All File Changes

v318_preview to v318_preview2 (2015-06-08 to 2015-06-15) v318

• src/hg/expMatrixToJson/expMatrixToJson.c
  • lines changed 101, context: html, text, full: html, text
    Changed the input/output. The program now takes an expression matrix as input and generates a .json and a .html
    
• src/hg/hgIntegrator/hgIntegrator.c
  • lines changed 1, context: html, text, full: html, text
    Use POST as queryForm's method, and use POST for ajax requests, because IE11 can't handle big URLs.
    refs #14579 note 84
    
• src/hg/hgMenubar/hgMenubar
  • lines changed 104, context: html, text, full: html, text
    Adding menubar CGI for static docs, refs #15389
    
• src/hg/hgMenubar/makefile
  • lines changed 29, context: html, text, full: html, text
    Adding menubar CGI for static docs, refs #15389
    
• src/hg/hgTables/userRegions.c
  • lines changed 6, context: html, text, full: html, text
    Fix a memory-usage bug that was leading to weird symptoms such as random
    data stored in the cart and possibly also bad end cookie when freeing.
    lineFileNext can trash the string passed to lineFileOnString, so pass
    in a copy instead of the original string.
    refs #15506
    
• src/hg/hgTracks/config.c
  • lines changed 1, context: html, text, full: html, text
    enlarged static buffer that overflowed on mouse strain browser (no redmine).
    
• src/hg/hgTracks/wigTrack.c
  • lines changed 2, context: html, text, full: html, text
    Adding a couple cloneString calls that I think are necessary;
    consider what may happen to wi->file, esp w/"freeMem(currentFile)".
    
• src/hg/htdocs/goldenPath/help/hgIntegratorHelp.html
  • lines changed 12, context: html, text, full: html, text
    Edits based on CR, refs #15484
    
  • lines changed 6, context: html, text, full: html, text
    Edits to choose region step, genome region is not default, refs #14579
    
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 37, context: html, text, full: html, text
    Adding announcement for hgIntegrator, refs #14579
    
• src/hg/htdocs/images/Manis_pentadactyla.jpg
  • lines changed 0, context: html, text, full: html, text
    photo from Caroline Härdter flicker dotpolka www.flickr.com/people/dotpolka/ refs #15515
    
• src/hg/htdocs/inc/globalNavBar.inc
  • lines changed 1, context: html, text, full: html, text
    Since Data Integrator is released, add it to globalNavBar.inc and
    remove the special case hook from web.c.
    refs #14579
    
• src/hg/htdocs/indexNews.html
  • lines changed 87, context: html, text, full: html, text
    Adding announcement for hgIntegrator, refs #14579
    
• src/hg/htdocs/style/nice_menu.css
  • lines changed 3, context: html, text, full: html, text
    Changing menu bar color to the new one selected by Jim, refs #15389
    
• src/hg/js/model/lib/UserRegionsMixin.js
  • lines changed 10, context: html, text, full: html, text
    Use POST as queryForm's method, and use POST for ajax requests, because IE11 can't handle big URLs.
    refs #14579 note 84
    
• src/hg/js/model/lib/cart.js
  • lines changed 62, context: html, text, full: html, text
    Use POST as queryForm's method, and use POST for ajax requests, because IE11 can't handle big URLs.
    refs #14579 note 84
    
• src/hg/lib/hAnno.c
  • lines changed 19, context: html, text, full: html, text
    annoStreamDbFactorSource assumes that 'type factorSource' implies a
    particular set of fields -- but on hgwdev it doesn't because there is
    an older 'type factorSource' table that has BED15 fields. So if the
    fields aren't what we expect for 'type factorSource', just treat it
    as a plain old db table.
    refs #14579 notes 145 & 146.
    
• src/hg/lib/web.c
  • lines changed 9, context: html, text, full: html, text
    Since Data Integrator is released, add it to globalNavBar.inc and
    remove the special case hook from web.c.
    refs #14579
    
• src/hg/makeDb/doc/bosTau8.txt
  • lines changed 1, context: html, text, full: html, text
    eliminate an extra -verbose=10 from many genbank load commands refs #15056
    
• src/hg/makeDb/doc/ce11/initialBuild.txt
  • lines changed 501, context: html, text, full: html, text
    running up genbank refs #15209
    
• src/hg/makeDb/doc/ce11/ucscCompositeAgp.pl
  • lines changed 62, context: html, text, full: html, text
    running up genbank refs #15209
    
• src/hg/makeDb/doc/danRer10/initialBuild.txt
  • lines changed 1, context: html, text, full: html, text
    eliminate an extra -verbose=10 from many genbank load commands refs #15056
    
• src/hg/makeDb/doc/hg19.txt
  • lines changed 59, context: html, text, full: html, text
    addingrn6 lastz/chain/net refs #15476
    
• src/hg/makeDb/doc/hg38/hg19MassiveLift.txt
  • lines changed 11, context: html, text, full: html, text
    Added in documentation for the wgEncode tracks
    
