDb/human/chainNetOtoGar1.ra
  • lines changed 16, context: html, text, full: html, text
    moving chainNetPrimate.ra up one so it can be used in hg38 too refs #11681
• src/hg/makeDb/trackDb/human/chainNetOtoGar3.ra
  • lines changed 15, context: html, text, full: html, text
    moving chainNetPrimate.ra up one so it can be used in hg38 too refs #11681
• src/hg/makeDb/trackDb/human/chainNetOviAri1.ra
  • lines changed 15, context: html, text, full: html, text
    moving chainNetPlacental up one level refs #11681
• src/hg/makeDb/trackDb/human/chainNetOviAri3.ra
  • lines changed 15, context: html, text, full: html, text
    moving chainNetPlacental up one level refs #11681
• src/hg/makeDb/trackDb/human/chainNetPlacental.ra
  • lines changed 388, context: html, text, full: html, text
    moving chainNetPlacental up one level refs #11681
  • lines changed 1, context: html, text, full: html, text
    correct usage of description html pages for vertebrate and placental chain nets refs #11681
  • lines changed 15, context: html, text, full: html, text
    adding felCat5 to the placental composite refs #11681
• src/hg/makeDb/trackDb/human/chainNetPrimate.ra
  • lines changed 204, context: html, text, full: html, text
    moving chainNetPrimate.ra up one so it can be used in hg38 too refs #11681
  • lines changed 1, context: html, text, full: html, text
    correct use of include html for chainNetPrimate refs #11681
• src/hg/makeDb/trackDb/human/chainNetRBestOtoGar1.ra
  • lines changed 16, context: html, text, full: html, text
    moving chainNetPrimate.ra up one so it can be used in hg38 too refs #11681
• src/hg/makeDb/trackDb/human/chainNetRBestOtoGar3.ra
  • lines changed 15, context: html, text, full: html, text
    moving chainNetPrimate.ra up one so it can be used in hg38 too refs #11681
• src/hg/makeDb/trackDb/human/chainNetRn4.ra
  • lines changed 15, context: html, text, full: html, text
    moving chainNetPlacental up one level refs #11681
• src/hg/makeDb/trackDb/human/chainNetRn5.ra
  • lines changed 15, context: html, text, full: html, text
    moving chainNetPlacental up one level refs #11681
• src/hg/makeDb/trackDb/human/chainNetSusScr2.ra
  • lines changed 16, context: html, text, full: html, text
    moving chainNetPlacental up one level refs #11681
• src/hg/makeDb/trackDb/human/chainNetSusScr3.ra
  • lines changed 15, context: html, text, full: html, text
    moving chainNetPlacental up one level refs #11681
• src/hg/makeDb/trackDb/human/chainNetTurTru1.ra
  • lines changed 15, context: html, text, full: html, text
    moving chainNetPlacental up one level refs #11681
• src/hg/makeDb/trackDb/human/chainNetTurTru2.ra
  • lines changed 15, context: html, text, full: html, text
    moving chainNetPlacental up one level refs #11681
• src/hg/makeDb/trackDb/human/chainNetVertebrate.ra
  • lines changed 340, context: html, text, full: html, text
    moving composite chainNetVertebrate up one level to use in hg38 also refs #11681
  • lines changed 1, context: html, text, full: html, text
    correct usage of description html pages for vertebrate and placental chain nets refs #11681
• src/hg/makeDb/trackDb/human/chainNetVicPac1.ra
  • lines changed 15, context: html, text, full: html, text
    moving chainNetPlacental up one level refs #11681
• src/hg/makeDb/trackDb/human/chainNetVicPac2.ra
  • lines changed 15, context: html, text, full: html, text
    moving chainNetPlacental up one level refs #11681
• src/hg/makeDb/trackDb/human/hg19/chainNetEchTel1.ra
  • lines changed 15, context: html, text, full: html, text
    moving chainNetPlacental up one level refs #11681
• src/hg/makeDb/trackDb/human/hg19/chainNetEchTel2.ra
  • lines changed 15, context: html, text, full: html, text
    moving chainNetPlacental up one level refs #11681
• src/hg/makeDb/trackDb/human/hg19/chainNetFr2.ra
  • lines changed 15, context: html, text, full: html, text
    moving composite chainNetVertebrate up one level to use in hg38 also refs #11681
• src/hg/makeDb/trackDb/human/hg19/chainNetFr3.ra
  • lines changed 15, context: html, text, full: html, text
    moving composite chainNetVertebrate up one level to use in hg38 also refs #11681
• src/hg/makeDb/trackDb/human/hg19/chainNetGalGal3.ra
  • lines changed 15, context: html, text, full: html, text
    moving composite chainNetVertebrate up one level to use in hg38 also refs #11681
• src/hg/makeDb/trackDb/human/hg19/chainNetGalGal4.ra
  • lines changed 15, context: html, text, full: html, text
    moving composite chainNetVertebrate up one level to use in hg38 also refs #11681
• src/hg/makeDb/trackDb/human/hg19/chainNetLegacy.ra
  • lines changed 546, context: html, text, full: html, text
