File Changes for hiram

v275_preview to v275_preview2 (2012-10-16 to 2012-10-23) v275

• src/hg/geneBounds/estLibStats/makefile
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    rearrange -lm to be after mysqllibs redmine 9101
• src/hg/makeDb/doc/allMis1.txt
  • lines changed 367, context: html, text, full: html, text
    trying to get a unique RM library from Robert Hubley
• src/hg/makeDb/doc/blastTab.txt
  • lines changed 399, context: html, text, full: html, text
    drBlastTab reload for danRer7 Ensembl update
• src/hg/makeDb/doc/braFlo2.txt
  • lines changed 418, context: html, text, full: html, text
    starting new Lancelet assembly v2.0
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    running genbank
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    done with genbank alignments
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    lastz Lamprey <-> Lancelet
• src/hg/makeDb/doc/cerSim1.txt
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    ready for default position and pushQ entry
• src/hg/makeDb/doc/hg19.txt
  • lines changed 137, context: html, text, full: html, text
    running lastz for petMar2 and cerSim1
• src/hg/makeDb/doc/mm10.txt
  • lines changed 29, context: html, text, full: html, text
    adding cytoband tables for Chromosome Band track
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    better generic location for these ideogram files
• src/hg/makeDb/doc/petMar1.txt
  • lines changed 19, context: html, text, full: html, text
    petMar2 liftOver constructed and blanks at ends of lines removed
• src/hg/makeDb/doc/petMar2.txt
  • lines changed 194, context: html, text, full: html, text
    resolve GIT conflict
  • lines changed 46, context: html, text, full: html, text
    lastz Lamprey <-> Lancelet
• src/hg/makeDb/genbank/etc/align.dbs
  • lines changed 1, context: html, text, full: html, text
    adding petMar2
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    Added braFlo2.
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 17, context: html, text, full: html, text
    adding petMar2 Lamprey redmine 9153
  • lines changed 17, context: html, text, full: html, text
    adding braFlo2 - Lancelet - Branchiostoma floridae
• src/hg/makeDb/genbank/etc/hgwdev.dbs
  • lines changed 1, context: html, text, full: html, text
    adding petMar2
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    Added braFlo2.
• src/hg/makeDb/genbank/src/lib/gbGenome.c
  • lines changed 1, context: html, text, full: html, text
    adding additional Lancelet names for Branchiostoma
• src/hg/makeDb/hgGcPercent/makefile
  • lines changed 8, context: html, text, full: html, text
    adding hgGcPercent to the userApps delivery
• src/hg/makeDb/schema/all.joiner
  • lines changed 31, context: html, text, full: html, text
    adding cerSim1 and petMar2 completely clean
  • lines changed 1, context: html, text, full: html, text
    do not need to check refLink with kgProtAlias on dm3
• src/hg/makeDb/trackDb/lancelet/braFlo2/description.html
  • lines changed 63, context: html, text, full: html, text
    adding Lancelet v2.0 braFlo2 to the build
• src/hg/makeDb/trackDb/lancelet/braFlo2/gap.html
  • lines changed 31, context: html, text, full: html, text
    adding Lancelet v2.0 braFlo2 to the build
• src/hg/makeDb/trackDb/lancelet/braFlo2/gold.html
  • lines changed 34, context: html, text, full: html, text
    adding Lancelet v2.0 braFlo2 to the build
• src/hg/makeDb/trackDb/lancelet/braFlo2/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    adding Lancelet v2.0 braFlo2 to the build
• src/hg/makeDb/trackDb/lizard/anoCar1/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    override for quality table maximum limit
• src/hg/makeDb/trackDb/makefile
  • lines changed 1, context: html, text, full: html, text
    adding petMar2 to the build
  • lines changed 1, context: html, text, full: html, text
    adding Lancelet v2.0 braFlo2 to the build
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.euarchontoglireChainNet.ra
  • lines changed 242, context: html, text, full: html, text
    renaming primatesChainNet to euarchontoglireChainNet
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.gliresChainNet.ra
  • lines changed 17, context: html, text, full: html, text
    renaming primatesChainNet to euarchontoglireChainNet
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.primatesChainNet.ra
  • lines changed 226, context: html, text, full: html, text
    renaming primatesChainNet to euarchontoglireChainNet
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    renaming primatesChainNet to euarchontoglireChainNet
• src/hg/utils/automation/configFiles/cerSim1.config.ra
  • lines changed 23, context: html, text, full: html, text
    adding recent new assemblies, rhino, chinchilla, lamprey
• src/hg/utils/automation/configFiles/chiLan1.config.ra
  • lines changed 23, context: html, text, full: html, text
    adding recent new assemblies, rhino, chinchilla, lamprey
• src/hg/utils/automation/configFiles/petMar2.config.ra
  • lines changed 23, context: html, text, full: html, text
    adding recent new assemblies, rhino, chinchilla, lamprey
• src/hg/utils/automation/configFiles/rn5.config.ra
  • lines changed 1, context: html, text, full: html, text
    corrected ncbiAssemblyId
• src/hg/utils/bedExtendRanges/makefile
  • lines changed 6, context: html, text, full: html, text
    adding bedExtendRanges and makeTableList to the build
• src/hg/utils/makefile
  • lines changed 2, context: html, text, full: html, text
    adding bedExtendRanges and makeTableList to the build
• src/makefile
  • lines changed 3, context: html, text, full: html, text
    adding hgGcPercent to the userApps delivery
• src/product/README.building.source
  • lines changed 12, context: html, text, full: html, text
    add note about dlopen routines in library -ldl
• src/utils/bedGraphToBigWig/bedGraphToBigWig.c
  • lines changed 1, context: html, text, full: html, text
    adding hgGcPercent to the userApps delivery
• src/utils/faRandomize/faRandomize.c
  • lines changed 8, context: html, text, full: html, text
    standardize usage message to place into the build
• src/utils/faRandomize/makefile
  • lines changed 3, context: html, text, full: html, text
    standardize usage message to place into the build
• src/utils/makefile
  • lines changed 1, context: html, text, full: html, text
    adding faRandomize to the build
  • lines changed 1, context: html, text, full: html, text
    adding paraSync to the build
• src/utils/ncbi/createNcbiCytoBand.pl
  • lines changed 3, context: html, text, full: html, text
    update to handle mm10 correctly
• src/utils/ncbi/cytoBandVerify.pl
  • lines changed 1, context: html, text, full: html, text
    update to handle mm10 correctly