Commits for tdreszer
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v243_base to v244_preview (2010-11-02 to 2010-11-16) v244
- Changed some antibodies from 'Input' to 'Control' for uniformity
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeBroadHistone.ra - lines changed 12, context: html, text, full: html, text
- Added 12 more fastq's as links to hg18
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeBroadHistone.ra - lines changed 241, context: html, text, full: html, text
- Added the color we use widely for sub headers
- Added a couple of useful macros for boolean settings
- Added raReadWithFilter to read an ra file and collect a set of related stanza. Useful for cv.ra processing to get all antibodies or all cells
- Added support for typOfTerm settings, allowing a table of contents of all important term types
- src/hg/encode/hgEncodeVocab/hgEncodeVocab.c - lines changed 111, context: html, text, full: html, text
- Added support for getting cv typeOfTerms hash and made the cv whitelist ise cv.ra
- The '...' metadata table now links to term definitions and specific cv defined terms
- Found recursive loop that wigMafs fell into with rightClick. The particular code may not actually be needed and has been ifdef'd OMITted.
- src/hg/hgTracks/hgTracks.c - lines changed 10, context: html, text, full: html, text
- Cricket noticed 15 fastqs missing. The update links 12 from hg18 but 3 remain for Broad to submit
- src/hg/makeDb/doc/encodeDccHg19/broadHistoneBernstein.hg19.txt - lines changed 146, context: html, text, full: html, text
- Added special case for mouse cell lines link showing up in typeOfTerms TOC
- src/hg/encode/hgEncodeVocab/hgEncodeVocab.c - lines changed 12, context: html, text, full: html, text
- Cleaned up unregistered labs and dataTypes. Removed parentTable.
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrHistone.ra - lines changed 12, context: html, text, full: html, text
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhHistone.ra - lines changed 64, context: html, text, full: html, text
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhTfbs.ra - lines changed 392, context: html, text, full: html, text
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeUwDnase.ra - lines changed 384, context: html, text, full: html, text
- Cleaned up unregistered labs and dataTypes. Removed parentTable.
- src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeBroadChipSeq.ra - lines changed 372, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeChromatinMap.ra - lines changed 527, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra - lines changed 25, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeCshlShortRnaSeq.ra - lines changed 55, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeGisDnaPet.ra - lines changed 62, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeGisPet.ra - lines changed 168, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeGisRnaSeq.ra - lines changed 30, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeHelicosRnaSeq.ra - lines changed 1, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeHudsonalphaChipSeq.ra - lines changed 343, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeHudsonalphaCnv.ra - lines changed 6, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeReg.ra - lines changed 5, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeRikenCage.ra - lines changed 101, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeSunyalbanyRnaGeneChip.ra - lines changed 7, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeUwAffyExonArray.ra - lines changed 71, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeUwChIPSeq.ra - lines changed 822, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeUwDGF.ra - lines changed 36, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeUwDnaseSeq.ra - lines changed 163, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeYaleChIPseq.ra - lines changed 278, context: html, text, full: html, text
- Cleaned up unregistered labs and dataTypes. Removed parentTable.
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeBroadHistone.ra - lines changed 529, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra - lines changed 165, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlShortRnaSeq.ra - lines changed 11, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisDnaPet.ra - lines changed 28, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisRnaSeq.ra - lines changed 6, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylSeq.ra - lines changed 44, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra - lines changed 719, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromChip.ra - lines changed 333, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromDnase.ra - lines changed 129, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromFaire.ra - lines changed 203, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeRikenCage.ra - lines changed 20, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhHistone.ra - lines changed 52, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra - lines changed 669, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwAffyExonArray.ra - lines changed 112, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDgf.ra - lines changed 19, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDnase.ra - lines changed 153, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwHistone.ra - lines changed 278, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwTfbs.ra - lines changed 384, context: html, text, full: html, text
- Forgot one instance of 'lab Uw' that should be 'lab UW'
- src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeUwDnaseSeq.ra - lines changed 401, context: html, text, full: html, text
- Adding labs CRG-Guigo and UCSC and grant UCSC as part of metaDb cleanup
- src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 26, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeReg.ra - lines changed 5, context: html, text, full: html, text
- Table of Grants needs to show grant Institution
- src/hg/encode/hgEncodeVocab/hgEncodeVocab.c - lines changed 17, context: html, text, full: html, text
- Validate daf lab and dataType. Remove obsolete parentTable.
