All File Changes

v251_preview2 to v251_base (2011-05-03 to 2011-05-10) v251

• src/ameme/ameme.c
  • lines changed 3, context: html, text, full: html, text
    A large set of tiny changes. These fix a lot of discrepencies with bgcolor and font color declarations which were tripping up docttype 4.01.
• src/ameme/amemeFloat.c
  • lines changed 3, context: html, text, full: html, text
    A large set of tiny changes. These fix a lot of discrepencies with bgcolor and font color declarations which were tripping up docttype 4.01.
• src/ameme/fixpAmeme.c
  • lines changed 3, context: html, text, full: html, text
    A large set of tiny changes. These fix a lot of discrepencies with bgcolor and font color declarations which were tripping up docttype 4.01.
• src/getgene/getgene.c
  • lines changed 2, context: html, text, full: html, text
    A large set of tiny changes. These fix a lot of discrepencies with bgcolor and font color declarations which were tripping up docttype 4.01.
• src/hg/altSplice/affySplice/altProbes.c
  • lines changed 1, context: html, text, full: html, text
    A large set of tiny changes. These fix a lot of discrepencies with bgcolor and font color declarations which were tripping up docttype 4.01.
• src/hg/altSplice/lib/affyPres.as
  • lines changed 10, context: html, text, full: html, text
    added n-scan track for oryCun2
  • lines changed 10, context: html, text, full: html, text
    revert commit that mistakenly deleted some files
• src/hg/altSplice/lib/affyPres.c
  • lines changed 152, context: html, text, full: html, text
    added n-scan track for oryCun2
  • lines changed 152, context: html, text, full: html, text
    revert commit that mistakenly deleted some files
• src/hg/altSplice/lib/affyProbe.as
  • lines changed 24, context: html, text, full: html, text
    added n-scan track for oryCun2
  • lines changed 24, context: html, text, full: html, text
    revert commit that mistakenly deleted some files
• src/hg/altSplice/lib/affyProbe.c
  • lines changed 230, context: html, text, full: html, text
    added n-scan track for oryCun2
  • lines changed 230, context: html, text, full: html, text
    revert commit that mistakenly deleted some files
• src/hg/altSplice/lib/altProbe.as
  • lines changed 20, context: html, text, full: html, text
    added n-scan track for oryCun2
  • lines changed 20, context: html, text, full: html, text
    revert commit that mistakenly deleted some files
• src/hg/altSplice/lib/altProbe.c
  • lines changed 252, context: html, text, full: html, text
    added n-scan track for oryCun2
  • lines changed 252, context: html, text, full: html, text
    revert commit that mistakenly deleted some files
• src/hg/altSplice/lib/altSpliceSite.as
  • lines changed 22, context: html, text, full: html, text
    added n-scan track for oryCun2
  • lines changed 22, context: html, text, full: html, text
    revert commit that mistakenly deleted some files
• src/hg/altSplice/lib/altSpliceSite.c
  • lines changed 333, context: html, text, full: html, text
    added n-scan track for oryCun2
  • lines changed 333, context: html, text, full: html, text
    revert commit that mistakenly deleted some files
• src/hg/altSplice/lib/altSpliceSite.sql
  • lines changed 28, context: html, text, full: html, text
    added n-scan track for oryCun2
  • lines changed 28, context: html, text, full: html, text
    revert commit that mistakenly deleted some files
• src/hg/altSplice/lib/dMatrix.c
  • lines changed 148, context: html, text, full: html, text
    added n-scan track for oryCun2
  • lines changed 148, context: html, text, full: html, text
    revert commit that mistakenly deleted some files
• src/hg/altSplice/lib/exonGraph.as
  • lines changed 58, context: html, text, full: html, text
    added n-scan track for oryCun2
  • lines changed 58, context: html, text, full: html, text
    revert commit that mistakenly deleted some files
• src/hg/altSplice/lib/exonGraph.c
  • lines changed 698, context: html, text, full: html, text
    added n-scan track for oryCun2
  • lines changed 698, context: html, text, full: html, text
    revert commit that mistakenly deleted some files
• src/hg/altSplice/lib/exonGraph.sql
  • lines changed 58, context: html, text, full: html, text
    added n-scan track for oryCun2
  • lines changed 58, context: html, text, full: html, text
    revert commit that mistakenly deleted some files
• src/hg/altSplice/lib/heap.c
  • lines changed 135, context: html, text, full: html, text
    added n-scan track for oryCun2
  • lines changed 135, context: html, text, full: html, text
    revert commit that mistakenly deleted some files
• src/hg/altSplice/lib/heapTest.c
  • lines changed 91, context: html, text, full: html, text
    added n-scan track for oryCun2
  • lines changed 91, context: html, text, full: html, text
    revert commit that mistakenly deleted some files
• src/hg/altSplice/lib/makefile
  • lines changed 38, context: html, text, full: html, text
    added n-scan track for oryCun2
  • lines changed 38, context: html, text, full: html, text
    revert commit that mistakenly deleted some files
• src/hg/altSplice/lib/mouseAPSetEventMap.c
  • lines changed 258, context: html, text, full: html, text
    added n-scan track for oryCun2
  • lines changed 258, context: html, text, full: html, text
    revert commit that mistakenly deleted some files
• src/hg/altSplice/lib/pfamDat.as
  • lines changed 37, context: html, text, full: html, text
    added n-scan track for oryCun2
  • lines changed 37, context: html, text, full: html, text
    revert commit that mistakenly deleted some files
• src/hg/altSplice/lib/pfamDat.c
  • lines changed 657, context: html, text, full: html, text
    added n-scan track for oryCun2
  • lines changed 657, context: html, text, full: html, text
    revert commit that mistakenly deleted some files
• src/hg/altSplice/lib/pfamDat.sql
  • lines changed 43, context: html, text, full: html, text
    added n-scan track for oryCun2
  • lines changed 43, context: html, text, full: html, text
    revert commit that mistakenly deleted some files
• src/hg/altSplice/lib/splice.as
  • lines changed 31, context: html, text, full: html, text
    added n-scan track for oryCun2
  • lines changed 31, context: html, text, full: html, text
    revert commit that mistakenly deleted some files
• src/hg/altSplice/lib/splice.c
  • lines changed 417, context: html, text, full: html, text
    added n-scan track for oryCun2
  • lines changed 417, context: html, text, full: html, text
    revert commit that mistakenly deleted some files
• src/hg/altSplice/lib/spliceGraph.as
  • lines changed 48, context: html, text, full: html, text
    added n-scan track for oryCun2
  • lines changed 48, context: html, text, full: html, text
    revert commit that mistakenly deleted some files
• src/hg/altSplice/lib/spliceGraph.c
  • lines changed 560, context: html, text, full: html, text
    added n-scan track for oryCun2
  • lines changed 560, context: html, text, full: html, text
    revert commit that mistakenly deleted some files
• src/hg/altSplice/lib/spliceGraph.sql
  • lines changed 52, context: html, text, full: html, text
    added n-scan track for oryCun2
  • lines changed 52, context: html, text, full: html, text
    revert commit that mistakenly deleted some files
• src/hg/encode/encodeExp/encodeExp.c
  • lines changed 5, context: html, text, full: html, text
    Nightly backup for experiment table
• src/hg/encode/encodeExp/encodeExpBackup.csh
  • lines changed 19, context: html, text, full: html, text
    Nightly backup for experiment table
• src/hg/encode/encodeValidate/config/labs.ra
  • lines changed 3, context: html, text, full: html, text
    Not sure why we still have this file, but we do.
