All File Changes

v280_preview2 to v280_base (2013-02-26 to 2013-03-05) v280

• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 34, context: html, text, full: html, text
    For Track #7043 (SNPs for mm10): Luvina noticed that mm10.snp137 hasseveral items that use a molType we haven't seen before, "mito";
    added filter and color options for that.
    
• src/hg/hgTracks/gencodeTracks.c
  • lines changed 74, context: html, text, full: html, text
    Added highlighting of GENCODE transcripts based on annotation method.Also fixed bug with annotation method filtering for `automatic'. Added
    support for filtering by `manual and automatic' method.
    
• src/hg/hgTracks/hgTracks.c
  • lines changed 88, context: html, text, full: html, text
    some assembly hub fixes (non-chrom sequence dump, don't open db when not needed) #8072
• src/hg/hgTracks/retroGene.c
  • lines changed 2, context: html, text, full: html, text
    Added trackHandler for ucscRetro v4 track tables.
• src/hg/hgc/hgc.c
  • lines changed 2, context: html, text, full: html, text
    some assembly hub fixes (non-chrom sequence dump, don't open db when not needed) #8072
• src/hg/hgc/retroClick.c
  • lines changed 4, context: html, text, full: html, text
    Removed oldScore column as no longer needed and renamed oldIntronCount to alignGapCount in ucscRetroInfo table so change code and variable names to match for details page display.
• src/hg/htdocs/ENCODE/contacts.html
  • lines changed 81, context: html, text, full: html, text
    Updating ENCODE contacts.html to look similar to ENCODE style, did not change content.
• src/hg/htdocs/ENCODE/contributors.html
  • lines changed 55, context: html, text, full: html, text
    Updating ENCODE contributors.html to look similar to ENCODE style
  • lines changed 1, context: html, text, full: html, text
    Removing extra </a> that was messing up indentation formatting for contributors.html
• src/hg/htdocs/ENCODE/downloads.html
  • lines changed 103, context: html, text, full: html, text
    Making changes to ENCODE download to have similar style of ENCODE pages, RM#10047
  • lines changed 18, context: html, text, full: html, text
    Clarification of links, data policy
  • lines changed 5, context: html, text, full: html, text
    Change page title for consistency with encodeProject style
  • lines changed 8, context: html, text, full: html, text
    Removing unneeded style definitions not used in ENCODE human downloads page, RM#10047
• src/hg/htdocs/ENCODE/downloadsMouse.html
  • lines changed 52, context: html, text, full: html, text
    Redoing HTML style ENCODE Mouse downloads page, related to RM# 10047
  • lines changed 7, context: html, text, full: html, text
    Removing unneeded old style definitions not used in ENCODE downloadsMouse page
  • lines changed 2, context: html, text, full: html, text
    Removing extra </a>, and extra </P> that was messing up indentation formatting for downloadsMouse.html
• src/hg/htdocs/ENCODE/terms.html
  • lines changed 84, context: html, text, full: html, text
    Updating Data Policy page for ENCODE to match new style
  • lines changed 14, context: html, text, full: html, text
    Cleaning up HTML, removing unneeded style stanza from ENCODE terms.html
  • lines changed 1, context: html, text, full: html, text
    Removing extra </a> that was messing up indentation formatting for terms.html
• src/hg/htdocs/ENCODE/usageResources.html
  • lines changed 53, context: html, text, full: html, text
    Updating usageResources.html to look similar to ENCODE style
  • lines changed 2, context: html, text, full: html, text
    Removing extra </a>, and missing <em> that was messing up indentation formatting for usageResources.html
• src/hg/htdocs/goldenPath/help/bigBed.html
  • lines changed 1, context: html, text, full: html, text
    changed help page for bigBed, there is no bedFields-option in bedToBigWig
• src/hg/htdocs/goldenPath/help/euroNode.html
  • lines changed 46, context: html, text, full: html, text
    Adds new euroNode doc page (redmine #9767)
  • lines changed 46, context: html, text, full: html, text
    Renamed euroNode.html to genomeEuro.html (redmine #9767)
• src/hg/htdocs/goldenPath/help/genomeEuro.html
  • lines changed 84, context: html, text, full: html, text
    Renamed euroNode.html to genomeEuro.html (redmine #9767)
• src/hg/htdocs/images/Pan_paniscus.jpg
  • lines changed 0, context: html, text, full: html, text
    from a-z-animals.com - Kabir Bakie
• src/hg/htdocs/images/server_selector.jpg
  • lines changed 0, context: html, text, full: html, text
    Adding server selector screen shot (redmine #9767)
• src/hg/htdocs/js/staticDoc.js
  • lines changed 1, context: html, text, full: html, text
    Updated the URL for the euroNode (redmine #3135)
• src/hg/inc/snp125Ui.h
  • lines changed 1, context: html, text, full: html, text
    For Track #7043 (SNPs for mm10): Luvina noticed that mm10.snp137 hasseveral items that use a molType we haven't seen before, "mito";
    added filter and color options for that.
    
