File Changes for hiram

v263_preview2 to v263_base (2011-02-07 to 2012-02-14) v263

• src/hg/hgGene/rgdInfo.c
  • lines changed 1, context: html, text, full: html, text
    fixup UniGene cluster ID to remove Rn. from the name redmine 29
• src/hg/hgTracks/hgTracks.c
  • lines changed 1, context: html, text, full: html, text
    hDbExists is not the function to use to see if a Db exists, that is only for hgcentral
• src/hg/lib/ensFace.c
  • lines changed 1, context: html, text, full: html, text
    hDbExists is only for assembly databases to see if they are in dbDb, to see if a database exists, use sqlDatabaseExists
• src/hg/makeDb/doc/fr3.txt
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    starting on 8-way multiz
• src/hg/makeDb/doc/gorGor3.txt
  • lines changed 4, context: html, text, full: html, text
    document upstreamGeneTbl choice
• src/hg/makeDb/doc/latCha1.txt
  • lines changed 2, context: html, text, full: html, text
    indicate windowmaskerSdust feature bits result
• src/hg/makeDb/doc/mm10.txt
  • lines changed 260, context: html, text, full: html, text
    getting ready to start genbank
  • lines changed 204, context: html, text, full: html, text
    genbank, cpgIslandExt, microsat, blatservers, default position done, running genscan
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    genscan done, featureBits complete, and in the pushQ
• src/hg/makeDb/doc/mm9.txt
  • lines changed 20, context: html, text, full: html, text
    done with mm9 to mm10 liftOver
• src/hg/makeDb/genbank/etc/align.dbs
  • lines changed 1, context: html, text, full: html, text
    Added mm10.
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 20, context: html, text, full: html, text
    adding mm10 definitions
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    set mm10.align.unplacedChroms = chr* since any of them can lift with the nonBridgedGap.lift file
  • lines changed 1, context: html, text, full: html, text
    incorrect spelling of mm10.nonBrided.lift file
• src/hg/makeDb/genbank/etc/hgwdev.dbs
  • lines changed 1, context: html, text, full: html, text
    Added mm10.
• src/hg/makeDb/schema/all.joiner
  • lines changed 23, context: html, text, full: html, text
    adding mm10 to the rules
• src/hg/makeDb/trackDb/fugu/fr3/description.html
  • lines changed 17, context: html, text, full: html, text
    update image include and assembly description
• src/hg/makeDb/trackDb/makefile
  • lines changed 1, context: html, text, full: html, text
    adding mm10 to the build
• src/hg/makeDb/trackDb/mouse/mm10/description.html
  • lines changed 132, context: html, text, full: html, text
    initial files from makeGenomeDb.pl
  • lines changed 95, context: html, text, full: html, text
    update description and gold and gap pages to better match reality
• src/hg/makeDb/trackDb/mouse/mm10/gap.html
  • lines changed 64, context: html, text, full: html, text
    initial files from makeGenomeDb.pl
  • lines changed 55, context: html, text, full: html, text
    update description and gold and gap pages to better match reality
• src/hg/makeDb/trackDb/mouse/mm10/gold.html
  • lines changed 23, context: html, text, full: html, text
    initial files from makeGenomeDb.pl
  • lines changed 17, context: html, text, full: html, text
    update description and gold and gap pages to better match reality
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    initial files from makeGenomeDb.pl
• src/hg/near/hgNear/hgNearData/Rat/rn4/genome.ra
  • lines changed 1, context: html, text, full: html, text
    fixup select statement for allTranscriptQuery
• src/hg/utils/genomeQuality/genomeQuality.pl
  • lines changed 1, context: html, text, full: html, text
    correct plural word
• src/utils/bedGraphToBigWig/bedGraphToBigWig.c
  • lines changed 2, context: html, text, full: html, text
    mention fetchChromSizes in these usage messages, redmine 6844
• src/utils/bedToBigBed/bedToBigBed.c
  • lines changed 2, context: html, text, full: html, text
    mention fetchChromSizes in these usage messages, redmine 6844
• src/utils/wigToBigWig/wigToBigWig.c
  • lines changed 2, context: html, text, full: html, text
    mention fetchChromSizes in these usage messages, redmine 6844