• src/hg/encode/encodeValidate/doEncodeValidate.pl
  • lines changed 1, context: html, text, full: html, text
    Added validation for tissueSourceType so that it can accept either Individual or Pooled or None when the term is not applicable.
  • lines changed 13, context: html, text, full: html, text
    Added support for uniquness as a cv term ofr mapability tracks. This will be experiment defining but not cv defined.
  • lines changed 13, context: html, text, full: html, text
    Backing out changes to support uniqueness as an expVar. While these changes may be useful in the future, I do not need them now and do not want to destabalize the rickety pipeline code.
• src/hg/encode/hgEncodeDataVersions/hgEncodeDataVersions.c
  • lines changed 1, context: html, text, full: html, text
    A large set of tiny changes. These fix a lot of discrepencies with bgcolor and font color declarations which were tripping up docttype 4.01.
• src/hg/encode/hgEncodeSubmit/app/views/layouts/main.rhtml
  • lines changed 1, context: html, text, full: html, text
    fixed contact and home link
• src/hg/encode/hgEncodeSubmit/public/help.html
  • lines changed 3, context: html, text, full: html, text
    fixed contact and home link
• src/hg/encode/lib/encodePatchTdb.c
  • lines changed 2, context: html, text, full: html, text
    Removed comment that was not true. No changes are needed to support continuation lines.
• src/hg/gigAssembler/ooGreedy/getgene/getgene.c
  • lines changed 2, context: html, text, full: html, text
    A large set of tiny changes. These fix a lot of discrepencies with bgcolor and font color declarations which were tripping up docttype 4.01.
• src/hg/gisaid/gisaidSample/gisaidSample.c
  • lines changed 7, context: html, text, full: html, text
    A large set of tiny changes. These fix a lot of discrepencies with bgcolor and font color declarations which were tripping up docttype 4.01.
• src/hg/gisaid/gisaidSubj/gisaidSubj.c
  • lines changed 7, context: html, text, full: html, text
    A large set of tiny changes. These fix a lot of discrepencies with bgcolor and font color declarations which were tripping up docttype 4.01.
• src/hg/gisaid/gisaidTable/gisaidTable.c
  • lines changed 9, context: html, text, full: html, text
    A large set of tiny changes. These fix a lot of discrepencies with bgcolor and font color declarations which were tripping up docttype 4.01.
• src/hg/gsid/gsidMember/gsidMember.c
  • lines changed 4, context: html, text, full: html, text
    A large set of tiny changes. These fix a lot of discrepencies with bgcolor and font color declarations which were tripping up docttype 4.01.
• src/hg/gsid/gsidPbGateway/gsidPbGateway.c
  • lines changed 6, context: html, text, full: html, text
    A large set of tiny changes. These fix a lot of discrepencies with bgcolor and font color declarations which were tripping up docttype 4.01.
  • lines changed 2, context: html, text, full: html, text
    Reverting span center to old style center tags because CSS didn't work as expected.
• src/hg/gsid/gsidSubj/clinical.c
  • lines changed 3, context: html, text, full: html, text
    A large set of tiny changes. These fix a lot of discrepencies with bgcolor and font color declarations which were tripping up docttype 4.01.
• src/hg/gsid/gsidSubj/gsidSubj.c
  • lines changed 6, context: html, text, full: html, text
    A large set of tiny changes. These fix a lot of discrepencies with bgcolor and font color declarations which were tripping up docttype 4.01.
• src/hg/gsid/gsidSubj3/clinical.c
  • lines changed 4, context: html, text, full: html, text
    A large set of tiny changes. These fix a lot of discrepencies with bgcolor and font color declarations which were tripping up docttype 4.01.
• src/hg/gsid/gsidSubj3/gsidSubj3.c
  • lines changed 6, context: html, text, full: html, text
    A large set of tiny changes. These fix a lot of discrepencies with bgcolor and font color declarations which were tripping up docttype 4.01.
• src/hg/gsid/gsidTable/gsidTable.c
  • lines changed 9, context: html, text, full: html, text
    A large set of tiny changes. These fix a lot of discrepencies with bgcolor and font color declarations which were tripping up docttype 4.01.
• src/hg/hgCert/hgCert.c
  • lines changed 4, context: html, text, full: html, text
    A large set of tiny changes. These fix a lot of discrepencies with bgcolor and font color declarations which were tripping up docttype 4.01.
• src/hg/hgCoordConv/hgCoordConv.c
  • lines changed 2, context: html, text, full: html, text
    A large set of tiny changes. These fix a lot of discrepencies with bgcolor and font color declarations which were tripping up docttype 4.01.
• src/hg/hgCustom/hgCustom.c
  • lines changed 4, context: html, text, full: html, text
    A large set of tiny changes. These fix a lot of discrepencies with bgcolor and font color declarations which were tripping up docttype 4.01.
  • lines changed 2, context: html, text, full: html, text
    Standardized replacement for <P> with cgiDown and worked out more spacing issues in hgFileUi and hgTrackUi.
• src/hg/hgFileSearch/hgFileSearch.c
  • lines changed 1, context: html, text, full: html, text
    Standardized replacement for <P> with cgiDown and worked out more spacing issues in hgFileUi and hgTrackUi.
  • lines changed 2, context: html, text, full: html, text
    Another tweek to hgFileSearch for spacing issues due to paragraph tags.
• src/hg/hgFileUi/hgFileUi.c
  • lines changed 16, context: html, text, full: html, text
    Fixes to spacing issues on hgTrackUi and hgFileUi where navlinks and description page resulted in extra lines. Created subheadingBar div to replace one of the many nested tables and use CSS.
  • lines changed 7, context: html, text, full: html, text
    Standardized replacement for <P> with cgiDown and worked out more spacing issues in hgFileUi and hgTrackUi.
• src/hg/hgGateway/hgGateway.c
  • lines changed 12, context: html, text, full: html, text
    A large set of tiny changes. These fix a lot of discrepencies with bgcolor and font color declarations which were tripping up docttype 4.01.
  • lines changed 8, context: html, text, full: html, text
    Reverting span center to old style center tags because CSS didn't work as expected.
• src/hg/hgGene/altSplice.c
  • lines changed 1, context: html, text, full: html, text
    A large set of tiny changes. These fix a lot of discrepencies with bgcolor and font color declarations which were tripping up docttype 4.01.
• src/hg/hgGeneRing/hgGeneRing.c
  • lines changed 30, context: html, text, full: html, text
    A large set of tiny changes. These fix a lot of discrepencies with bgcolor and font color declarations which were tripping up docttype 4.01.
  • lines changed 17, context: html, text, full: html, text
    Reverting span center to old style center tags because CSS didn't work as expected.
