All File Changes

v307_base to v308_preview (2014-10-13 to 2014-10-20) v308

• src/browserbox/home/browser/README.txt
  • lines changed 41, context: html, text, full: html, text
    gbib gets its readme file
• src/browserbox/root/updateBrowser.sh
  • lines changed 21, context: html, text, full: html, text
    removing the ENCODE link from the gbib index.html, adding a little helpmessage. Also not pulling beta htmls for alpha boxes anymore, not
    needed.
    
• src/browserbox/usr/local/apache/cgi-bin/hgNear
  • lines changed 19, context: html, text, full: html, text
    removing the now superfluous hgNear replacement script for gbib
• src/hg/hgMirror/hgMirror
  • lines changed 18, context: html, text, full: html, text
    fixing conservation track not being hidden after hgMirror run followedby cartReset. refs #14121 note 11
    
• src/hg/hgTracks/rmskJoinedTrack.c
  • lines changed 40, context: html, text, full: html, text
    fixup font sizing issues refs #9741
• src/hg/hgTracks/wigTrack.c
  • lines changed 5, context: html, text, full: html, text
    fix #14168 fix custom wiggle tracks on assembly hubs
• src/hg/hgc/retroClick.c
  • lines changed 4, context: html, text, full: html, text
    Corrected off by 1 errors in position starts. Added a link from the Breaks in Orthology table to the description for this feature.
• src/hg/htdocs/goldenPath/help/gbib.html
  • lines changed 1, context: html, text, full: html, text
    fixing typoe, refs #14151
  • lines changed 140, context: html, text, full: html, text
    Interim check-in of edits to allow others to edit. Not finished with editing pass yet.
  • lines changed 5, context: html, text, full: html, text
    Tweaking point about BIOS virtualization, refs #12843
  • lines changed 1, context: html, text, full: html, text
    Jorge pointed out that genbank etc are updated weekly, not daily.
• src/hg/htdocs/indexNews.html
  • lines changed 2, context: html, text, full: html, text
    fixed two mispellings of October
• src/hg/lib/customFactory.c
  • lines changed 9, context: html, text, full: html, text
    fix #14168 fix custom wiggle tracks on assembly hubs
• src/hg/makeDb/doc/bosTau8.txt
  • lines changed 155, context: html, text, full: html, text
    Added bosTau8 <-> hg38,mm10 chain/net tracks, liftOvers; refs #13852
• src/hg/makeDb/doc/dm6.txt
  • lines changed 64, context: html, text, full: html, text
    finalize the 27-way conservation track refs #4049
• src/hg/makeDb/doc/eboVir3/phastCons160way.txt
  • lines changed 173, context: html, text, full: html, text
    running up phastCons and mostConserved for 160-way refs #10411
  • lines changed 102, context: html, text, full: html, text
    adding phyloP construction refs #10411
  • lines changed 23, context: html, text, full: html, text
    adding loading of tables for strain display track refs #14011
• src/hg/makeDb/doc/hg38.txt
  • lines changed 1, context: html, text, full: html, text
    fixup negative strand underscore genomicSuperDups track refs #13580
  • lines changed 108, context: html, text, full: html, text
    Ugh, in ad6b5c875 I got a couple chrX_*_alt IDs swizzled, so my update to the par table wasincorrect; so when I rebuilt everything in e829f902a3, it didn't fix the MultipleAlignments
    problems, it only masked a few. Thank you Matt for noticing that! Now par is correct and
    as far as I can tell, the MultipleAlignments problems are truly fixed.
    refs #13309
    
  • lines changed 56, context: html, text, full: html, text
    Added bosTau8 <-> hg38,mm10 chain/net tracks, liftOvers; refs #13852
• src/hg/makeDb/doc/mm10.txt
  • lines changed 55, context: html, text, full: html, text
    Added bosTau8 <-> hg38,mm10 chain/net tracks, liftOvers; refs #13852
• src/hg/makeDb/genbank/etc/align.dbs
  • lines changed 1, context: html, text, full: html, text
    Added bosTau8 - Cow; refs #13852
• src/hg/makeDb/genbank/etc/hgwdev.dbs
  • lines changed 1, context: html, text, full: html, text
    Added bosTau8 - Cow; refs #13852
• src/hg/makeDb/hgLoadWiggle/hgLoadWiggle.c
  • lines changed 9, context: html, text, full: html, text
    fix #14168 fix custom wiggle tracks on assembly hubs
• src/hg/makeDb/schema/all.joiner
  • lines changed 8, context: html, text, full: html, text
    adding dm6 to the rule book refs #4049
  • lines changed 7, context: html, text, full: html, text
    adding dm6 to the rule book refs #4049
  • lines changed 2, context: html, text, full: html, text
    Added bosTau8; also corrected some ordering; refs #13852
• src/hg/makeDb/trackDb/ebola/eboVir3/cons160way.html
  • lines changed 0, context: html, text, full: html, text
    Minor tweak as part of CR, refs #14147
• src/hg/makeDb/trackDb/ebola/eboVir3/trackDb.160way.ra
  • lines changed 2, context: html, text, full: html, text
    Commenting out lines for Hirams test frames tables
  • lines changed 2, context: html, text, full: html, text
    revert to the single species frame table refs #10411
  • lines changed 66, context: html, text, full: html, text
    adding phastCons and phyloP for the 160-way refs #14011
• src/hg/makeDb/trackDb/ebola/eboVir3/trackDb.strainName160way.ra
  • lines changed 2, context: html, text, full: html, text
    Commenting out lines for Hirams test frames tables
  • lines changed 2, context: html, text, full: html, text
    revert to the single species frame table refs #10411
  • lines changed 66, context: html, text, full: html, text
    adding phastCons and phyloP to strain track refs #14011
• src/hg/makeDb/trackDb/genomicSuperDups.html
  • lines changed 4, context: html, text, full: html, text
    Changing people under Credits, removing emails for people no longer with Eichler lab, refs #13580
• src/hg/makeDb/trackDb/human/hg19/affyExonArray.html
  • lines changed 1, context: html, text, full: html, text
    Changing URL to fix error found by hgTablesTest
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    hiding snp138 on hg19. Making snp141 tracks highest priority for Variation group
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    hiding snp138 on hg19. Making snp141 tracks highest priority for Variation group
• src/hg/makeDb/trackDb/trackDb.chainNet.insects.ra
  • lines changed 60, context: html, text, full: html, text
    adding triCas2 for dm6 refs #13461
• src/hg/makeDb/trackDb/trackDb.chainNet.ra
  • lines changed 51, context: html, text, full: html, text
    Added bosTau8 <-> hg38,mm10 chain/net tracks, liftOvers; refs #13852
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    v308 preview1 refs #14072

• lines changed: 1332
• files changed: 42