File Changes for hiram

v306_preview2 to v306_base (2014-09-15 to 2014-09-22) v306

• src/hg/hgTracks/wigMafTrack.c
  • lines changed 1, context: html, text, full: html, text
    species group names are getting longer than 24 characters refs #13411
• src/hg/htdocs/images/Filoviridae_ebolavirus.jpg
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    same photo from eboVir2 for eboVir3 under a more generic name refs #14011
• src/hg/inc/trackLayout.h
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    allow hg.conf override of 5000 pixel wide limit refs #10411
• src/hg/inc/versionInfo.h
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    New version number v306
• src/hg/lib/hui.c
  • lines changed 5, context: html, text, full: html, text
    species group names are getting longer than 24 characters refs #13411
• src/hg/lib/trackLayout.c
  • lines changed 8, context: html, text, full: html, text
    allow hg.conf override of 5000 pixel wide limit refs #10411
• src/hg/makeDb/doc/eboVir2/153.strain.descriptions.txt
  • lines changed 153, context: html, text, full: html, text
    extracted descriptions from genbank records refs #13996
  • lines changed 153, context: html, text, full: html, text
    adding UCSC naming scheme refs #13996
• src/hg/makeDb/doc/eboVir2/158.strain.descriptions.txt
  • lines changed 158, context: html, text, full: html, text
    adding five more from the Baize paper refs #13996
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    corrected 1966 date to 1996 refs #13996
• src/hg/makeDb/doc/eboVir2/ordinaryTracks.txt
  • lines changed 82, context: html, text, full: html, text
    document regular track construction refs #13996
  • lines changed 15, context: html, text, full: html, text
    document regular track construction refs #13996
• src/hg/makeDb/doc/eboVir2/ucscName.strainName.sed
  • lines changed 104, context: html, text, full: html, text
    adding 102-way strain name cross reference refs #13996
  • lines changed 48, context: html, text, full: html, text
    adding Angie names from yesterday refs #13996
  • lines changed 13, context: html, text, full: html, text
    eliminate duplicate entries, add duplicate sequences, add Marburg all names accounted for refs #13996
  • lines changed 104, context: html, text, full: html, text
    adding five more from the Baize paper refs #13996
• src/hg/makeDb/doc/eboVir2/virus.strain.descriptions.txt
  • lines changed 155, context: html, text, full: html, text
    eliminate duplicate entries, add duplicate sequences, add Marburg all names accounted for refs #13996
• src/hg/makeDb/doc/eboVir3/fetchSequence.txt
  • lines changed 101, context: html, text, full: html, text
    fetching sequence information refs #14011
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    running 160-way on eboVir3 refs 4011
• src/hg/makeDb/doc/eboVir3/gbkDefinition.pl
  • lines changed 55, context: html, text, full: html, text
    fetching sequence information refs #14011
• src/hg/makeDb/doc/eboVir3/lastz160way.txt
  • lines changed 120, context: html, text, full: html, text
    initial track building refs #14011
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    running 160-way on eboVir3 refs 4011
• src/hg/makeDb/doc/eboVir3/multiz160way.txt
  • lines changed 124, context: html, text, full: html, text
    running 160-way on eboVir3 refs 4011
  • lines changed 101, context: html, text, full: html, text
    first view of 160-way refs #14011
  • lines changed 16, context: html, text, full: html, text
    16-way now showing strain names refs #14011
  • lines changed 21, context: html, text, full: html, text
    catch up with the stray outcast KJ660347v2 which had the incorrect db name in its pairwise refs #14011
• src/hg/makeDb/doc/eboVir3/ordinaryTracks.txt
  • lines changed 154, context: html, text, full: html, text
    initial track building refs #14011
  • lines changed 7, context: html, text, full: html, text
    first view of 160-way refs #14011
  • lines changed 2, context: html, text, full: html, text
    add blat servers refs #14011
• src/hg/makeDb/doc/eboVir3/ucscName.strainName.sed
