File Changes for hiram

v265_preview to v265_preview2 (2012-03-13 to 2012-03-20) v265

• src/hg/makeDb/doc/ailMel1.txt
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    adding URL information to NCBI information pages
• src/hg/makeDb/doc/bosTau7.txt
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    adding URL information to NCBI information pages
• src/hg/makeDb/doc/canFam3.txt
  • lines changed 3, context: html, text, full: html, text
    adding URL information to NCBI information pages
• src/hg/makeDb/doc/choHof1.txt
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    adding URL information to NCBI information pages
• src/hg/makeDb/doc/dasNov2.txt
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    adding URL information to NCBI information pages
• src/hg/makeDb/doc/echTel1.txt
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    adding URL information to NCBI information pages
• src/hg/makeDb/doc/eriEur1.txt
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    adding URL information to NCBI information pages
• src/hg/makeDb/doc/felCat4.txt
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    adding URL information to NCBI information pages
• src/hg/makeDb/doc/galGal4.txt
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    adding URL information to NCBI information pages
• src/hg/makeDb/doc/loxAfr3.txt
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    adding URL information to NCBI information pages
• src/hg/makeDb/doc/macEug2.txt
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    adding URL information to NCBI information pages
• src/hg/makeDb/doc/micMur1.txt
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    adding URL information to NCBI information pages
• src/hg/makeDb/doc/mm10.txt
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    panTro3, otoGar3, micMur1 lastz done
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    done with speTri2 hetGla1 dipOrd1 lastz
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    running equCab3 cavPor3 vicPac1 lastz
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    lastz running oryCun2 susScr2 tupBel1 turTru1 vicPac1 and cavPor3
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    starting lastz runs for choHof1 pteVam1 loxAfr3 felCat4 ailMel1 and canFam3
• src/hg/makeDb/doc/myoLuc2.txt
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    adding URL information to NCBI information pages
• src/hg/makeDb/doc/ochPri2.txt
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    adding URL information to NCBI information pages
• src/hg/makeDb/doc/ornAna1.txt
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    adding URL information to NCBI information pages
• src/hg/makeDb/doc/oryCun2.txt
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    adding URL information to NCBI information pages
• src/hg/makeDb/doc/otoGar3.txt
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    masking done
• src/hg/makeDb/doc/oviAri1.txt
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    adding URL information to NCBI information pages
• src/hg/makeDb/doc/panTro3.txt
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    adding URL information to NCBI information pages
• src/hg/makeDb/doc/petMar1.txt
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    adding URL information to NCBI information pages
• src/hg/makeDb/doc/proCap1.txt
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    adding URL information to NCBI information pages
• src/hg/makeDb/doc/pteVam1.txt
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    adding URL information to NCBI information pages
• src/hg/makeDb/doc/rn5.obsolete.txt
  • lines changed 361, context: html, text, full: html, text
    previous rn5 experiment is now obsolete with new rn5 release
• src/hg/makeDb/doc/rn5.txt
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    buildign a new RN5 release
• src/hg/makeDb/doc/sarHar1.txt
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    add NCBI URL information
• src/hg/makeDb/doc/sorAra1.txt
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    adding URL information to NCBI information pages
• src/hg/makeDb/doc/speTri1.txt
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    adding URL information to NCBI information pages
• src/hg/makeDb/doc/speTri2.txt
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    initial browser build
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    starting masking procedures
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    adding URL information to NCBI information pages
• src/hg/makeDb/doc/susScr2.txt
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    adding URL information to NCBI information pages
• src/hg/makeDb/doc/taeGut1.txt
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    adding URL information to NCBI information pages
• src/hg/makeDb/doc/tarSyr1.txt
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    adding URL information to NCBI information pages
• src/hg/makeDb/doc/tupBel1.txt
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    adding URL information to NCBI information pages
• src/hg/makeDb/doc/turTru1.txt
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    adding URL information to NCBI information pages
• src/hg/makeDb/doc/vicPac1.txt
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    adding URL information to NCBI information pages
• src/hg/makeDb/trackDb/makefile
  • lines changed 1, context: html, text, full: html, text
    adding speTri2 to the build
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    adding rn5 to the build
• src/hg/makeDb/trackDb/rat/rn5/gap.html
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    updated with new rn5 build original files from makeGenomeDb.pl
• src/hg/makeDb/trackDb/rat/rn5/gold.html
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    updated with new rn5 build original files from makeGenomeDb.pl
• src/hg/makeDb/trackDb/rat/rn5/trackDb.ra
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    updated with new rn5 build original files from makeGenomeDb.pl
• src/hg/makeDb/trackDb/squirrel/speTri2/description.html
  • lines changed 132, context: html, text, full: html, text
    initial files from makeGenomeDb.pl
• src/hg/makeDb/trackDb/squirrel/speTri2/gap.html
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    initial files from makeGenomeDb.pl
• src/hg/makeDb/trackDb/squirrel/speTri2/gold.html
  • lines changed 23, context: html, text, full: html, text
    initial files from makeGenomeDb.pl
• src/hg/makeDb/trackDb/squirrel/speTri2/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    initial files from makeGenomeDb.pl
• src/hg/makeDb/trackDb/trackDb.chainNet.ra
  • lines changed 51, context: html, text, full: html, text
    adding chainNetMm10
• src/hg/utils/automation/fastaSubseq
  • lines changed 49, context: html, text, full: html, text
    shell script to replace fasta-subseq command
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    do not need the test reference to fasta-subseq
• src/hg/utils/automation/makeGenomeDb.pl
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    there are new included trackDb ra files
• src/utils/bedGraphToBigWig/bedGraphToBigWig.c
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    the sort usage message was incorrect