File Changes for hiram

v260_preview to v260_preview2 (2011-11-15 to 2011-11-22) v260

• src/hg/htdocs/images/phylo/gorGor3_11way.png
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    phylo tree for Gorilla 11-way primate alignment
• src/hg/lib/hgFind.c
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    allow refLink searches to work when accessions have version numbers (ignore the accession version number) RedMine issue 6040
• src/hg/makeDb/doc/anoCar2.txt
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    add link to WGS Traces information for these assemblies
• src/hg/makeDb/doc/calJac3.txt
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    add link to WGS Traces information for these assemblies
• src/hg/makeDb/doc/danRer7.txt
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    add link to WGS Traces information for these assemblies
• src/hg/makeDb/doc/fr3.txt
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    initial genome build with repeat masker, simple repeats, and gaps fixed up
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    windowMasker and blat server now running
• src/hg/makeDb/doc/gorGor3.txt
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    running synNet maf split for 11-way alignment
• src/hg/makeDb/doc/melGal1.txt
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    add link to WGS Traces information for these assemblies
• src/hg/makeDb/doc/micMur1.txt
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    add link to WGS Traces information for these assemblies
• src/hg/makeDb/doc/otoGar1.txt
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    add link to WGS Traces information for these assemblies
• src/hg/makeDb/doc/panTro3.txt
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    add link to WGS Traces information for these assemblies
• src/hg/makeDb/doc/papHam1.txt
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    catch up some ancient instructions for Baboon
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    add link to WGS Traces information for these assemblies
• src/hg/makeDb/doc/ponAbe2.txt
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    add link to WGS Traces information for these assemblies
• src/hg/makeDb/doc/rheMac2.txt
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    add link to WGS Traces information for these assemblies
• src/hg/makeDb/doc/tarSyr1.txt
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    add link to WGS Traces information for these assemblies
• src/hg/makeDb/genbank/etc/genbank.conf
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    no refseq natives for gorGor3
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    adding definitions for fr3 Fugu
• src/hg/makeDb/schema/all.joiner
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    eliminate felCat3 from identifier ensemblTranscriptId checks
• src/hg/makeDb/trackDb/fugu/fr3/description.html
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    initial files from makeGenomeDb.pl
• src/hg/makeDb/trackDb/fugu/fr3/gap.html
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    initial files from makeGenomeDb.pl
• src/hg/makeDb/trackDb/fugu/fr3/gold.html
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    initial files from makeGenomeDb.pl
• src/hg/makeDb/trackDb/fugu/fr3/trackDb.ra
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    initial files from makeGenomeDb.pl
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    proper searching for gold table
• src/hg/makeDb/trackDb/gibbon/nomLeu1/trackDb.ra
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    remove all_mrna and all_est and fixup gold search
• src/hg/makeDb/trackDb/gibbon/trackDb.chainNet.ra
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    overrides for hg19 and gorGor3
• src/hg/makeDb/trackDb/gibbon/trackDb.ra
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    overrides for hg19 and gorGor3
• src/hg/makeDb/trackDb/gorilla/gorGor3/description.html
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    add a two item name between region display example
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    indicate NM version number searches ignore the version extension
• src/hg/makeDb/trackDb/gorilla/gorGor3/trackDb.chainNet.ra
  • lines changed 40, context: html, text, full: html, text
    adding chainNet overrides and proper search for gold track
• src/hg/makeDb/trackDb/gorilla/gorGor3/trackDb.ra
  • lines changed 7, context: html, text, full: html, text
    adding proper search rule for gold table
  • lines changed 7, context: html, text, full: html, text
    adding chainNet overrides and proper search for gold track
• src/hg/makeDb/trackDb/human/hg19/altSeqComposite5.ra
  • lines changed 2, context: html, text, full: html, text
    fixup URL for alternate sequence
• src/hg/makeDb/trackDb/makefile
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    adding fr3 fugu to the build
• src/hg/makeDb/trackDb/orangutan/trackDb.chainNet.ra
  • lines changed 4, context: html, text, full: html, text
    set priorities for gorGor3 chain net tracks
• src/hg/makeDb/trackDb/rhesus/trackDb.chainNet.ra
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    set priorities for gorGor3 chain net tracks
• src/hg/makeDb/trackDb/xenTro/xenTro3/cons9way.html
  • lines changed 8, context: html, text, full: html, text
    clarify language issues and formatting
• src/hg/utils/automation/doRepeatMasker.pl
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    load a sorted fa.out file to satisify the QA ordered table check
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    one line too much in the head to sorted operation
• src/hg/utils/automation/makeGenomeDb.pl
  • lines changed 37, context: html, text, full: html, text
    eliminate teh obsolete all_mrna and all_est entries in the initial trackDb.ra file