  • lines changed 160, context: html, text, full: html, text
    16-way now showing strain names refs #14011
• src/hg/makeDb/trackDb/ebola/eboVir2/trackDb.102way.ra
  • lines changed 103, context: html, text, full: html, text
    adding 102-way multiz alignment refs #13996
  • lines changed 2, context: html, text, full: html, text
    setting mafDot on refs #13996
  • lines changed 5, context: html, text, full: html, text
    West Africa instead of Sierra Leone refs #13396
• src/hg/makeDb/trackDb/ebola/eboVir2/trackDb.49way.ra
  • lines changed 1, context: html, text, full: html, text
    better short label refs #13996
  • lines changed 2, context: html, text, full: html, text
    better short label refs #13996
  • lines changed 1, context: html, text, full: html, text
    setting mafDot on refs #13996
  • lines changed 1, context: html, text, full: html, text
    experiment with name.name maf file spec refs #13996
• src/hg/makeDb/trackDb/ebola/eboVir2/trackDb.49wayStrainNames.ra
  • lines changed 3, context: html, text, full: html, text
    better short label refs #13996
  • lines changed 1, context: html, text, full: html, text
    setting mafDot on refs #13996
• src/hg/makeDb/trackDb/ebola/eboVir2/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    adding 102-way multiz alignment refs #13996
  • lines changed 14, context: html, text, full: html, text
    comment out self chain tracks and rename those tables refs #13996
  • lines changed 18, context: html, text, full: html, text
    cpgIsland override refs #13996
• src/hg/makeDb/trackDb/ebola/eboVir3/description.html
  • lines changed 62, context: html, text, full: html, text
    initial files from makeGenomeDb.pl refs #14011
  • lines changed 2, context: html, text, full: html, text
    correct nucleotide reference refs #14011
• src/hg/makeDb/trackDb/ebola/eboVir3/gap.html
  • lines changed 29, context: html, text, full: html, text
    initial files from makeGenomeDb.pl refs #14011
• src/hg/makeDb/trackDb/ebola/eboVir3/gold.html
  • lines changed 33, context: html, text, full: html, text
    initial files from makeGenomeDb.pl refs #14011
• src/hg/makeDb/trackDb/ebola/eboVir3/trackDb.160way.ra
  • lines changed 38, context: html, text, full: html, text
    first view of 160-way refs #14011
  • lines changed 2, context: html, text, full: html, text
    now with strain names, missing one for some odd reason refs 4011
  • lines changed 8, context: html, text, full: html, text
    ordered by visual similarity and grouped refs #14011
• src/hg/makeDb/trackDb/ebola/eboVir3/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    initial files from makeGenomeDb.pl refs #14011
  • lines changed 4, context: html, text, full: html, text
    setting default viz refs #14011
  • lines changed 2, context: html, text, full: html, text
    first view of 160-way refs #14011
  • lines changed 1, context: html, text, full: html, text
    now with strain names, missing one for some odd reason refs 4011
• src/hg/makeDb/trackDb/ebola/eboVir3/trackDb.strainName160way.ra
  • lines changed 38, context: html, text, full: html, text
    now with strain names, missing one for some odd reason refs 4011
  • lines changed 10, context: html, text, full: html, text
    ordered by visual similarity and grouped refs #14011
• src/hg/makeDb/trackDb/human/chainNetPlacental.ra
  • lines changed 3, context: html, text, full: html, text
    sloth was out of order refs #11681
• src/hg/makeDb/trackDb/makefile
  • lines changed 1, context: html, text, full: html, text
    adding eboVir3 refs #14011
• src/hg/makeDb/trackDb/tagTypes.tab
  • lines changed 10, context: html, text, full: html, text
    ordered by visual similarity and grouped refs #14011
• src/hg/utils/phyloTrees/eboVir2.49way.nh
  • lines changed 44, context: html, text, full: html, text
    correct first two nodes that multiz did not understand refs #13996
• src/product/ex.hg.conf
  • lines changed 4, context: html, text, full: html, text
    allow hg.conf override of 5000 pixel wide limit refs #10411
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 3, context: html, text, full: html, text
    v306 final build refs #13832