    moving chainNetLegacy.ra up refs #11681
• src/hg/makeDb/trackDb/human/hg19/chainNetOtoGar1.ra
  • lines changed 16, context: html, text, full: html, text
    moving chainNetPrimate.ra up one so it can be used in hg38 too refs #11681
• src/hg/makeDb/trackDb/human/hg19/chainNetOtoGar3.ra
  • lines changed 15, context: html, text, full: html, text
    moving chainNetPrimate.ra up one so it can be used in hg38 too refs #11681
• src/hg/makeDb/trackDb/human/hg19/chainNetOviAri1.ra
  • lines changed 15, context: html, text, full: html, text
    moving chainNetPlacental up one level refs #11681
• src/hg/makeDb/trackDb/human/hg19/chainNetOviAri3.ra
  • lines changed 15, context: html, text, full: html, text
    moving chainNetPlacental up one level refs #11681
• src/hg/makeDb/trackDb/human/hg19/chainNetPlacental.ra
  • lines changed 388, context: html, text, full: html, text
    moving chainNetPlacental up one level refs #11681
• src/hg/makeDb/trackDb/human/hg19/chainNetPrimate.ra
  • lines changed 204, context: html, text, full: html, text
    moving chainNetPrimate.ra up one so it can be used in hg38 too refs #11681
• src/hg/makeDb/trackDb/human/hg19/chainNetRBestOtoGar1.ra
  • lines changed 16, context: html, text, full: html, text
    moving chainNetPrimate.ra up one so it can be used in hg38 too refs #11681
• src/hg/makeDb/trackDb/human/hg19/chainNetRBestOtoGar3.ra
  • lines changed 15, context: html, text, full: html, text
    moving chainNetPrimate.ra up one so it can be used in hg38 too refs #11681
• src/hg/makeDb/trackDb/human/hg19/chainNetRn4.ra
  • lines changed 15, context: html, text, full: html, text
    moving chainNetPlacental up one level refs #11681
• src/hg/makeDb/trackDb/human/hg19/chainNetRn5.ra
  • lines changed 15, context: html, text, full: html, text
    moving chainNetPlacental up one level refs #11681
• src/hg/makeDb/trackDb/human/hg19/chainNetSusScr2.ra
  • lines changed 16, context: html, text, full: html, text
    moving chainNetPlacental up one level refs #11681
• src/hg/makeDb/trackDb/human/hg19/chainNetSusScr3.ra
  • lines changed 15, context: html, text, full: html, text
    moving chainNetPlacental up one level refs #11681
• src/hg/makeDb/trackDb/human/hg19/chainNetTurTru1.ra
  • lines changed 15, context: html, text, full: html, text
    moving chainNetPlacental up one level refs #11681
• src/hg/makeDb/trackDb/human/hg19/chainNetTurTru2.ra
  • lines changed 15, context: html, text, full: html, text
    moving chainNetPlacental up one level refs #11681
• src/hg/makeDb/trackDb/human/hg19/chainNetVertebrate.ra
  • lines changed 340, context: html, text, full: html, text
    moving composite chainNetVertebrate up one level to use in hg38 also refs #11681
• src/hg/makeDb/trackDb/human/hg19/chainNetVicPac1.ra
  • lines changed 15, context: html, text, full: html, text
    moving chainNetPlacental up one level refs #11681
• src/hg/makeDb/trackDb/human/hg19/chainNetVicPac2.ra
  • lines changed 15, context: html, text, full: html, text
    moving chainNetPlacental up one level refs #11681
• src/hg/makeDb/trackDb/human/hg19/hg19ContigDiff.html
  • lines changed 21, context: html, text, full: html, text
    Edited hg39 and hg19 diffs tracks. Fixed inconsistent longLabel capitalization for several tracks in trackDb.ra.
• src/hg/makeDb/trackDb/human/hg19/hg19mammalChainNet.html
  • lines changed 160, context: html, text, full: html, text
    correct usage of description html pages for vertebrate and placental chain nets refs #11681
• src/hg/makeDb/trackDb/human/hg19/hg19primateChainNet.html
  • lines changed 202, context: html, text, full: html, text
    correct use of include html for chainNetPrimate refs #11681
• src/hg/makeDb/trackDb/human/hg19/hg19vertChainNet.html
  • lines changed 206, context: html, text, full: html, text
    correct usage of description html pages for vertebrate and placental chain nets refs #11681
• src/hg/makeDb/trackDb/human/hg19/hg38ContigDiff.html
  • lines changed 19, context: html, text, full: html, text
    Edited hg39 and hg19 diffs tracks. Fixed inconsistent longLabel capitalization for several tracks in trackDb.ra.
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    moving chainNetLegacy.ra up one to share with hg19 and hg38 refs #11681
  • lines changed 48, context: html, text, full: html, text
    Edited hg39 and hg19 diffs tracks. Fixed inconsistent longLabel capitalization for several tracks in trackDb.ra.
  • lines changed 53, context: html, text, full: html, text
    Added Retroposed genes version 5 back as this is the track on the RR.
  • lines changed 0, context: html, text, full: html, text
    Added back spaces in trackDb entry for retrogenes.
