Commits for tdreszer
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v251_preview2 to v251_base (2011-05-03 to 2011-05-10) v251
- Removed obsolete support for ra files that don't tolerate continuation lines.
- Removed obsolete support for ra files that don't tolerate continuation lines.
- Undoing a number of changes added by Cricket, as she was unaware that I was working on this track.
- src/hg/makeDb/trackDb/human/hg19/wgEncodeMapability.new.ra - lines changed 87, 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/cv/alpha/cv.ra - lines changed 4, context: html, text, full: html, text
- Not sure why we still have this file, but we do.
- src/hg/encode/encodeValidate/config/labs.ra - lines changed 3, 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.
- src/hg/encode/encodeValidate/doEncodeValidate.pl - lines changed 13, 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/wgEncodeBroadChipSeq.ra - lines changed 550, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeBroadHmm.ra - lines changed 10, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeChromatinMap.ra - lines changed 534, context: html, text, full: html, text
- Anshul's blacklist is being added to mapability
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeMapability.ra - lines changed 17, context: html, text, full: html, text
- Removed dateUnrestricted because mapability tracks have no restrictions on them
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeMapability.ra - lines changed 2, context: html, text, full: html, text
- Adding in Anshul's blacklisted regions to the Mapability composite
- src/hg/makeDb/trackDb/human/hg19/wgEncodeMapability.new.html - lines changed 31, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg19/wgEncodeMapability.new.ra - lines changed 21, context: html, text, full: html, text
- Greg found this one was supposed to be color: not font-color:
- Fixed a couple of color settings which require a '#' before the color.
- src/hg/near/hgNear/hgNear.c - lines changed 2, context: html, text, full: html, text
- Noticed possible bug in raFoldInOneRetName and made simple case of raNextTagVal more efficient.
- 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
- src/hg/encode/hgEncodeDataVersions/hgEncodeDataVersions.c - lines changed 1, context: html, text, full: html, text
- src/hg/gigAssembler/ooGreedy/getgene/getgene.c - lines changed 2, context: html, text, full: html, text
- src/hg/gisaid/gisaidSample/gisaidSample.c - lines changed 7, context: html, text, full: html, text
- src/hg/gisaid/gisaidSubj/gisaidSubj.c - lines changed 7, context: html, text, full: html, text
- src/hg/gisaid/gisaidTable/gisaidTable.c - lines changed 9, context: html, text, full: html, text
- src/hg/gsid/gsidMember/gsidMember.c - lines changed 4, context: html, text, full: html, text
- src/hg/gsid/gsidPbGateway/gsidPbGateway.c - lines changed 6, context: html, text, full: html, text
- src/hg/gsid/gsidSubj/clinical.c - lines changed 3, context: html, text, full: html, text
- src/hg/gsid/gsidSubj/gsidSubj.c - lines changed 6, context: html, text, full: html, text
- src/hg/gsid/gsidSubj3/clinical.c - lines changed 4, context: html, text, full: html, text
- src/hg/gsid/gsidSubj3/gsidSubj3.c - lines changed 6, context: html, text, full: html, text
- src/hg/gsid/gsidTable/gsidTable.c - lines changed 9, context: html, text, full: html, text
- src/hg/hgCoordConv/hgCoordConv.c - lines changed 2, context: html, text, full: html, text
- src/hg/hgCustom/hgCustom.c - lines changed 4, context: html, text, full: html, text
- src/hg/hgGateway/hgGateway.c - lines changed 12, context: html, text, full: html, text
- src/hg/hgGene/altSplice.c - lines changed 1, context: html, text, full: html, text
- src/hg/hgGeneRing/hgGeneRing.c - lines changed 30, context: html, text, full: html, text
- src/hg/hgHubConnect/hgHubConnect.c - lines changed 1, context: html, text, full: html, text
- src/hg/hgKnownGeneList/hgKnownGeneList.c - lines changed 2, context: html, text, full: html, text
- src/hg/hgTables/correlate.c - lines changed 16, context: html, text, full: html, text
- src/hg/hgText/hgText.c - lines changed 21, context: html, text, full: html, text
- src/hg/hgText/hgWigText.c - lines changed 2, context: html, text, full: html, text
- src/hg/hgTracks/config.c - lines changed 2, context: html, text, full: html, text
- src/hg/hgTracks/searchTracks.c - lines changed 6, context: html, text, full: html, text
- src/hg/hgc/rnaFoldClick.c - lines changed 11, context: html, text, full: html, text
- src/hg/lib/wigDataStream.c - lines changed 2, context: html, text, full: html, text
- src/hg/lib/wiggleUtils.c - lines changed 4, context: html, text, full: html, text
- src/hg/protein/lib/pbUtil.c - lines changed 3, context: html, text, full: html, text
- src/hg/protein/pbGlobal/pbGlobal.c - lines changed 1, context: html, text, full: html, text
- src/hg/protein/pbTracks/pbTracks.c - lines changed 1, context: html, text, full: html, text
- src/hg/qaPushQ/qaPushQ.c - lines changed 5, context: html, text, full: html, text
- Missing newline at end ??