• src/hg/hgHubConnect/hgHubConnect.c
  • lines changed 21, context: html, text, full: html, text
    changed some things around in response to Greg's comments #704
  • lines changed 1, context: html, text, full: html, text
    A large set of tiny changes. These fix a lot of discrepencies with bgcolor and font color declarations which were tripping up docttype 4.01.
• src/hg/hgKnownGeneList/hgKnownGeneList.c
  • lines changed 2, context: html, text, full: html, text
    A large set of tiny changes. These fix a lot of discrepencies with bgcolor and font color declarations which were tripping up docttype 4.01.
  • lines changed 1, context: html, text, full: html, text
    Missing newline at end ??
• src/hg/hgTables/bedList.c
  • lines changed 2, context: html, text, full: html, text
    Standardized replacement for <P> with cgiDown and worked out more spacing issues in hgFileUi and hgTrackUi.
• src/hg/hgTables/correlate.c
  • lines changed 16, context: html, text, full: html, text
    A large set of tiny changes. These fix a lot of discrepencies with bgcolor and font color declarations which were tripping up docttype 4.01.
• src/hg/hgTables/filterFields.c
  • lines changed 2, context: html, text, full: html, text
    Spacing change requested by Mary. redmine 2864.
  • lines changed 4, context: html, text, full: html, text
    Standardized replacement for <P> with cgiDown and worked out more spacing issues in hgFileUi and hgTrackUi.
• src/hg/hgTables/identifiers.c
  • lines changed 2, context: html, text, full: html, text
    Standardized replacement for <P> with cgiDown and worked out more spacing issues in hgFileUi and hgTrackUi.
• src/hg/hgTables/seqOut.c
  • lines changed 2, context: html, text, full: html, text
    Standardized replacement for <P> with cgiDown and worked out more spacing issues in hgFileUi and hgTrackUi.
• src/hg/hgText/hgText.c
  • lines changed 21, context: html, text, full: html, text
    A large set of tiny changes. These fix a lot of discrepencies with bgcolor and font color declarations which were tripping up docttype 4.01.
  • lines changed 6, context: html, text, full: html, text
    Reverting span center to old style center tags because CSS didn't work as expected.
• src/hg/hgText/hgWigText.c
  • lines changed 2, context: html, text, full: html, text
    A large set of tiny changes. These fix a lot of discrepencies with bgcolor and font color declarations which were tripping up docttype 4.01.
• src/hg/hgTrackUi/encodePeakUi.c
  • lines changed 1, context: html, text, full: html, text
    Added some spacing before the first control.
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 13, context: html, text, full: html, text
    Fixes to spacing issues on hgTrackUi and hgFileUi where navlinks and description page resulted in extra lines. Created subheadingBar div to replace one of the many nested tables and use CSS.
  • lines changed 8, context: html, text, full: html, text
    Standardized replacement for <P> with cgiDown and worked out more spacing issues in hgFileUi and hgTrackUi.
• src/hg/hgTracks/config.c
  • lines changed 2, context: html, text, full: html, text
    A large set of tiny changes. These fix a lot of discrepencies with bgcolor and font color declarations which were tripping up docttype 4.01.
  • lines changed 1, context: html, text, full: html, text
    Standardized replacement for <P> with cgiDown and worked out more spacing issues in hgFileUi and hgTrackUi.
• src/hg/hgTracks/hgTracks.c
  • lines changed 1, context: html, text, full: html, text
    Standardized replacement for <P> with cgiDown and worked out more spacing issues in hgFileUi and hgTrackUi.
• src/hg/hgTracks/searchTracks.c
  • lines changed 6, context: html, text, full: html, text
    A large set of tiny changes. These fix a lot of discrepencies with bgcolor and font color declarations which were tripping up docttype 4.01.
  • lines changed 1, context: html, text, full: html, text
    Standardized replacement for <P> with cgiDown and worked out more spacing issues in hgFileUi and hgTrackUi.
• src/hg/hgTracks/simpleTracks.c
  • lines changed 1, context: html, text, full: html, text
    pgSnp's extra mapbox over the bases covered only the bottom one;tweaked it to cover both top and bottom.
• src/hg/hgTracks/vcfTrack.c
  • lines changed 168, context: html, text, full: html, text
    Feature #3711 (center-weighted alpha haplo sorting for vcfTabix):Performance improvement for hacTree: if caller passes in comparison function, then pre-sort the items and pre-cluster adjacent identical items before generating pairs. When many of the inputs are identical, this greatly reduces the number of pairs that the main clustering algorithm starts with. For example, a 1000 Genomes file has genotypes for 1360 people (2720 haplotypes), and starting with all pairs of 2720 haps was impossibly slow for hgTracks. However, in regions of a few tens of thousands of bases and a few tens of variants, in practice there's usually less than 100 distinct haplotypes, which makes it possible to cluster in tenths of seconds instead of timing out. The pre-clustering also makes nice balanced trees; the main clustering step still seems prone to chaining to me, so there's probably still more room for improvement there.
  • lines changed 28, context: html, text, full: html, text
    Feature #2823 (VCF track handler): removing some code that won't be used.
  • lines changed 42, context: html, text, full: html, text
    Feature #3711 (vcfTabix haplotype clustering): added pgSnp-like mouseovertext, but with genotype counts instead of allele counts.
• src/hg/hgc/dbRIP.c
  • lines changed 9, context: html, text, full: html, text
    A large set of tiny changes. These fix a lot of discrepencies with bgcolor and font color declarations which were tripping up docttype 4.01.
• src/hg/hgc/expClick.c
  • lines changed 2, context: html, text, full: html, text
    A large set of tiny changes. These fix a lot of discrepencies with bgcolor and font color declarations which were tripping up docttype 4.01.
  • lines changed 2, context: html, text, full: html, text
    Missing newline at end ??
• src/hg/hgc/hgc.c
  • lines changed 52, context: html, text, full: html, text
    A large set of tiny changes. These fix a lot of discrepencies with bgcolor and font color declarations which were tripping up docttype 4.01.
• src/hg/hgc/lowelab.c
  • lines changed 15, context: html, text, full: html, text
    A large set of tiny changes. These fix a lot of discrepencies with bgcolor and font color declarations which were tripping up docttype 4.01.
• src/hg/hgc/mafClick.c
  • lines changed 4, context: html, text, full: html, text
    A large set of tiny changes. These fix a lot of discrepencies with bgcolor and font color declarations which were tripping up docttype 4.01.
• src/hg/hgc/mgcClick.c
  • lines changed 1, context: html, text, full: html, text
    A large set of tiny changes. These fix a lot of discrepencies with bgcolor and font color declarations which were tripping up docttype 4.01.
• src/hg/hgc/peakClusters.c
  • lines changed 2, context: html, text, full: html, text
    Trimming a couple of unused lines of code that Angie noticed in review.
• src/hg/hgc/regMotif.c
  • lines changed 2, context: html, text, full: html, text
    A large set of tiny changes. These fix a lot of discrepencies with bgcolor and font color declarations which were tripping up docttype 4.01.