  • lines changed 0, context: html, text, full: html, text
    Added more spaces that were removed in retrogenes entry.
  • lines changed 1, context: html, text, full: html, text
    Added version number for Retroposed Genes 6.0.
  • lines changed 0, context: html, text, full: html, text
    Added extra space between track and track name for version 5.
  • lines changed 0, context: html, text, full: html, text
    Added in another missing space.
  • lines changed 0, context: html, text, full: html, text
    Added in another missing space.
  • lines changed 0, context: html, text, full: html, text
    Added in another missing space.
  • lines changed 0, context: html, text, full: html, text
    Added in another missing space.
  • lines changed 1, context: html, text, full: html, text
    moving composite chainNetVertebrate up one level to use in hg38 also refs #11681
  • lines changed 1, context: html, text, full: html, text
    moving chainNetPrimate.ra up one so it can be used in hg38 too refs #11681
  • lines changed 1, context: html, text, full: html, text
    moving chainNetPlacental up one level refs #11681
  • lines changed 1, context: html, text, full: html, text
    Settting Retroposed genes version 5 to hide from pack
  • lines changed 1, context: html, text, full: html, text
    Settting Retroposed genes version 5 to have no priority
• src/hg/makeDb/trackDb/human/hg38/altSequence.html
  • lines changed 7, context: html, text, full: html, text
    Edited these files.
  • lines changed 43, context: html, text, full: html, text
    Made a few more edits.
  • lines changed 2, context: html, text, full: html, text
    One last small edit.
• src/hg/makeDb/trackDb/human/hg38/chainNetPrimate.ra
  • lines changed 215, context: html, text, full: html, text
    chainNetPrimate has moved up one level refs #11681
• src/hg/makeDb/trackDb/human/hg38/ctgPos2.html
  • lines changed 8, context: html, text, full: html, text
    Edited these files.
  • lines changed 5, context: html, text, full: html, text
    Made a few more edits.
• src/hg/makeDb/trackDb/human/hg38/defaultPriority.ra
  • lines changed 4, context: html, text, full: html, text
    default on for knownGene and refGene refs #11681
• src/hg/makeDb/trackDb/human/hg38/description.html
  • lines changed 8, context: html, text, full: html, text
    Made final addition about analysis set (redmine #11706)
  • lines changed 193, context: html, text, full: html, text
    Preliminary editing pass on gateway page.
  • lines changed 15, context: html, text, full: html, text
    A few more edits.
  • lines changed 37, context: html, text, full: html, text
    More editing work on this page.
  • lines changed 6, context: html, text, full: html, text
    Modified info about Karen Miga's work, per input from Karen + Jim.
• src/hg/makeDb/trackDb/human/hg38/gap.html
  • lines changed 19, context: html, text, full: html, text
    Edited these files.
  • lines changed 1, context: html, text, full: html, text
    Made a few more edits.
• src/hg/makeDb/trackDb/human/hg38/gold.html
  • lines changed 19, context: html, text, full: html, text
    Edited these files.
  • lines changed 1, context: html, text, full: html, text
    Made a few more edits.
• src/hg/makeDb/trackDb/human/hg38/hg38ContigDiff.html
  • lines changed 21, context: html, text, full: html, text
    Edited hg39 and hg19 diffs tracks. Fixed inconsistent longLabel capitalization for several tracks in trackDb.ra.
• src/hg/makeDb/trackDb/human/hg38/scaffolds.html
  • lines changed 7, context: html, text, full: html, text
    Edited these files.
  • lines changed 8, context: html, text, full: html, text
    Made a few more edits.
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 12, context: html, text, full: html, text
    Edited hg39 and hg19 diffs tracks. Fixed inconsistent longLabel capitalization for several tracks in trackDb.ra.
  • lines changed 3, context: html, text, full: html, text
    now using same chain net composites as hg19 refs #11681
  • lines changed 1, context: html, text, full: html, text
    adding felCat5 to the placental composite refs #11681
• src/hg/makeDb/trackDb/human/placentalChainNet.html
  • lines changed 160, context: html, text, full: html, text
    correct usage of description html pages for vertebrate and placental chain nets refs #11681
• src/hg/makeDb/trackDb/human/primateChainNet.html
  • lines changed 202, context: html, text, full: html, text
    correct use of include html for chainNetPrimate refs #11681
• src/hg/makeDb/trackDb/human/vertebrateChainNet.html
  • lines changed 206, context: html, text, full: html, text
    correct usage of description html pages for vertebrate and placental chain nets refs #11681