  • lines changed 1, context: html, text, full: html, text
    Added an ENCODE tag to the ENCODE track db
    
• src/hg/makeDb/doc/hg38/hg38.txt
  • lines changed 5, context: html, text, full: html, text
    Add ref to make doc. refs #14733
    
  • lines changed 3, context: html, text, full: html, text
    Modified entry for ENCODE Regulation tracks in main hg38 make doc; added Chris' entries to reg.txt from hg19MassiveLift.txt; refs #14568
    
• src/hg/makeDb/doc/hg38/reg.txt
  • lines changed 10, context: html, text, full: html, text
    Move vocab tables to hg38 as they are human-specific. refs #14353
    
  • lines changed 11, context: html, text, full: html, text
    Modified entry for ENCODE Regulation tracks in main hg38 make doc; added Chris' entries to reg.txt from hg19MassiveLift.txt; refs #14568
    
• src/hg/makeDb/doc/macFas5/initialBuild.txt
  • lines changed 1, context: html, text, full: html, text
    eliminate an extra -verbose=10 from many genbank load commands refs #15056
    
• src/hg/makeDb/doc/micMur2/initialBuild.txt
  • lines changed 34, context: html, text, full: html, text
    wrapped up and in the pushQ 007598 refs #15292
    
• src/hg/makeDb/doc/micMur2/lastzRuns.txt
  • lines changed 81, context: html, text, full: html, text
    wrapped up and in the pushQ 007598 refs #15292
    
• src/hg/makeDb/doc/nasLar1/initialBuild.txt
  • lines changed 1, context: html, text, full: html, text
    eliminate an extra -verbose=10 from many genbank load commands refs #15056
    
• src/hg/makeDb/doc/rhiRox1/initialBuild.txt
  • lines changed 1, context: html, text, full: html, text
    eliminate an extra -verbose=10 from many genbank load commands refs #15056
    
• src/hg/makeDb/doc/rn6.txt
  • lines changed 26, context: html, text, full: html, text
    addingrn6 lastz/chain/net refs #15476
    
• src/hg/makeDb/doc/tarSyr2/initialBuild.txt
  • lines changed 1, context: html, text, full: html, text
    eliminate an extra -verbose=10 from many genbank load commands refs #15056
    
• src/hg/makeDb/genbank/etc/align.dbs
  • lines changed 1, context: html, text, full: html, text
    Added ornAna2 - platypus refs #15098
    
  • lines changed 1, context: html, text, full: html, text
    Added nanPar1 - Tibetan frog refs #15056
    
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 18, context: html, text, full: html, text
    Added manPen1/Pangolin; refs #15515
    
  • lines changed 21, context: html, text, full: html, text
    Added ce11; refs #15209
    
• src/hg/makeDb/genbank/etc/hgwdev.dbs
  • lines changed 2, context: html, text, full: html, text
    Added ornAna2 - platypus refs #15098
    
  • lines changed 1, context: html, text, full: html, text
    Added nanPar1 - Tibetan frog refs #15056
    
• src/hg/makeDb/genbank/src/lib/gbGenome.c
  • lines changed 2, context: html, text, full: html, text
    Added manPen Pangolin/Manis pentadactyla (javanica) refs #15515
    
• src/hg/makeDb/schema/all.joiner
  • lines changed 11, context: html, text, full: html, text
    Added bisBis1 - Bison bison bison refs #15388
    
  • lines changed 1, context: html, text, full: html, text
    updated for ornAna2 table coverage refs #15098
    
  • lines changed 12, context: html, text, full: html, text
    adding nanPar1 - Tibetan frog refs #15056
    
• src/hg/makeDb/trackDb/bonobo/panPan1/trackDb.chainNet.ra
  • lines changed 5, context: html, text, full: html, text
    Forgot to add chainNet.ra, refs #8231
    
• src/hg/makeDb/trackDb/bonobo/panPan1/trackDb.ra
  • lines changed 7, context: html, text, full: html, text
    Making some bonobo tracks more visible at default position since there's not much to see
    
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg.html
  • lines changed 22, context: html, text, full: html, text
    Round 1 of description page changes for ENCODE Regulation tracks; refs #14568,##14731,#14732,#14733
    
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg.ra
  • lines changed 1, context: html, text, full: html, text
    Shorted long label for H3K27Ac parent entry; refs #14568
    
• src/hg/makeDb/trackDb/human/hg38/wgEncodeRegDnase.ra
  • lines changed 6, context: html, text, full: html, text
    Move vocab tables to hg38 as they are human-specific. refs #14353
    
  • lines changed 49, context: html, text, full: html, text
    Trim label lengths for QA. Refs #14733
    
  • lines changed 4, context: html, text, full: html, text
    Alpha sort subgroup lists for QA. refs #14353
    
  • lines changed 6, context: html, text, full: html, text
    More offending labels. refs #14733
    
  • lines changed 6, context: html, text, full: html, text
    Fix misspelled tissue, tnx eagle-eyed Steve H. refs #14353
    