• src/hg/hgc/rnaFoldClick.c
  • lines changed 9, context: html, text, full: html, text
    Added link to Jakob's lab mirror site page which has Java applet with more viewing options.
  • lines changed 11, context: html, text, full: html, text
    A large set of tiny changes. These fix a lot of discrepencies with bgcolor and font color declarations which were tripping up docttype 4.01.
• src/hg/hgc/t2g.c
  • lines changed 2, context: html, text, full: html, text
    A large set of tiny changes. These fix a lot of discrepencies with bgcolor and font color declarations which were tripping up docttype 4.01.
• src/hg/htdocs/ENCODE/index.html
  • lines changed 25, context: html, text, full: html, text
    Improvements to warning messages for test server and preview server. Will handle hgwdev-user and variants of genome-preview
  • lines changed 1, context: html, text, full: html, text
    Fix typo
• src/hg/htdocs/admin/mirror.html
  • lines changed 12, context: html, text, full: html, text
    removing 'z' from rsync commands
• src/hg/htdocs/images/phylo/calJac3_13way.png
  • lines changed 0, context: html, text, full: html, text
    changed aspect ratio of image
  • lines changed 0, context: html, text, full: html, text
    use png image from Bob with better aspect ratio
• src/hg/htdocs/indexIntro.html
  • lines changed 15, context: html, text, full: html, text
    Improvements to warning messages for test server and preview server. Will handle hgwdev-user and variants of genome-preview
  • lines changed 1, context: html, text, full: html, text
    Fix typo
• src/hg/htdocs/indexNews.html
  • lines changed 17, context: html, text, full: html, text
    Add ENCODE survey and publication links
  • lines changed 2, context: html, text, full: html, text
    Add link to PLoS article
• src/hg/htdocs/style/HGStyle.css
  • lines changed 4, context: html, text, full: html, text
    Fixes to spacing issues on hgTrackUi and hgFileUi where navlinks and description page resulted in extra lines. Created subheadingBar div to replace one of the many nested tables and use CSS.
  • lines changed 1, context: html, text, full: html, text
    Another tweek to hgFileSearch for spacing issues due to paragraph tags.
  • lines changed 1, context: html, text, full: html, text
    Can't set height on light blue subheadingBar.
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    New version number v251
• src/hg/js/hui.js
  • lines changed 7, context: html, text, full: html, text
    Fixes to spacing issues on hgTrackUi and hgFileUi where navlinks and description page resulted in extra lines. Created subheadingBar div to replace one of the many nested tables and use CSS.
  • lines changed 1, context: html, text, full: html, text
    The nav links are appearing too big in the new CSS scheme.
  • lines changed 1, context: html, text, full: html, text
    One final adjustment for navLinks which ensures the subheadingBar spans the entire page even when it is wider than the window.
• src/hg/lib/cv.c
  • lines changed 5, context: html, text, full: html, text
    Jim wanted this little bit of cleanup to more stadardized function name.
• src/hg/lib/fileUi.c
  • lines changed 12, context: html, text, full: html, text
    Standardized replacement for <P> with cgiDown and worked out more spacing issues in hgFileUi and hgTrackUi.
• src/hg/lib/hdb.c
  • lines changed 3, context: html, text, full: html, text
    make hHostHasPrefix work when run from command line in a non-csh shell
• src/hg/lib/hui.c
  • lines changed 1, context: html, text, full: html, text
    A large set of tiny changes. These fix a lot of discrepencies with bgcolor and font color declarations which were tripping up docttype 4.01.
  • lines changed 7, context: html, text, full: html, text
    Fixes to spacing issues on hgTrackUi and hgFileUi where navlinks and description page resulted in extra lines. Created subheadingBar div to replace one of the many nested tables and use CSS.
  • lines changed 55, context: html, text, full: html, text
    Standardized replacement for <P> with cgiDown and worked out more spacing issues in hgFileUi and hgTrackUi.
• src/hg/lib/tableList.sql
  • lines changed 6, context: html, text, full: html, text
    table list cache; see redmine 3780
• src/hg/lib/web.c
  • lines changed 46, context: html, text, full: html, text
    A large set of tiny changes. These fix a lot of discrepencies with bgcolor and font color declarations which were tripping up docttype 4.01.
  • lines changed 6, context: html, text, full: html, text
    Fixes to spacing issues on hgTrackUi and hgFileUi where navlinks and description page resulted in extra lines. Created subheadingBar div to replace one of the many nested tables and use CSS.
  • lines changed 1, context: html, text, full: html, text
    Nav lonks were broken an large matrices.
  • lines changed 2, context: html, text, full: html, text
    One final adjustment for navLinks which ensures the subheadingBar spans the entire page even when it is wider than the window.
  • lines changed 3, context: html, text, full: html, text
    Blue menubar must be squeezed left with a final empty TD. However some output pages are giant so the width must be not 80 but 95 percent to foce the columns as far left as they need to go.
• src/hg/lib/wigDataStream.c
  • lines changed 2, context: html, text, full: html, text
    A large set of tiny changes. These fix a lot of discrepencies with bgcolor and font color declarations which were tripping up docttype 4.01.
• src/hg/lib/wiggleUtils.c
  • lines changed 4, context: html, text, full: html, text
    A large set of tiny changes. These fix a lot of discrepencies with bgcolor and font color declarations which were tripping up docttype 4.01.
• src/hg/makeDb/doc/bosTau6.txt
  • lines changed 745, context: html, text, full: html, text
    Initial bosTau6 (UMD3.1) assembly setup.
• src/hg/makeDb/doc/calJac3.txt
  • lines changed 215, context: html, text, full: html, text
    Finished GAP and GENE annotation using fixed mafAddIRows
• src/hg/makeDb/doc/danRer7.txt
  • lines changed 1, context: html, text, full: html, text
    finished with 12-way for panTro3
• src/hg/makeDb/doc/encodeDccHg18/broadBernstein.txt
  • lines changed 7, context: html, text, full: html, text
    Checking in the historical documents
• src/hg/makeDb/doc/encodeDccHg18/dukeUtaUncCrawford.txt
  • lines changed 3, context: html, text, full: html, text
    Checking in the historical documents
• src/hg/makeDb/doc/encodeDccHg19/broadHistoneBernstein.hg19.txt
  • lines changed 8, context: html, text, full: html, text
    Checking in the historical documents
• src/hg/makeDb/doc/encodeDccHg19/openChromCrawford.hg19.txt
  • lines changed 55, context: html, text, full: html, text
    Checking in the historical documents
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeHaibMethylRrbs.release2.notes
  • lines changed 12, context: html, text, full: html, text
    DoubleChecking that the realease notes got the last few fastqs
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeYaleRnaSeq.release1.notes
  • lines changed 52, context: html, text, full: html, text
    Dropping all datasets that are suspect and replaceing in the pushQ
• src/hg/makeDb/doc/hg18.txt
  • lines changed 26, context: html, text, full: html, text
    Updating wgEncodeReg TFBS and DNase components so they don't crash on the details page.
