File Changes for tdreszer

v243_base to v244_preview (2010-11-02 to 2010-11-16) v244

• src/hg/encode/encodeValidate/doEncodeValidate.pl
  • lines changed 26, context: html, text, full: html, text
    Validate daf lab and dataType. Remove obsolete parentTable.
• src/hg/encode/hgEncodeVocab/hgEncodeVocab.c
  • lines changed 111, context: html, text, full: html, text
    Added support for typOfTerm settings, allowing a table of contents of all important term types
  • lines changed 12, context: html, text, full: html, text
    Added special case for mouse cell lines link showing up in typeOfTerms TOC
  • lines changed 17, context: html, text, full: html, text
    Table of Grants needs to show grant Institution
  • lines changed 6, context: html, text, full: html, text
    Multiple protocols should appear on separate lines.
• src/hg/hgTracks/config.c
  • lines changed 6, context: html, text, full: html, text
    Added support for pennantIcon as requested by b0b. First use flagging hg18 to hg19 liftOver tracks.
• src/hg/hgTracks/hgTracks.c
  • lines changed 10, context: html, text, full: html, text
    Found recursive loop that wigMafs fell into with rightClick. The particular code may not actually be needed and has been ifdef'd OMITted.
  • lines changed 16, context: html, text, full: html, text
    Fixed bug 32 in 1071. Repeated vis changes in track search had unpredictable consequences.
  • lines changed 66, context: html, text, full: html, text
    Added support for pennantIcon as requested by b0b. First use flagging hg18 to hg19 liftOver tracks.
  • lines changed 7, context: html, text, full: html, text
    Simultaneous reshaping and composite cleanup no longer conflict if reshaping goes first.
• src/hg/htdocs/images/eye.png
  • lines changed 0, context: html, text, full: html, text
    New16x16 icon for rightClick view
  • 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/inc/hui.h
  • lines changed 3, context: html, text, full: html, text
    Added support for pennantIcon as requested by b0b. First use flagging hg18 to hg19 liftOver tracks.
• src/hg/inc/mdb.h
  • lines changed 4, context: html, text, full: html, text
    Added support for getting cv typeOfTerms hash and made the cv whitelist ise cv.ra
• src/hg/js/hgTracks.js
  • lines changed 10, context: html, text, full: html, text
    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.
• src/hg/lib/cart.c
  • lines changed 52, context: html, text, full: html, text
    Fixed bug 32 in 1071. Repeated vis changes in track search had unpredictable consequences.
  • lines changed 22, context: html, text, full: html, text
    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.
• src/hg/lib/hui.c
  • lines changed 50, context: html, text, full: html, text
    The '...' metadata table now links to term definitions and specific cv defined terms
  • lines changed 10, context: html, text, full: html, text
    Fixed 1480 repoort of show stopper by Mary. mRNA checkboxes were not working.
  • lines changed 1, 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
  • lines changed 36, context: html, text, full: html, text
    Added support for pennantIcon as requested by b0b. First use flagging hg18 to hg19 liftOver tracks.
  • lines changed 1, context: html, text, full: html, text
    Removed an erroneous freeMem
• src/hg/lib/mdb.c
  • lines changed 122, context: html, text, full: html, text
    Added support for getting cv typeOfTerms hash and made the cv whitelist ise cv.ra
  • lines changed 5, context: html, text, full: html, text
    Fixed bug where cell was not showing up in whitelist to track search
• src/hg/makeDb/doc/encodeDccHg19/broadHistoneBernstein.hg19.txt
  • lines changed 146, context: html, text, full: html, text
    Cricket noticed 15 fastqs missing. The update links 12 from hg18 but 3 remain for Broad to submit
  • lines changed 652, context: html, text, full: html, text
    Broad submitted hg19 peaks (finally) and resubmitted most bamsand bigWigs AND 3 missing fastqs
• src/hg/makeDb/trackDb/README
  • lines changed 5, context: html, text, full: html, text
    Added pennantIcon to README
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 26, context: html, text, full: html, text
    Adding labs CRG-Guigo and UCSC and grant UCSC as part of metaDb cleanup
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeBroadChipSeq.ra
  • lines changed 372, context: html, text, full: html, text
    Cleaned up unregistered labs and dataTypes. Removed parentTable.
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeChromatinMap.ra
  • lines changed 527, context: html, text, full: html, text
    Cleaned up unregistered labs and dataTypes. Removed parentTable.
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra
  • lines changed 25, context: html, text, full: html, text
    Cleaned up unregistered labs and dataTypes. Removed parentTable.
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeCshlShortRnaSeq.ra
  • lines changed 55, context: html, text, full: html, text
    Cleaned up unregistered labs and dataTypes. Removed parentTable.
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeGisDnaPet.ra
  • lines changed 62, context: html, text, full: html, text
    Cleaned up unregistered labs and dataTypes. Removed parentTable.
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeGisPet.ra
  • lines changed 168, context: html, text, full: html, text
    Cleaned up unregistered labs and dataTypes. Removed parentTable.
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeGisRnaSeq.ra
  • lines changed 30, context: html, text, full: html, text
    Cleaned up unregistered labs and dataTypes. Removed parentTable.
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeHelicosRnaSeq.ra
  • lines changed 1, context: html, text, full: html, text
    Cleaned up unregistered labs and dataTypes. Removed parentTable.
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeHudsonalphaChipSeq.ra
  • lines changed 343, context: html, text, full: html, text
    Cleaned up unregistered labs and dataTypes. Removed parentTable.
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeHudsonalphaCnv.ra
  • lines changed 6, context: html, text, full: html, text
    Cleaned up unregistered labs and dataTypes. Removed parentTable.