• src/hg/inc/ucscRetroInfo.h
  • lines changed 20, context: html, text, full: html, text
    Removed oldScore column as no longer needed and renamed oldIntronCount to alignGapCount in ucscRetroInfo table so change code and variable names to match.
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    New version number v280
• src/hg/js/hgTracks.js
  • lines changed 1, context: html, text, full: html, text
    Remove debug label, ugh
  • lines changed 1, context: html, text, full: html, text
    support drag-select in ideogram even if it has only one bar (#10285)
• src/hg/lib/snp125Ui.c
  • lines changed 5, context: html, text, full: html, text
    For Track #7043 (SNPs for mm10): Luvina noticed that mm10.snp137 hasseveral items that use a molType we haven't seen before, "mito";
    added filter and color options for that.
    
  • lines changed 1, context: html, text, full: html, text
    Fixing stupid sin of omission bug found by Brian R -- forgot to test w/clean cart.
• src/hg/lib/trackHub.c
  • lines changed 1, context: html, text, full: html, text
    move hasProtocol() function from common.c to net.c (code review #10278)
• src/hg/lib/ucscRetroInfo.c
  • lines changed 29, context: html, text, full: html, text
    Removed oldScore column as no longer needed and renamed oldIntronCount to alignGapCount in ucscRetroInfo table so change code and variable names to match.
• src/hg/lib/ucscRetroInfo.sql
  • lines changed 20, context: html, text, full: html, text
    Removed oldScore column as no longer needed and renamed oldIntronCount to alignGapCount.
• src/hg/makeDb/doc/bosTau6.txt
  • lines changed 2, context: html, text, full: html, text
    Track #8533 NumtS tracks for cow bosTau6 and horse equCab2.
• src/hg/makeDb/doc/equCab2.txt
  • lines changed 25, context: html, text, full: html, text
    Track #8533 NumtS tracks for cow bosTau6 and horse equCab2.
• src/hg/makeDb/doc/hg19.txt
  • lines changed 29, context: html, text, full: html, text
    adding rows to cytoBandIdeo for odd chroms with no entries. just for navigation/orientation
• src/hg/makeDb/doc/mm10.txt
  • lines changed 29, context: html, text, full: html, text
    adding rows to cytoBandIdeo for odd chroms with no entries. just for navigation/orientation
• src/hg/makeDb/doc/nomLeu3.txt
  • lines changed 212, context: html, text, full: html, text
    Updating makedoc with additional completed steps.
  • lines changed 15, context: html, text, full: html, text
    Checking up on gaps.
  • lines changed 24, context: html, text, full: html, text
    Adding more progress to the makedoc for the new assembly.
• src/hg/makeDb/doc/panPan1.txt
  • lines changed 2814, context: html, text, full: html, text
    Initial panPan1 browser.
  • lines changed 10, context: html, text, full: html, text
    Add panPan1 assembly back.
• src/hg/makeDb/doc/susScr2.txt
  • lines changed 1, context: html, text, full: html, text
    Track #8533 NumtS tracks for cow bosTau6 and horse equCab2.
• src/hg/makeDb/schema/all.joiner
  • lines changed 2, context: html, text, full: html, text
    Added nomLeu3 (new db) to relevant places
  • lines changed 1, context: html, text, full: html, text
    joinerCheck reported 202431 of 3276242 elements of canFam2.snp131Seq.acc are not in key snp131.name line 2861; the old threshold was 0.98; changing to 0.93 fixed the issue; since this is an old dog assembly and an old SNP track and it's been three years since this was last checked, I deem this to be an acceptable change