• src/hg/makeDb/doc/oryCun2.txt
  • lines changed 25, context: html, text, full: html, text
    added n-scan track for oryCun2
  • lines changed 25, context: html, text, full: html, text
    revert commit that mistakenly deleted some files
  • lines changed 25, context: html, text, full: html, text
    added n-scan track for oryCun2
• src/hg/makeDb/doc/panTro3.txt
  • lines changed 39, context: html, text, full: html, text
    reworking the 12way anno mafs
  • lines changed 73, context: html, text, full: html, text
    working on the 12way downloads
  • lines changed 63, context: html, text, full: html, text
    finished with 12-way for panTro3
• src/hg/makeDb/doc/ucscGenes/mm9.ucscGenes12.csh
  • lines changed 50, context: html, text, full: html, text
    Updating instructions for various pathway things to make them mouse instead of human!
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 2, context: html, text, full: html, text
    adding upstreamGeneTbl for panTro3
• src/hg/makeDb/schema/all.joiner
  • lines changed 3, context: html, text, full: html, text
    adding some ucscToEnsembl definitions for other dbs
  • lines changed 5, context: html, text, full: html, text
    Updating all.joiner for mm9.ucscGene
  • lines changed 20, context: html, text, full: html, text
    Updated/Added IDs related to new OMIM tracks.
• src/hg/makeDb/trackDb/cow/bosTau6/description.html
  • lines changed 129, context: html, text, full: html, text
    Initial descriptions for bosTau6.
• src/hg/makeDb/trackDb/cow/bosTau6/gap.html
  • lines changed 64, context: html, text, full: html, text
    Initial descriptions for bosTau6.
• src/hg/makeDb/trackDb/cow/bosTau6/gold.html
  • lines changed 23, context: html, text, full: html, text
    Initial descriptions for bosTau6.
• src/hg/makeDb/trackDb/cow/bosTau6/trackDb.ra
  • lines changed 40, context: html, text, full: html, text
    Initial descriptions for bosTau6.
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 1, context: html, text, full: html, text
    Added validation list for the attic meta-data variable.
  • lines changed 37, context: html, text, full: html, text
    Registered 2 cell lines Patski and ZhBTc4. As a consequence had to register strain 129/Ola.
  • lines changed 9, context: html, text, full: html, text
    Accepting several provisional stanzas, with a minor change in the labPi line in one stanza
  • lines changed 1, context: html, text, full: html, text
    Added validation for tissueSourceType so that it can accept either Individual or Pooled or None when the term is not applicable.
  • lines changed 57, context: html, text, full: html, text
    Adding several new cell lines, and validation documents for other cell lines. Also adding the type category, so that Morgan's validation scripts have known categories to validate against
  • lines changed 17, context: html, text, full: html, text
    Added a new mouse cell line: ES-Bruce4
  • lines changed 23, context: html, text, full: html, text
    Changed the terms for the cell line, tissue, and primary cell category to conform with Tim's camel case standard
  • lines changed 4, context: html, text, full: html, text
    uniqueness term which is only used by mapability composite, needs expansion to include blacklist/excluded regions distinctions.
  • lines changed 5, context: html, text, full: html, text
    Adding differentiation as a treatment for Wold
  • lines changed 51, context: html, text, full: html, text
    registering three new human cell types
  • lines changed 2, context: html, text, full: html, text
    Added strain information for ES-Bruce4 and updated registered sex for ZhBTc4 from U -> M.
  • lines changed 5, context: html, text, full: html, text
    Added tissueSourceType for each experiment as provided by the lab. Added new term Both, that identifies that processed data was made from replicates using pooled and individual sampling of tissues.
  • lines changed 31, context: html, text, full: html, text
    Added attic terms into the cv, so that validation is against cv and not a list. Fulfills redmine issue: #3830.
  • lines changed 170, context: html, text, full: html, text
    First draft of NHGRI edits
• src/hg/makeDb/trackDb/cv/beta/cv.ra
  • lines changed 114, context: html, text, full: html, text
    Copying CV changes from alpha to beta
• src/hg/makeDb/trackDb/human/evofold.html
  • lines changed 1, context: html, text, full: html, text
    Added VARNA link to the Credit section.
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeBroadChipSeq.ra
  • lines changed 550, context: html, text, full: html, text
    Removed dccAccessions because we will actively block dccAccessions from going out on hg18
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeBroadHmm.ra
  • lines changed 10, context: html, text, full: html, text
    Removed dccAccessions because we will actively block dccAccessions from going out on hg18
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeChromatinMap.ra
  • lines changed 534, context: html, text, full: html, text
    Removed dccAccessions because we will actively block dccAccessions from going out on hg18
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeHudsonalphaChipSeq.ra
  • lines changed 17, context: html, text, full: html, text
    Updated the CTCF meta-data to be associated with the correct antibody name CTCF_(SC-5916)
  • lines changed 4278, context: html, text, full: html, text
    Updated the metaData to include controlId and labExpId to match hg19. Update meta-data in trackDb and mdb.ra for protocol changes. Dropped meta-data and tracks for data that lab requested to revoke.
  • lines changed 336, context: html, text, full: html, text
    Updated labVersion based on lab recomended information. If lab removed information from field, field was deleted.
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeHudsonalphaMethylSeq.ra
  • lines changed 108, context: html, text, full: html, text
    Made a lot of changes according to the labs spreadsheet, issue 55
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeSangerGencode.ra
  • lines changed 6, context: html, text, full: html, text
    Adding a composite stanza with my first draft of expVars
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeYaleRNAseq.ra
  • lines changed 2, context: html, text, full: html, text
    Adding rnaExtract as an expVar to work with hg19 data
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
  • lines changed 5, context: html, text, full: html, text
    Moving to less fragile system for displaying table of metadata in cluster tracks details page on hg18.
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaChipSeq.new.ra
  • lines changed 581, context: html, text, full: html, text
    Updated the metaData to include controlId and labExpId to match hg19. Update meta-data in trackDb and mdb.ra for protocol changes. Dropped meta-data and tracks for data that lab requested to revoke.
