File Changes for tdreszer

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/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 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/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 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/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/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 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/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/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/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/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/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/trackDb/cv/alpha/cv.ra
  • 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.
• 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/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/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 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/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/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/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/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/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/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/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.