• src/hg/makeDb/trackDb/lamprey/petMar2/lampreyGene.html
  • lines changed 47, context: html, text, full: html, text
    adding lamprey genes from Carson Holt/Jeramiah Smith refs #9153
• src/hg/makeDb/trackDb/lamprey/petMar2/trackDb.ra
  • lines changed 11, context: html, text, full: html, text
    adding lamprey genes from Carson Holt/Jeramiah Smith refs #9153
• src/hg/makeDb/trackDb/mouse/mm10/hg19ChainNet.ra
  • lines changed 2, context: html, text, full: html, text
    Made changes so hg19 and hg38 chain/net tracks could co-exist with unique labels (redmine #11681)
• src/hg/makeDb/trackDb/mouse/mm10/hg38ChainNet.ra
  • lines changed 2, context: html, text, full: html, text
    Made changes so hg19 and hg38 chain/net tracks could co-exist with unique labels (redmine #11681)
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.euarchontoglireChainNet.ra
  • lines changed 2, context: html, text, full: html, text
    Adjusting human release tags after staging hg38 on beta (redmine #11681)
  • lines changed 2, context: html, text, full: html, text
    Per Bob, Ann and Hiram, added both hg19 and hg38 to euarchontoglire composite track (redmine #11681)
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.previousVersionsChainNet.ra
  • lines changed 16, context: html, text, full: html, text
    Per Bob, Ann and Hiram, added both hg19 and hg38 to euarchontoglire composite track (redmine #11681)
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    removing GENCODE priority, refs #12701
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM2.ra
  • lines changed 13, context: html, text, full: html, text
    Fixing search regex for mm10 GENCODE tracks, refs #12701
• src/hg/makeDb/trackDb/orangutan/ponAbe2/description.html
  • lines changed 4, context: html, text, full: html, text
    Fixing links on orangutan (ponAbe2) track description pages
• src/hg/makeDb/trackDb/orangutan/ponAbe2/multiz8way.html
  • lines changed 25, context: html, text, full: html, text
    Fixing links on orangutan (ponAbe2) track description pages
• src/hg/makeDb/trackDb/orangutan/ponAbe2/nscanGene.html
  • lines changed 31, context: html, text, full: html, text
    Fixing links on orangutan (ponAbe2) track description pages
• src/hg/makeDb/trackDb/orangutan/ponAbe2/phastConsElements8way.html
  • lines changed 19, context: html, text, full: html, text
    Fixing links on orangutan (ponAbe2) track description pages
• src/hg/makeDb/trackDb/rhesus/rheMac3/trackDb.chainNet.ra
  • lines changed 17, context: html, text, full: html, text
    Made changes so hg19 and hg38 chain/net tracks could co-exist with unique labels (redmine #11681)
• src/hg/makeDb/trackDb/rhesus/rheMac3/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    Made changes so hg19 and hg38 chain/net tracks could co-exist with unique labels (redmine #11681)
• src/hg/makeDb/trackDb/ucscToINSDC.html
  • lines changed 6, context: html, text, full: html, text
    Edited these files.
  • lines changed 6, context: html, text, full: html, text
    Made a few more edits.
• src/hg/near/hgNear/hgNearData/Rat/rn4/gnfAtlas2RgdGene2.html
  • lines changed 62, context: html, text, full: html, text
    Added HTML files to silence rn4 errors in hgNearTest, refs #7129
• src/hg/near/hgNear/hgNearData/Rat/rn4/gnfAtlas2RgdGene2Distance.html
  • lines changed 12, context: html, text, full: html, text
    Added HTML files to silence rn4 errors in hgNearTest, refs #7129
• src/hg/near/hgNear/hgNearData/Rat/rn4/rgdGene2ToRAE230.html
  • lines changed 15, context: html, text, full: html, text
    Added HTML files to silence rn4 errors in hgNearTest, refs #7129
• src/hg/near/hgNear/hgNearData/Rat/rn4/rgdGene2ToU34A.html
  • lines changed 15, context: html, text, full: html, text
    Added HTML files to silence rn4 errors in hgNearTest, refs #7129
• src/hg/protein/kgBioCyc1/kgBioCyc1.c
  • lines changed 8, context: html, text, full: html, text
    more UCSC genes changes.
• src/hg/utils/automation/EnsGeneAutomate.pm
  • lines changed 4, context: html, text, full: html, text
    fixup a couple of the URLs refs #12796
• src/hg/utils/automation/doEnsGeneUpdate.pl
  • lines changed 1, context: html, text, full: html, text
    add geneNameAsName2 option to the gtfToGenePred refs #12796
• src/hg/utils/gtfToGenePred/tests/expected/ensemblSplicedStop.gp
  • lines changed 1, context: html, text, full: html, text
    Fixed bug in GTF to genePred conversion where an assertion was triggered when theGTF had a spliced stop codon where the exon containing the first part of the
    stop codon only consisted of the stop codon bases. For example, a two-base exon where
    with two bases are the first two bases of the stop codon.
    