• src/hg/makeDb/trackDb/human/hg19/acembly.html
  • lines changed 17, context: html, text, full: html, text
    Fixed some grammar errors. Added two links in the text that seemed helpful. Moved one sentence into a more appropriate location
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeAffyRnaChip.ra
  • lines changed 5308, context: html, text, full: html, text
    Correcting two mdbPrint's gone wrong. This is an attempt to return the status of these files to having the dccAccession numbers
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisDnaPet.ra
  • lines changed 70, context: html, text, full: html, text
    Correcting two mdbPrint's gone wrong. This is an attempt to return the status of these files to having the dccAccession numbers
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisRnaPet.ra
  • lines changed 1277, context: html, text, full: html, text
    Adding the new submissions, some of which are replacements
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibGenotype.ra
  • lines changed 9, context: html, text, full: html, text
    Added the GM12878 back in with the new file
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylRrbs.ra
  • lines changed 2, context: html, text, full: html, text
    Changed the expVars
  • lines changed 2, context: html, text, full: html, text
    removed 2 suspicious geoAccession numbers
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylSeq.ra
  • lines changed 168, context: html, text, full: html, text
    began the cleanup of the metaData for this track including adding fileSortOrder to the trackDb
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra
  • lines changed 142, context: html, text, full: html, text
    Changed antibody=Control to antibody=Input to match hg18 data.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeMapability.ra
  • lines changed 17, context: html, text, full: html, text
    Anshul's blacklist is being added to mapability
  • lines changed 2, context: html, text, full: html, text
    Removed dateUnrestricted because mapability tracks have no restrictions on them
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeRikenCage.ra
  • lines changed 174, context: html, text, full: html, text
    Adding new submissions, mostly clusters and some replacement GM12878, cleaning up metaData so that the table looks clear byt filiing in missing information
  • lines changed 1060, context: html, text, full: html, text
    massive rename to make sure Signals were not called Clusters or Raw
  • lines changed 26, context: html, text, full: html, text
    adding the Clusters for the I40
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSunyRipSeq.ra
  • lines changed 41, context: html, text, full: html, text
    Final clean up for the pushQ, added the antibody information, changed to mean+whiskers, changed the Input to being off, cleaned up the fileSortOrder
  • lines changed 54, context: html, text, full: html, text
    Added md5sums
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUmassDekker5C.ra
  • lines changed 6, context: html, text, full: html, text
    Adding the expVars
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDnase.ra
  • lines changed 169, context: html, text, full: html, text
    Removed Version 1 file meta-data so as not to show up on the RR in fileUi, since deprecated files are still present on the RR.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeYaleRnaSeq.ra
  • lines changed 228, context: html, text, full: html, text
    Dropping all datasets that are suspect and replaceing in the pushQ
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/makefile
  • lines changed 1, context: html, text, full: html, text
    staging metadata for Regulation super track on beta, redmine #3454
  • lines changed 1, context: html, text, full: html, text
    staging SYDH Histone on beta, redmine# 68
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeReg.ra
  • lines changed 233, context: html, text, full: html, text
    staging metadata for Regulation super track on beta, redmine #3454
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeSydhHistone.ra
  • lines changed 1762, context: html, text, full: html, text
    staging SYDH Histone on beta, redmine# 68
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeUwDnase.ra
  • lines changed 169, context: html, text, full: html, text
    venkat removed 8 deprecated files from the metaDb, redmine# 2397
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeUwDnase.ra
  • lines changed 5977, context: html, text, full: html, text
    preparing release of UW DNaseI HS (release 2), redmine# 2397
  • lines changed 169, context: html, text, full: html, text
    venkat removed 8 deprecated files from the metaDb, redmine# 2397
• src/hg/makeDb/trackDb/human/hg19/omimGene2.html
  • lines changed 91, context: html, text, full: html, text
    Created omimGene2.html.
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
  • lines changed 4, context: html, text, full: html, text
    changed the right release tags this time around! staging UW DNaseI (release 2), redmine #2397
  • lines changed 8, context: html, text, full: html, text
    Adding .new files for the trackDb so that we can add fileSortOrder to these tracks
  • lines changed 2, context: html, text, full: html, text
    preparing release of UW DNaseI HS (release 2), redmine# 2397
  • lines changed 1, context: html, text, full: html, text
    staging SYDH Histone on beta, redmine# 68
  • lines changed 1, context: html, text, full: html, text
    Changing the release tags to be with the include statement
• src/hg/makeDb/trackDb/human/hg19/wgEncodeAffyRnaChip.new.ra
  • lines changed 247, context: html, text, full: html, text
    Correcting two mdbPrint's gone wrong. This is an attempt to return the status of these files to having the dccAccession numbers
  • lines changed 1, context: html, text, full: html, text
    Adding .new files for the trackDb so that we can add fileSortOrder to these tracks
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCaltechRnaSeq.new.ra
  • lines changed 36, context: html, text, full: html, text
    Changed the default on/off
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.ra
  • lines changed 258, context: html, text, full: html, text
    Changed the defualt on and off and the celltype for ordering
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.new.ra
  • lines changed 22, context: html, text, full: html, text
    Changed the default on/off
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGisDnaPet.new.ra
  • lines changed 81, context: html, text, full: html, text
    Adding .new files for the trackDb so that we can add fileSortOrder to these tracks
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGisRnaPet.ra
  • lines changed 67, context: html, text, full: html, text
    Changed the cellline names to improve the sort
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGisRnaSeq.new.ra
  • lines changed 174, context: html, text, full: html, text
    Correcting two mdbPrint's gone wrong. This is an attempt to return the status of these files to having the dccAccession numbers
  • lines changed 1, context: html, text, full: html, text
    Adding .new files for the trackDb so that we can add fileSortOrder to these tracks
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibGenotype.ra
  • lines changed 4, context: html, text, full: html, text
    Added the GM12878 back in with the new file
  • lines changed 2, context: html, text, full: html, text
    Fixed the parent name and cell line to merge properly
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylSeq.ra
  • lines changed 1, context: html, text, full: html, text
    began the cleanup of the metaData for this track including adding fileSortOrder to the trackDb
  • lines changed 11, context: html, text, full: html, text
    Changed the cellline names to improve the sort
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibRnaSeq.ra
  • lines changed 16, context: html, text, full: html, text
    Added the A549 cell line as defualt on
• src/hg/makeDb/trackDb/human/hg19/wgEncodeMapability.new.html
  • lines changed 31, context: html, text, full: html, text
    Adding in Anshul's blacklisted regions to the Mapability composite
  • lines changed 11, context: html, text, full: html, text
    Anshul's edit of the methods section.
  • lines changed 26, context: html, text, full: html, text
    Another tweek from Anshul.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeMapability.new.ra
  • lines changed 86, context: html, text, full: html, text
    Correcting two mdbPrint's gone wrong. This is an attempt to return the status of these files to having the dccAccession numbers
  • lines changed 2, context: html, text, full: html, text
    Adding .new files for the trackDb so that we can add fileSortOrder to these tracks
  • lines changed 87, context: html, text, full: html, text
    Undoing a number of changes added by Cricket, as she was unaware that I was working on this track.
  • lines changed 21, context: html, text, full: html, text
    Adding in Anshul's blacklisted regions to the Mapability composite
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromSynth.html
  • lines changed 14, context: html, text, full: html, text
    rearranging a few sentences for better user understanding, redmine #2881
  • lines changed 1, context: html, text, full: html, text
    minor edit, redmine #2881
  • lines changed 1, context: html, text, full: html, text
    changing release month, redmine #2881
• src/hg/makeDb/trackDb/human/hg19/wgEncodeReg.ra
  • lines changed 1, context: html, text, full: html, text
    Showing antibody as well as cell in TFbS details.