- src/hg/hgKnownGeneList/hgKnownGeneList.c - lines changed 1, context: html, text, full: html, text
- Reverting span center to old style center tags because CSS didn't work as expected.
- src/hg/gsid/gsidPbGateway/gsidPbGateway.c - lines changed 2, context: html, text, full: html, text
- src/hg/hgGateway/hgGateway.c - lines changed 8, context: html, text, full: html, text
- src/hg/hgGeneRing/hgGeneRing.c - lines changed 17, context: html, text, full: html, text
- Jim wanted this little bit of cleanup to more stadardized function name.
- Removed comment that was not true. No changes are needed to support continuation lines.
- src/hg/encode/lib/encodePatchTdb.c - lines changed 2, context: html, text, full: html, text
- Checking in the historical documents
- src/hg/makeDb/doc/encodeDccHg18/broadBernstein.txt - lines changed 7, context: html, text, full: html, text
- src/hg/makeDb/doc/encodeDccHg18/dukeUtaUncCrawford.txt - lines changed 3, context: html, text, full: html, text
- src/hg/makeDb/doc/encodeDccHg19/broadHistoneBernstein.hg19.txt - lines changed 8, context: html, text, full: html, text
- src/hg/makeDb/doc/encodeDccHg19/openChromCrawford.hg19.txt - lines changed 55, 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/encodeValidate/doEncodeValidate.pl - lines changed 13, context: html, text, full: html, text
- Spacing change requested by Mary. redmine 2864.
- src/hg/hgTables/filterFields.c - lines changed 2, context: html, text, full: html, text
- Another insignificant font color change that I forgot to check in yesterday.
- src/xenoAli/smithWat/smithWat.c - lines changed 2, context: html, text, full: html, text
- Anshul's edit of the methods section.
- src/hg/makeDb/trackDb/human/hg19/wgEncodeMapability.new.html - lines changed 11, context: html, text, full: html, text
- Another tweek from Anshul.
- src/hg/makeDb/trackDb/human/hg19/wgEncodeMapability.new.html - lines changed 26, 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.
- src/hg/hgFileUi/hgFileUi.c - lines changed 16, context: html, text, full: html, text
- src/hg/hgTrackUi/hgTrackUi.c - lines changed 13, context: html, text, full: html, text
- src/hg/htdocs/style/HGStyle.css - 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/hgCustom/hgCustom.c - lines changed 2, context: html, text, full: html, text
- src/hg/hgFileSearch/hgFileSearch.c - lines changed 1, context: html, text, full: html, text
- src/hg/hgFileUi/hgFileUi.c - lines changed 7, context: html, text, full: html, text
- src/hg/hgTables/bedList.c - lines changed 2, context: html, text, full: html, text
- src/hg/hgTables/filterFields.c - lines changed 4, context: html, text, full: html, text
- src/hg/hgTables/identifiers.c - lines changed 2, context: html, text, full: html, text
- src/hg/hgTables/seqOut.c - lines changed 2, context: html, text, full: html, text
- src/hg/hgTrackUi/hgTrackUi.c - lines changed 8, context: html, text, full: html, text
- src/hg/hgTracks/config.c - lines changed 1, context: html, text, full: html, text
- src/hg/hgTracks/hgTracks.c - lines changed 1, context: html, text, full: html, text
- src/hg/hgTracks/searchTracks.c - lines changed 1, context: html, text, full: html, text
- Another tweek to hgFileSearch for spacing issues due to paragraph tags.
- src/hg/hgFileSearch/hgFileSearch.c - lines changed 2, context: html, text, full: html, text
- src/hg/htdocs/style/HGStyle.css - lines changed 1, context: html, text, full: html, text
- The nav links are appearing too big in the new CSS scheme.
- Nav lonks were broken an large matrices.
- One final adjustment for navLinks which ensures the subheadingBar spans the entire page even when it is wider than the window.
- VisiGene uses frames and needed appropriate doctype. Also, needed javascript to set image height.
- src/hg/visiGene/hgVisiGene/hgVisiGene.c - lines changed 10, context: html, text, full: html, text
- Can't set height on light blue subheadingBar.
- src/hg/htdocs/style/HGStyle.css - lines changed 1, 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.
- Added some spacing before the first control.
- src/hg/hgTrackUi/encodePeakUi.c - lines changed 1, context: html, text, full: html, text
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