  • lines changed 1, context: html, text, full: html, text
    commit 5a7542dced0497f6d08a503a95eba87619b23a8aAuthor: Mark Diekhans <markd@soe.ucsc.edu>
    Date: Wed Mar 5 19:35:34 2014 -0800
    
    Fixed bug in GTF to genePred conversion where an assertion was triggered when the
    GTF had a spliced stop codon where the exon containing the first part of the
    stop codon only consisted of the stop codon bases. For example, a two-base exon where
    with two bases are the first two bases of the stop codon. This commit handle negative
    strand case.
    
• src/hg/utils/gtfToGenePred/tests/input/ensemblSplicedStop.gp
  • lines changed 71, context: html, text, full: html, text
    Fixed bug in GTF to genePred conversion where an assertion was triggered when theGTF had a spliced stop codon where the exon containing the first part of the
    stop codon only consisted of the stop codon bases. For example, a two-base exon where
    with two bases are the first two bases of the stop codon.
    
  • lines changed 31, context: html, text, full: html, text
    commit 5a7542dced0497f6d08a503a95eba87619b23a8aAuthor: Mark Diekhans <markd@soe.ucsc.edu>
    Date: Wed Mar 5 19:35:34 2014 -0800
    
    Fixed bug in GTF to genePred conversion where an assertion was triggered when the
    GTF had a spliced stop codon where the exon containing the first part of the
    stop codon only consisted of the stop codon bases. For example, a two-base exon where
    with two bases are the first two bases of the stop codon. This commit handle negative
    strand case.
    