- src/hg/encode/encodeValidate/doEncodeValidate.pl - lines changed 26, context: html, text, full: html, text
- As long as mdbs are being cleaned up... removed some labVersions which were duplicate with labExpId
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra - lines changed 17, context: html, text, full: html, text
- Change protocol from 'HudsoneAlpha' to 'HAIB-p1' to avoid term conflict with lab 'HidsonAlpha'
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylRrbs.ra - lines changed 14, context: html, text, full: html, text
- Fixed bug where cell was not showing up in whitelist to track search
- Fixed bug 32 in 1071. Repeated vis changes in track search had unpredictable consequences.
- src/hg/hgTracks/hgTracks.c - lines changed 16, context: html, text, full: html, text
- Brian caught me bugging out. case insensitive sort should really be case insensitive
- Fixed 1480 repoort of show stopper by Mary. mRNA checkboxes were not working.
- Resubmission of almost all Broad hg19 and new submission of peaks and a couple missing fastq
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeBroadHistone.ra - lines changed 3544, context: html, text, full: html, text
- Removed parentTables that snuck back in
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeBroadHistone.ra - lines changed 14, context: html, text, full: html, text
- Added all but one peak tracks. Reorganized a little bit.
- src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHistone.ra - lines changed 1354, context: html, text, full: html, text
- Added broadPeak to signalFilter allowed types
- src/hg/makeDb/trackDb/tagTypes.tab - lines changed 2, context: html, text, full: html, text
- Broad submitted hg19 peaks (finally) and resubmitted most bamsand bigWigs AND 3 missing fastqs
- src/hg/makeDb/doc/encodeDccHg19/broadHistoneBernstein.hg19.txt - lines changed 652, context: html, text, full: html, text
- Had to change tdbVisLimitedByAncestors, because it didn't handle subtracks where view or composite was not at default vis
- Multiple protocols should appear on separate lines.
- src/hg/encode/hgEncodeVocab/hgEncodeVocab.c - lines changed 6, context: html, text, full: html, text
- New16x16 icon for rightClick view
- src/hg/htdocs/images/eye.png - lines changed 0, context: html, text, full: html, text
- Eye needs to be at the bottom, not the middle of the 16x16 png
- src/hg/htdocs/images/eye.png - lines changed 0, context: html, text, full: html, text
- Added some standard bit mask macros
- Added support for pennantIcon as requested by b0b. First use flagging hg18 to hg19 liftOver tracks.
- src/hg/hgTracks/config.c - lines changed 6, context: html, text, full: html, text
- src/hg/hgTracks/hgTracks.c - lines changed 66, context: html, text, full: html, text
- src/hg/makeDb/trackDb/tagTypes.tab - lines changed 1, context: html, text, full: html, text
- Added pennantIcon to README
- src/hg/makeDb/trackDb/README - lines changed 5, context: html, text, full: html, text
- Removed an erroneous freeMem
- Fixed part of redmine 1071.35 where subtrack not selected is made visible. Also half of fix where selecting both composite and subtrack simultaneously will do composite cleanup but not subtrack shaping. That is, composite vis will override selected subtrack vis.
- Support for AJAX callback at initial load to retrieve individual tracks. This is useful if a track has a remote data source and will take a long time to retrieve, then draw the image.
- Simultaneous reshaping and composite cleanup no longer conflict if reshaping goes first.
- src/hg/hgTracks/hgTracks.c - lines changed 7, context: html, text, full: html, text
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