  • lines changed 3, context: html, text, full: html, text
    Trim more long labels. refs #14733
    
• src/hg/makeDb/trackDb/human/hg38/wgEncodeRegMarkH3k27ac.html
  • lines changed 6, context: html, text, full: html, text
    Round 1 of description page changes for ENCODE Regulation tracks; refs #14568,##14731,#14732,#14733
    
• src/hg/makeDb/trackDb/human/hg38/wgEncodeRegMarkH3k4me1.html
  • lines changed 6, context: html, text, full: html, text
    Round 1 of description page changes for ENCODE Regulation tracks; refs #14568,##14731,#14732,#14733
    
• src/hg/makeDb/trackDb/human/hg38/wgEncodeRegMarkH3k4me3.html
  • lines changed 6, context: html, text, full: html, text
    Round 1 of description page changes for ENCODE Regulation tracks; refs #14568,##14731,#14732,#14733
    
• src/hg/makeDb/trackDb/human/hg38/wgEncodeRegTxn.html
  • lines changed 3, context: html, text, full: html, text
    Round 1 of description page changes for ENCODE Regulation tracks; refs #14568,##14731,#14732,#14733
    
• src/hg/makeDb/trackDb/human/lovd.html
  • lines changed 10, context: html, text, full: html, text
    pointer to beacon from LOVD track, refs #15555
    
• src/hg/makeDb/trackDb/makefile
  • lines changed 1, context: html, text, full: html, text
    initial files from makeGenomeDb.pl for manPen1 refs #15515
    
  • lines changed 1, context: html, text, full: html, text
    adding ce11 to the build refs #15209
    
• src/hg/makeDb/trackDb/pangolin/manPen1/description.html
  • lines changed 63, context: html, text, full: html, text
    initial files from makeGenomeDb.pl for manPen1 refs #15515
    
• src/hg/makeDb/trackDb/pangolin/manPen1/gap.html
  • lines changed 30, context: html, text, full: html, text
    initial files from makeGenomeDb.pl for manPen1 refs #15515
    
• src/hg/makeDb/trackDb/pangolin/manPen1/gold.html
  • lines changed 34, context: html, text, full: html, text
    initial files from makeGenomeDb.pl for manPen1 refs #15515
    
• src/hg/makeDb/trackDb/pangolin/manPen1/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    initial files from makeGenomeDb.pl for manPen1 refs #15515
    
• src/hg/makeDb/trackDb/worm/ce11/description.html
  • lines changed 63, context: html, text, full: html, text
    adding ce11 to the build refs #15209
    
• src/hg/makeDb/trackDb/worm/ce11/gap.html
  • lines changed 29, context: html, text, full: html, text
    adding ce11 to the build refs #15209
    
• src/hg/makeDb/trackDb/worm/ce11/gold.html
  • lines changed 33, context: html, text, full: html, text
    adding ce11 to the build refs #15209
    
• src/hg/makeDb/trackDb/worm/ce11/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    adding ce11 to the build refs #15209
    
  • lines changed 5, context: html, text, full: html, text
    add search rule for gold table refs #15209
    
• src/hg/utils/gff3ToGenePred/gff3ToGenePred.c
  • lines changed 4, context: html, text, full: html, text
    more tweaks to support NCBI RefSeq #13673
    
  • lines changed 4, context: html, text, full: html, text
    more changes to support NCBI RefSeq #13673
    
• src/hg/utils/gff3ToGenePred/tests/expected/noIdTest.gp
  • lines changed 3, context: html, text, full: html, text
    more tweaks to support NCBI RefSeq #13673
    
• src/hg/utils/liftList/bigWigList.ra
  • lines changed 113, context: html, text, full: html, text
    A file that is needed for lifting documentation
    
• src/hg/utils/liftList/liftList.c
  • lines changed 106, context: html, text, full: html, text
    Renamed the file liftList to liftManyBigWigs as part of the doc entry for hg19 to hg38 lifts
    
• src/hg/utils/liftList/liftManyBigWigs.c
  • lines changed 106, context: html, text, full: html, text
    Renamed the file liftList to liftManyBigWigs as part of the doc entry for hg19 to hg38 lifts
    
• src/hg/utils/liftList/liftManyBigWigsScript
  • lines changed 6, context: html, text, full: html, text
    renaming a script that was used in lifting bigWigs
    
• src/hg/utils/liftList/liftingScript
  • lines changed 6, context: html, text, full: html, text
    renaming a script that was used in lifting bigWigs
    
• src/lib/udc.c
  • lines changed 12, context: html, text, full: html, text
    Revert "allowing a single redirect in udc info requests, refs #12728"
    
    This reverts commit a90b80696b95a7af02251c0206a11f7e24f3e0c3.
    
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    v318 preview2 refs #15485
    
• src/utils/qa/weeklybld/doHgNearTestRobot.csh
  • lines changed 2, context: html, text, full: html, text
    Replaced bashism with csh-compliant setenv. Thanks Hiram! refs #15485
    

• lines changed: 2149
• files changed: 83