  • lines changed 1, context: html, text, full: html, text
    Encountered numerous errors with duplicates in ensGene.name; these are actually valid duplicates, so added the dupeOk tag
• src/hg/makeDb/trackDb/bonobo/description.html
  • lines changed 63, context: html, text, full: html, text
    Initial descriptions for panPan1.
  • lines changed 63, context: html, text, full: html, text
    Put the *.html *.ra file into panPan1 directory
• src/hg/makeDb/trackDb/bonobo/gap.html
  • lines changed 30, context: html, text, full: html, text
    Initial descriptions for panPan1.
  • lines changed 30, context: html, text, full: html, text
    Put the *.html *.ra file into panPan1 directory
• src/hg/makeDb/trackDb/bonobo/gold.html
  • lines changed 34, context: html, text, full: html, text
    Initial descriptions for panPan1.
  • lines changed 34, context: html, text, full: html, text
    Put the *.html *.ra file into panPan1 directory
• src/hg/makeDb/trackDb/bonobo/panPan1/description.html
  • lines changed 63, context: html, text, full: html, text
    Put the *.html *.ra file into panPan1 directory
• src/hg/makeDb/trackDb/bonobo/panPan1/gap.html
  • lines changed 30, context: html, text, full: html, text
    Put the *.html *.ra file into panPan1 directory
• src/hg/makeDb/trackDb/bonobo/panPan1/gold.html
  • lines changed 34, context: html, text, full: html, text
    Put the *.html *.ra file into panPan1 directory
• src/hg/makeDb/trackDb/bonobo/panPan1/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    Put the *.html *.ra file into panPan1 directory
• src/hg/makeDb/trackDb/bonobo/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    Initial descriptions for panPan1.
  • lines changed 8, context: html, text, full: html, text
    Put the *.html *.ra file into panPan1 directory
• src/hg/makeDb/trackDb/cow/bosTau6/trackDb.ra
  • lines changed 23, context: html, text, full: html, text
    Track #8533 NumtS tracks for cow bosTau6 and horse equCab2.
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 1, context: html, text, full: html, text
    Updating cv.ra to fix broken link for term iPS, reported on chronjob
• src/hg/makeDb/trackDb/cv/beta/cv.ra
  • lines changed 1, context: html, text, full: html, text
    Updating cv.ra to fix broken link for term iPS, reported on chronjob
• src/hg/makeDb/trackDb/cv/public/cv.ra
  • lines changed 1, context: html, text, full: html, text
    Updating cv.ra to fix broken link for term iPS, reported on chronjob
• src/hg/makeDb/trackDb/horse/equCab2/trackDb.ra
  • lines changed 40, context: html, text, full: html, text
    Track #8533 NumtS tracks for cow bosTau6 and horse equCab2.
• src/hg/makeDb/trackDb/human/hg19/cosmic.html
  • lines changed 1, context: html, text, full: html, text
    Updating link to cosmic as per code review #10284
  • lines changed 7, context: html, text, full: html, text
    Whitespace changes.
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
  • lines changed 2, context: html, text, full: html, text
    Added highlighting of GENCODE transcripts based on annotation method.Also fixed bug with annotation method filtering for `automatic'. Added
    support for filtering by `manual and automatic' method.
    