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeReg.ra
  • lines changed 5, context: html, text, full: html, text
    Cleaned up unregistered labs and dataTypes. Removed parentTable.
  • lines changed 5, context: html, text, full: html, text
    Adding labs CRG-Guigo and UCSC and grant UCSC as part of metaDb cleanup
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeRikenCage.ra
  • lines changed 101, context: html, text, full: html, text
    Cleaned up unregistered labs and dataTypes. Removed parentTable.
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeSunyalbanyRnaGeneChip.ra
  • lines changed 7, context: html, text, full: html, text
    Cleaned up unregistered labs and dataTypes. Removed parentTable.
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeUwAffyExonArray.ra
  • lines changed 71, context: html, text, full: html, text
    Cleaned up unregistered labs and dataTypes. Removed parentTable.
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeUwChIPSeq.ra
  • lines changed 822, context: html, text, full: html, text
    Cleaned up unregistered labs and dataTypes. Removed parentTable.
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeUwDGF.ra
  • lines changed 36, context: html, text, full: html, text
    Cleaned up unregistered labs and dataTypes. Removed parentTable.
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeUwDnaseSeq.ra
  • lines changed 163, context: html, text, full: html, text
    Cleaned up unregistered labs and dataTypes. Removed parentTable.
  • lines changed 401, 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/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 12, context: html, text, full: html, text
    Changed some antibodies from 'Input' to 'Control' for uniformity
  • lines changed 241, context: html, text, full: html, text
    Added 12 more fastq's as links to hg18
  • lines changed 529, context: html, text, full: html, text
    Cleaned up unregistered labs and dataTypes. Removed parentTable.
  • lines changed 3544, context: html, text, full: html, text
    Resubmission of almost all Broad hg19 and new submission of peaks and a couple missing fastq
  • lines changed 14, context: html, text, full: html, text
    Removed parentTables that snuck back in
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra
  • lines changed 165, context: html, text, full: html, text
    Cleaned up unregistered labs and dataTypes. Removed parentTable.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlShortRnaSeq.ra
  • lines changed 11, context: html, text, full: html, text
    Cleaned up unregistered labs and dataTypes. Removed parentTable.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisDnaPet.ra
  • lines changed 28, context: html, text, full: html, text
    Cleaned up unregistered labs and dataTypes. Removed parentTable.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisRnaSeq.ra
  • lines changed 6, context: html, text, full: html, text
    Cleaned up unregistered labs and dataTypes. Removed parentTable.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylRrbs.ra
  • lines changed 14, 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/wgEncodeHaibMethylSeq.ra
  • lines changed 44, context: html, text, full: html, text
    Cleaned up unregistered labs and dataTypes. Removed parentTable.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra
  • lines changed 719, context: html, text, full: html, text
    Cleaned up unregistered labs and dataTypes. Removed parentTable.
  • lines changed 17, 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/wgEncodeOpenChromChip.ra
  • lines changed 333, context: html, text, full: html, text
    Cleaned up unregistered labs and dataTypes. Removed parentTable.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromDnase.ra
  • lines changed 129, context: html, text, full: html, text
    Cleaned up unregistered labs and dataTypes. Removed parentTable.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromFaire.ra
  • lines changed 203, context: html, text, full: html, text
    Cleaned up unregistered labs and dataTypes. Removed parentTable.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeRikenCage.ra
  • lines changed 20, context: html, text, full: html, text
    Cleaned up unregistered labs and dataTypes. Removed parentTable.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhHistone.ra
  • lines changed 52, context: html, text, full: html, text
    Cleaned up unregistered labs and dataTypes. Removed parentTable.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra
  • lines changed 669, context: html, text, full: html, text
    Cleaned up unregistered labs and dataTypes. Removed parentTable.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwAffyExonArray.ra
  • lines changed 112, context: html, text, full: html, text
    Cleaned up unregistered labs and dataTypes. Removed parentTable.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDgf.ra
  • lines changed 19, context: html, text, full: html, text
    Cleaned up unregistered labs and dataTypes. Removed parentTable.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDnase.ra
  • lines changed 153, context: html, text, full: html, text
    Cleaned up unregistered labs and dataTypes. Removed parentTable.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwHistone.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/wgEncodeUwTfbs.ra
  • lines changed 384, context: html, text, full: html, text
    Cleaned up unregistered labs and dataTypes. Removed parentTable.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHistone.ra
  • lines changed 1354, context: html, text, full: html, text
    Added all but one peak tracks. Reorganized a little bit.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrHistone.ra
  • 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/wgEncodeSydhHistone.ra
  • lines changed 64, context: html, text, full: html, text
    Cleaned up unregistered labs and dataTypes. Removed parentTable.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhTfbs.ra
  • lines changed 392, context: html, text, full: html, text
    Cleaned up unregistered labs and dataTypes. Removed parentTable.
• 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/tagTypes.tab
  • lines changed 2, context: html, text, full: html, text
    Added broadPeak to signalFilter allowed types
  • lines changed 1, context: html, text, full: html, text
    Added support for pennantIcon as requested by b0b. First use flagging hg18 to hg19 liftOver tracks.
• src/inc/cheapcgi.h
  • lines changed 1, context: html, text, full: html, text
    Added the color we use widely for sub headers
• src/inc/common.h
  • lines changed 6, context: html, text, full: html, text
    Added a couple of useful macros for boolean settings
  • lines changed 6, context: html, text, full: html, text
    Added some standard bit mask macros
• src/inc/ra.h
  • lines changed 5, context: html, text, full: html, text
    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
• src/lib/common.c
  • lines changed 1, context: html, text, full: html, text
    Brian caught me bugging out. case insensitive sort should really be case insensitive
• src/lib/ra.c
  • lines changed 34, context: html, text, full: html, text
    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