  • lines changed 2, context: html, text, full: html, text
    making default value in score filter 100 and changing range of score filter to 100-1000 to reflect the scores included in the track, redmine #3454
• src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.new.ra
  • lines changed 702, context: html, text, full: html, text
    Adding new submissions, mostly clusters and some replacement GM12878, cleaning up metaData so that the table looks clear byt filiing in missing information
  • lines changed 286, context: html, text, full: html, text
    massive rename to make sure Signals were not called Clusters or Raw
  • lines changed 1, context: html, text, full: html, text
    Adding UCSC accesion to the fileSortOrder
  • lines changed 237, context: html, text, full: html, text
    Changed the labels and the defualt on tracks
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyRipSeq.html
  • lines changed 102, context: html, text, full: html, text
    Combined the .new and the .html and added contact information
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyRipSeq.new.html
  • lines changed 136, context: html, text, full: html, text
    Combined the .new and the .html and added contact information
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyRipSeq.ra
  • lines changed 26, context: html, text, full: html, text
    Final clean up for the pushQ, added the antibody information, changed to mean+whiskers, changed the Input to being off, cleaned up the fileSortOrder
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhHistone.html
  • lines changed 17, context: html, text, full: html, text
    fixed grammar issues, rearranged references for SYDH Histone, redmine#68
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhHistone.ra
  • lines changed 28, context: html, text, full: html, text
    Truncated longLabel ENCODE/Stanford/Yale/Davis/Harvard -> ENCODE/SYDH
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.html
  • lines changed 20, context: html, text, full: html, text
    preparing release of UW DNaseI HS (release 2), redmine# 2397
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.new.html
  • lines changed 1, context: html, text, full: html, text
    added release date, redmine # 2397
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.ra
  • lines changed 1567, context: html, text, full: html, text
    preparing release of UW DNaseI HS (release 2), redmine# 2397
• src/hg/makeDb/trackDb/human/hg19/wgEncodeYaleRnaSeq.html
  • lines changed 26, context: html, text, full: html, text
    Dropping all datasets that are suspect and replaceing in the pushQ
• src/hg/makeDb/trackDb/human/hg19/wgEncodeYaleRnaSeq.ra
  • lines changed 93, context: html, text, full: html, text
    Dropping all datasets that are suspect and replaceing in the pushQ
  • lines changed 11, context: html, text, full: html, text
    Changing the release tags to be with the include statement
• src/hg/makeDb/trackDb/initTableList
  • lines changed 18, context: html, text, full: html, text
    init table list cache; see redmine 3780
  • lines changed 11, context: html, text, full: html, text
    utility for making/refreshing tableList (see redmine 3780)
• src/hg/makeDb/trackDb/makeTableList
  • lines changed 27, context: html, text, full: html, text
    utility for making/refreshing tableList (see redmine 3780)
• src/hg/makeDb/trackDb/makefile
  • lines changed 1, context: html, text, full: html, text
    Added bosTau6 to DBS.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrHistone.ra
  • lines changed 443, context: html, text, full: html, text
    Added 8 experiments for TFBS and Histone Track. Update long and short labels. Errors in long labels were 'TFBS TFBS' and 'Histone Histone'.
  • lines changed 154, context: html, text, full: html, text
    Added tissueSourceType for each experiment as provided by the lab. Added new term Both, that identifies that processed data was made from replicates using pooled and individual sampling of tissues.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrTfbs.ra
  • lines changed 157, context: html, text, full: html, text
    Added experiment Spleen Pol2.
  • lines changed 755, context: html, text, full: html, text
    Added 8 experiments for TFBS and Histone Track. Update long and short labels. Errors in long labels were 'TFBS TFBS' and 'Histone Histone'.
  • lines changed 164, context: html, text, full: html, text
    Added tissueSourceType for each experiment as provided by the lab. Added new term Both, that identifies that processed data was made from replicates using pooled and individual sampling of tissues.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodePsuHistone.ra
  • lines changed 1, context: html, text, full: html, text
    adding the Clusters for the I40
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrHistone.ra
  • lines changed 27, context: html, text, full: html, text
    Updated Short label abbreviation for Signal from Sig -> Sg.
  • lines changed 39, context: html, text, full: html, text
    Added 8 experiments for TFBS and Histone Track. Update long and short labels. Errors in long labels were 'TFBS TFBS' and 'Histone Histone'.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrTfbs.ra
  • lines changed 18, context: html, text, full: html, text
    Added experiment Spleen Pol2.
  • lines changed 27, context: html, text, full: html, text
    Updated Short label abbreviation for Signal from Sig -> Sg.
  • lines changed 94, context: html, text, full: html, text
    Added 8 experiments for TFBS and Histone Track. Update long and short labels. Errors in long labels were 'TFBS TFBS' and 'Histone Histone'.
• src/hg/makeDb/trackDb/rabbit/oryCun2/trackDb.ra
  • lines changed 4, context: html, text, full: html, text
    added n-scan track for oryCun2
  • lines changed 4, context: html, text, full: html, text
    revert commit that mistakenly deleted some files
  • lines changed 4, context: html, text, full: html, text
    added n-scan track for oryCun2
• src/hg/makeDb/trackDb/zebrafish/danRer5/trackDb.ra
  • lines changed 29, context: html, text, full: html, text
    Changed U Mass ChIP-Seq from super to composite track.
  • lines changed 27, context: html, text, full: html, text
    Changed color of U Mass ChIP-Seq sub-tracks per data source provider's request.
• src/hg/makeDb/trackDb/zebrafish/danRer7/trackDb.ra
  • lines changed 29, context: html, text, full: html, text
    Changed U Mass ChIP-Seq from super to composite track.
  • lines changed 27, context: html, text, full: html, text
    Changed color of U Mass ChIP-Seq sub-tracks per data source provider's request.
• src/hg/near/hgNear/hgNear.c
  • lines changed 2, context: html, text, full: html, text
    Fixed a couple of color settings which require a '#' before the color.
• src/hg/protein/lib/pbUtil.c
  • lines changed 3, context: html, text, full: html, text
    A large set of tiny changes. These fix a lot of discrepencies with bgcolor and font color declarations which were tripping up docttype 4.01.
• src/hg/protein/pbGlobal/pbGlobal.c
  • lines changed 1, context: html, text, full: html, text
    A large set of tiny changes. These fix a lot of discrepencies with bgcolor and font color declarations which were tripping up docttype 4.01.
• src/hg/protein/pbTracks/pbTracks.c
  • lines changed 1, context: html, text, full: html, text
    A large set of tiny changes. These fix a lot of discrepencies with bgcolor and font color declarations which were tripping up docttype 4.01.
• src/hg/qaPushQ/qaPushQ.c
  • lines changed 5, context: html, text, full: html, text
    A large set of tiny changes. These fix a lot of discrepencies with bgcolor and font color declarations which were tripping up docttype 4.01.
• src/hg/regulate/regClusterTreeCells/makefile
  • lines changed 1, context: html, text, full: html, text
    Fixing test case and improving a comment.
• src/hg/regulate/regClusterTreeCells/regClusterTreeCells.c
  • lines changed 2, context: html, text, full: html, text
    Fixing test case and improving a comment.
• src/hg/txGraph/txBedToGraph/makeGraph.c
  • lines changed 14, context: html, text, full: html, text
    Added more verbose messages, for debugging a problem with a mis-assigned Rfam transcript
• src/hg/visiGene/hgVisiGene/hgVisiGene.c
  • lines changed 10, context: html, text, full: html, text
    VisiGene uses frames and needed appropriate doctype. Also, needed javascript to set image height.
