File Changes for hiram

v265_base to v266_preview (2012-03-27 to 2012-04-10) v266

• src/hg/makeDb/doc/chrPic1.txt
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    masking underway
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    done with masking, used the WM result
• src/hg/makeDb/doc/melUnd1.txt
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    download sequence for new browsers
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    initial browser build
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    masking underway
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    done with masking, used the WM result
• src/hg/makeDb/doc/mm10.txt
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    rn5 lastz done with abridged repeats
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    running reciprocal bests and starting triMan1 monDom5 sarHar1 melUnd1 lastz runs
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    done with lastz chain net runs for ornAna1 chrPic1 triMan1 monDom5 sarHar1 melUnd1 and most recip bests
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    starting lastz runs for the final set: galGal4 taeGut1 anoCar2 melGal1 xenTro3 latCha1 gadMor1 oreNil1 gasAcu1 fr3 tetNig2 danRer7 oryLat2 petMar1
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    done with all 60 lastz chain net alignments with swaps
• src/hg/makeDb/doc/triMan1.txt
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    download sequence for new browsers
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    initial browser build
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    masking underway
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    completed masking operations, used the RM result
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    starting genbank
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    completed genbank run
• src/hg/makeDb/genbank/etc/align.dbs
  • lines changed 1, context: html, text, full: html, text
    Added triMan1 - Manatee
• src/hg/makeDb/genbank/etc/genbank.conf
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    adding Trichechus manatus latirostris (Florida manatee) triMan1
  • lines changed 1, context: html, text, full: html, text
    adding Trichechus manatus latirostris (Florida manatee) triMan1
• src/hg/makeDb/genbank/etc/hgwdev.dbs
  • lines changed 1, context: html, text, full: html, text
    Added triMan1 - Manatee
• src/hg/makeDb/genbank/src/lib/gbGenome.c
  • lines changed 3, context: html, text, full: html, text
    adding Trichechus manatus latirostris (Florida manatee) triMan1
• src/hg/makeDb/trackDb/birds/melUnd1/description.html
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    original source from makeGenomeDb.pl
• src/hg/makeDb/trackDb/birds/melUnd1/gap.html
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    original source from makeGenomeDb.pl
• src/hg/makeDb/trackDb/birds/melUnd1/gold.html
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    original source from makeGenomeDb.pl
• src/hg/makeDb/trackDb/birds/melUnd1/trackDb.ra
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    original source from makeGenomeDb.pl
• src/hg/makeDb/trackDb/makefile
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    adding manatee, painted turtle, budgerigar
• src/hg/makeDb/trackDb/manatee/triMan1/description.html
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    original source from makeGenomeDb.pl
• src/hg/makeDb/trackDb/manatee/triMan1/gap.html
  • lines changed 64, context: html, text, full: html, text
    original source from makeGenomeDb.pl
• src/hg/makeDb/trackDb/manatee/triMan1/gold.html
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    original source from makeGenomeDb.pl
• src/hg/makeDb/trackDb/manatee/triMan1/trackDb.ra
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    original source from makeGenomeDb.pl
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.chainNet.ra
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    contents split up into separate files
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.gliersChainNet.ra
  • lines changed 66, context: html, text, full: html, text
    initial contents
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    glier subset
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.placentalsChainNet.ra
  • lines changed 338, context: html, text, full: html, text
    initial contents
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.previousVersionsChainNet.ra
  • lines changed 226, context: html, text, full: html, text
    initial contents
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    moved older genome release chain nets to this package
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.primatesChainNet.ra
  • lines changed 226, context: html, text, full: html, text
    initial contents
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    using otoGar3 instead of otoGar1
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    correct netOtoGar3 instead of netOtoGar1
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
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    five primary groups for chain net definitions
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.vertebrateChainNet.ra
  • lines changed 354, context: html, text, full: html, text
    initial contents
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    setting priority to get in line
• src/hg/makeDb/trackDb/turtle/chrPic1/description.html
  • lines changed 132, context: html, text, full: html, text
    original source from makeGenomeDb.pl
• src/hg/makeDb/trackDb/turtle/chrPic1/gap.html
  • lines changed 64, context: html, text, full: html, text
    original source from makeGenomeDb.pl
• src/hg/makeDb/trackDb/turtle/chrPic1/gold.html
  • lines changed 23, context: html, text, full: html, text
    original source from makeGenomeDb.pl
• src/hg/makeDb/trackDb/turtle/chrPic1/trackDb.ra
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    original source from makeGenomeDb.pl
• src/hg/utils/automation/grcIncidentDb.pl
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    issue.sql has added two new fields
• src/hg/utils/automation/ncbiIncidentDb.pl
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    issue.sql has added two new fields
• src/hg/utils/phyloTrees/61way.nh
  • lines changed 25, context: html, text, full: html, text
    adding manatee triMan1
• src/hg/utils/phyloTrees/62way.nh
  • lines changed 25, context: html, text, full: html, text
    adding melUnd1 budgie
• src/hg/utils/phyloTrees/primates.txt
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    updated with newer listings from NCBI taxonomy