• src/hg/utils/gtfToGenePred/tests/makefile
  • lines changed 7, context: html, text, full: html, text
    Fixed bug in GTF to genePred conversion where an assertion was triggered when theGTF had a spliced stop codon where the exon containing the first part of the
    stop codon only consisted of the stop codon bases. For example, a two-base exon where
    with two bases are the first two bases of the stop codon.
    
• src/inc/vcf.h
  • lines changed 5, context: html, text, full: html, text
    Adding support for plain VCF custom tracks (as opposed to VCF+tabix),since users seem to want to upload VCF, and as long as the file is
    not too big it will work OK. This means adding a new track type
    vcf (as opposed to vcfTabix) and supporting it in hgTracks, hgTrackUi,
    hgc, hgTables and hgVai. (and others I've forgotten?)
    refs #12416
    
  • lines changed 9, context: html, text, full: html, text
    In addition to trimming the left padding base from VCF indels,now we trim identical bases on the right of all alleles, if there
    are any. I've seen multiple cases of user VCF with indels that
    have inflated size due to including right flanking bases; when
    trying to determine functional consequences, it's misleading to
    have an indel sized larger than it has to be.
    
• src/lib/annoStreamVcf.c
  • lines changed 1, context: html, text, full: html, text
    Adding support for plain VCF custom tracks (as opposed to VCF+tabix),since users seem to want to upload VCF, and as long as the file is
    not too big it will work OK. This means adding a new track type
    vcf (as opposed to vcfTabix) and supporting it in hgTracks, hgTrackUi,
    hgc, hgTables and hgVai. (and others I've forgotten?)
    refs #12416
    
  • lines changed 1, context: html, text, full: html, text
    In addition to trimming the left padding base from VCF indels,now we trim identical bases on the right of all alleles, if there
    are any. I've seen multiple cases of user VCF with indels that
    have inflated size due to including right flanking bases; when
    trying to determine functional consequences, it's misleading to
    have an indel sized larger than it has to be.
    
• src/lib/bamFile.c
  • lines changed 3, context: html, text, full: html, text
    Fixing an incomplete renaming of a variable that caused a compile errorfor a mirror admin using USE_BAM w/samtools but not using KNETFILE_HOOKS.
    refs #12827
    
• src/lib/gff3.c
  • lines changed 1, context: html, text, full: html, text
    fixed check for include escape in GFF3 files
• src/lib/vcf.c
  • lines changed 65, context: html, text, full: html, text
    Adding support for plain VCF custom tracks (as opposed to VCF+tabix),since users seem to want to upload VCF, and as long as the file is
    not too big it will work OK. This means adding a new track type
    vcf (as opposed to vcfTabix) and supporting it in hgTracks, hgTrackUi,
    hgc, hgTables and hgVai. (and others I've forgotten?)
    refs #12416
    
  • lines changed 114, context: html, text, full: html, text
    In addition to trimming the left padding base from VCF indels,now we trim identical bases on the right of all alleles, if there
    are any. I've seen multiple cases of user VCF with indels that
    have inflated size due to including right flanking bases; when
    trying to determine functional consequences, it's misleading to
    have an indel sized larger than it has to be.
    
• src/product/ex.hg.conf
  • lines changed 6, context: html, text, full: html, text
    Fixing RNAplot problem with newer versions, refs #11957, note 178 andrefs #6382
    
  • lines changed 6, context: html, text, full: html, text
    Allow special value HTTPHOST for central.domain and wiki.host, so aserver can be reached under multiple names. Might be a good default
    value for our example hg.conf? refs #11957
    
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    v297 preview2 refs #12656

• lines changed: 11477
• files changed: 293