File Changes for hiram

v266_preview2 to v266_base (2012-04-17 to 2012-04-24) v266

• src/hg/htdocs/images/phylo/mm10_60way.png
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    first pass an a 60-way tree diagram
• src/hg/makeDb/doc/fr3.txt
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    adding cpgIsland and genscan tracks
• src/hg/makeDb/doc/hg19.txt
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    added windowMasker track
• src/hg/makeDb/doc/mm10.txt
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    loading up the first 60-way result
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    the multiz60waySummary table is loaded and fix a bunch of broken path names
• src/hg/makeDb/trackDb/mouse/mm10/chainNet.html
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    updated with reference to one single html page
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.60way.ra
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    initial look at the 60way alignment
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    fixup Glire group display and treeImage
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.gliersChainNet.ra
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    updated to new assemblies
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    changed name of file
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.gliresChainNet.ra
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    updated with reference to one single html page
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.placentalsChainNet.ra
  • lines changed 24, context: html, text, full: html, text
    updated to new assemblies
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    updated with reference to one single html page
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.previousVersionsChainNet.ra
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    updated to new assemblies
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    updated with reference to one single html page
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.primatesChainNet.ra
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    updated to new assemblies
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    updated with reference to one single html page
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
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    initial look at the 60way alignment
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.vertebrateChainNet.ra
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    updated to new assemblies
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    update reference to html file
• src/hg/utils/automation/doCpgIslands.pl
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    masking and cpg operation are now kluster jobs to take care of the gigantic contig count genomes
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    correctly specify paraHub for the doCpg script
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    add run time calculation
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    add featureBits measurement of result
• src/utils/cpgIslandExt/README
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    UCSC source from CVS source tree 2005 version
• src/utils/cpgIslandExt/cpg.c
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    UCSC source from CVS source tree 2005 version
• src/utils/cpgIslandExt/cpg_lh.c
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    UCSC source from CVS source tree 2005 version
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    fixup compile errors with modern environment
• src/utils/cpgIslandExt/makefile
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    UCSC source from CVS source tree 2005 version
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    fixup compile errors with modern environment
• src/utils/cpgIslandExt/readseq.c
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    UCSC source from CVS source tree 2005 version
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    fixup compile errors with modern environment
• src/utils/cpgIslandExt/readseq.h
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    UCSC source from CVS source tree 2005 version