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV14.release2.ra
  • lines changed 264, context: html, text, full: html, text
    Added highlighting of GENCODE transcripts based on annotation method.Also fixed bug with annotation method filtering for `automatic'. Added
    support for filtering by `manual and automatic' method.
    
• src/hg/makeDb/trackDb/makefile
  • lines changed 1, context: html, text, full: html, text
    Added panPan1 to DBS.
  • lines changed 1, context: html, text, full: html, text
    Remove panPan1 from the build.
  • lines changed 1, context: html, text, full: html, text
    Add panPan1 assembly back.
• src/hg/makeDb/trackDb/other/repeats2/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    set emboss in repeats2 to pack
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    changed publications track group to pub
  • lines changed 1, context: html, text, full: html, text
    changed visibility of snp track to dense
  • lines changed 1, context: html, text, full: html, text
    setting sequences to dense, hide the others
  • lines changed 2, context: html, text, full: html, text
    setting sequences to dense, hide the others (trying parent stanza)
• src/hg/utils/automation/configFiles/nomLeu3.config.ra
  • lines changed 23, context: html, text, full: html, text
    adding nomLeu3 config file
• src/hg/utils/automation/doEnsGeneUpdate.pl
  • lines changed 6, context: html, text, full: html, text
    Feedback from CR #10241, made the MT liftover faster.
• src/inc/common.h
  • lines changed 3, context: html, text, full: html, text
    move hasProtocol() function from common.c to net.c (code review #10278)
• src/inc/net.h
  • lines changed 2, context: html, text, full: html, text
    move hasProtocol() function from common.c to net.c (code review #10278)
• src/lib/common.c
  • lines changed 7, context: html, text, full: html, text
    move hasProtocol() function from common.c to net.c (code review #10278)
• src/lib/net.c
  • lines changed 5, context: html, text, full: html, text
    move hasProtocol() function from common.c to net.c (code review #10278)
• src/lib/twoBit.c
  • lines changed 1, context: html, text, full: html, text
    move hasProtocol() function from common.c to net.c (code review #10278)
• src/utils/qa/checkMachineName.csh
  • lines changed 1, context: html, text, full: html, text
    added genome-euro to realTime.csh and adjusted a few other scripts to enable it. added verbose mode to realTime.csh so you can get machine names instead of just a dot
• src/utils/qa/getTableStatus.csh
  • lines changed 8, context: html, text, full: html, text
    added genome-euro to realTime.csh and adjusted a few other scripts to enable it. added verbose mode to realTime.csh so you can get machine names instead of just a dot
• src/utils/qa/getVersion.csh
  • lines changed 4, context: html, text, full: html, text
    added genome-euro to realTime.csh and adjusted a few other scripts to enable it. added verbose mode to realTime.csh so you can get machine names instead of just a dot
• src/utils/qa/makeCytoBandIdeo.csh
  • lines changed 2, context: html, text, full: html, text
    pulled a statement outside a loop so it only writes to the file once at the end
• src/utils/qa/realTime.csh
  • lines changed 32, context: html, text, full: html, text
    added genome-euro to realTime.csh and adjusted a few other scripts to enable it. added verbose mode to realTime.csh so you can get machine names instead of just a dot
  • lines changed 17, context: html, text, full: html, text
    removed MySQL version-checking, now that all machines are on ver5.0 or later. speeds up the script considerably
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 1, context: html, text, full: html, text
    redmine #10179 Change replyto address of code summary email from build@soe.ucsc.edu to ann@soe.ucsc.edu
  • lines changed 3, context: html, text, full: html, text
    v280 final build
• src/utils/qa/weeklybld/doNewBranch.csh
  • lines changed 1, context: html, text, full: html, text
    To Do #10179 Change replyto address of code summary email from build@soe.ucsc.edu to ann@soe.ucsc.edu.

• lines changed: 4983
• files changed: 96