• src/inc/cheapcgi.h
  • lines changed 2, context: html, text, full: html, text
    A large set of tiny changes. These fix a lot of discrepencies with bgcolor and font color declarations which were tripping up docttype 4.01.
  • lines changed 3, context: html, text, full: html, text
    Standardized replacement for <P> with cgiDown and worked out more spacing issues in hgFileUi and hgTrackUi.
• src/inc/hacTree.h
  • lines changed 19, context: html, text, full: html, text
    Feature #3711 (center-weighted alpha haplo sorting for vcfTabix):Performance improvement for hacTree: if caller passes in comparison function, then pre-sort the items and pre-cluster adjacent identical items before generating pairs. When many of the inputs are identical, this greatly reduces the number of pairs that the main clustering algorithm starts with. For example, a 1000 Genomes file has genotypes for 1360 people (2720 haplotypes), and starting with all pairs of 2720 haps was impossibly slow for hgTracks. However, in regions of a few tens of thousands of bases and a few tens of variants, in practice there's usually less than 100 distinct haplotypes, which makes it possible to cluster in tenths of seconds instead of timing out. The pre-clustering also makes nice balanced trees; the main clustering step still seems prone to chaining to me, so there's probably still more room for improvement there.
• src/inc/ra.h
  • lines changed 20, context: html, text, full: html, text
    Removed obsolete support for ra files that don't tolerate continuation lines.
• src/lib/bwgCreate.c
  • lines changed 28, context: html, text, full: html, text
    Making wigToBigWig detect overlaps in input.
• src/lib/cheapcgi.c
  • lines changed 6, context: html, text, full: html, text
    Standardized replacement for <P> with cgiDown and worked out more spacing issues in hgFileUi and hgTrackUi.
• src/lib/hacTree.c
  • lines changed 109, context: html, text, full: html, text
    Feature #3711 (center-weighted alpha haplo sorting for vcfTabix):Performance improvement for hacTree: if caller passes in comparison function, then pre-sort the items and pre-cluster adjacent identical items before generating pairs. When many of the inputs are identical, this greatly reduces the number of pairs that the main clustering algorithm starts with. For example, a 1000 Genomes file has genotypes for 1360 people (2720 haplotypes), and starting with all pairs of 2720 haps was impossibly slow for hgTracks. However, in regions of a few tens of thousands of bases and a few tens of variants, in practice there's usually less than 100 distinct haplotypes, which makes it possible to cluster in tenths of seconds instead of timing out. The pre-clustering also makes nice balanced trees; the main clustering step still seems prone to chaining to me, so there's probably still more room for improvement there.
  • lines changed 1, context: html, text, full: html, text
    Fix for warning message produced only when -O is used: compiler thinksa variable might be used uninitialized, although it is initialized in all if/else cases. Thanks Tim for catching that!
  • lines changed 64, context: html, text, full: html, text
    Code Review #3822: Added long explanatory comment for main clusteringstep based on Jim's suggestions. In the process, I realized that I'm using a pool not a true heap, so I changed variable names and comments accordingly.
• src/lib/htmshell.c
  • lines changed 1, context: html, text, full: html, text
    Fixed a couple of color settings which require a '#' before the color.
• src/lib/peakCluster.c
  • lines changed 3, context: html, text, full: html, text
    Improving comment.
• src/lib/ra.c
  • lines changed 62, context: html, text, full: html, text
    Removed obsolete support for ra files that don't tolerate continuation lines.
  • lines changed 15, context: html, text, full: html, text
    Noticed possible bug in raFoldInOneRetName and made simple case of raNextTagVal more efficient.
• src/lib/seqOut.c
  • lines changed 1, context: html, text, full: html, text
    Greg found this one was supposed to be color: not font-color:
• src/lib/tests/expected/hacTreeTest.out
  • lines changed 63, context: html, text, full: html, text
    Feature #3711 (center-weighted alpha haplo sorting for vcfTabix):Performance improvement for hacTree: if caller passes in comparison function, then pre-sort the items and pre-cluster adjacent identical items before generating pairs. When many of the inputs are identical, this greatly reduces the number of pairs that the main clustering algorithm starts with. For example, a 1000 Genomes file has genotypes for 1360 people (2720 haplotypes), and starting with all pairs of 2720 haps was impossibly slow for hgTracks. However, in regions of a few tens of thousands of bases and a few tens of variants, in practice there's usually less than 100 distinct haplotypes, which makes it possible to cluster in tenths of seconds instead of timing out. The pre-clustering also makes nice balanced trees; the main clustering step still seems prone to chaining to me, so there's probably still more room for improvement there.
• src/lib/tests/hacTreeTest.c
  • lines changed 11, context: html, text, full: html, text
    Feature #3711 (center-weighted alpha haplo sorting for vcfTabix):Performance improvement for hacTree: if caller passes in comparison function, then pre-sort the items and pre-cluster adjacent identical items before generating pairs. When many of the inputs are identical, this greatly reduces the number of pairs that the main clustering algorithm starts with. For example, a 1000 Genomes file has genotypes for 1360 people (2720 haplotypes), and starting with all pairs of 2720 haps was impossibly slow for hgTracks. However, in regions of a few tens of thousands of bases and a few tens of variants, in practice there's usually less than 100 distinct haplotypes, which makes it possible to cluster in tenths of seconds instead of timing out. The pre-clustering also makes nice balanced trees; the main clustering step still seems prone to chaining to me, so there's probably still more room for improvement there.
• src/lib/tests/input/hacTreeTest.txt
  • lines changed 20, context: html, text, full: html, text
    Feature #3711 (center-weighted alpha haplo sorting for vcfTabix):Performance improvement for hacTree: if caller passes in comparison function, then pre-sort the items and pre-cluster adjacent identical items before generating pairs. When many of the inputs are identical, this greatly reduces the number of pairs that the main clustering algorithm starts with. For example, a 1000 Genomes file has genotypes for 1360 people (2720 haplotypes), and starting with all pairs of 2720 haps was impossibly slow for hgTracks. However, in regions of a few tens of thousands of bases and a few tens of variants, in practice there's usually less than 100 distinct haplotypes, which makes it possible to cluster in tenths of seconds instead of timing out. The pre-clustering also makes nice balanced trees; the main clustering step still seems prone to chaining to me, so there's probably still more room for improvement there.
• src/product/README.QuickStart
  • lines changed 4, context: html, text, full: html, text
    removing the -z argument from any mention of the rsync command since it only causes trouble
• src/product/README.install
  • lines changed 3, context: html, text, full: html, text
    removing the -z argument from any mention of the rsync command since it only causes trouble
• src/product/scripts/browserEnvironment.txt
  • lines changed 1, context: html, text, full: html, text
    removing the -z argument from any mention of the rsync command since it only causes trouble
• src/utils/qa/countPerChrom.csh
  • lines changed 1, context: html, text, full: html, text
    Fixed the file cleanup at the end so that files are not left around when not debugging.
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 3, context: html, text, full: html, text
    v251 final build
• src/xenoAli/smithWat/smithWat.c
  • lines changed 2, context: html, text, full: html, text
    Another insignificant font color change that I forgot to check in yesterday.

• lines changed: 42605
• files changed: 336