All File Changes

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

• confs/hgwbeta.hg.conf
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    Added trackLog lines; made corrections to reflect additions to hg.conf files that were not added here; refs #8383
• confs/hgwdev.hg.conf
  • lines changed 3, context: html, text, full: html, text
    Added trackLog lines; made corrections to reflect additions to hg.conf files that were not added here; refs #8383
  • lines changed 1, context: html, text, full: html, text
    Made one more correction to synchronize hg.conf files; refs #8383
• confs/rr.hg.conf
  • lines changed 3, context: html, text, full: html, text
    Added trackLog lines; made corrections to reflect additions to hg.conf files that were not added here; refs #8383
• src/hg/hgTracks/mafTrack.c
  • lines changed 3, context: html, text, full: html, text
    color mismatches as red ticks in mafs
  • lines changed 23, context: html, text, full: html, text
    show SNPs as red in maf and wigMaf tracks if "showSnp on" is set in the trackDb
• src/hg/hgTracks/mafTrack.h
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    show SNPs as red in maf and wigMaf tracks if "showSnp on" is set in the trackDb
• src/hg/hgTracks/vcfTrack.c
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    Use vcfGenotype's isHaploid field instead of comparing chrom to chrY (that was messing up display of ebola which is haploid).
• src/hg/hgTracks/wigMafTrack.c
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    species group names are getting longer than 24 characters refs #13411
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    show SNPs as red in maf and wigMaf tracks if "showSnp on" is set in the trackDb
• src/hg/hgc/hgc.c
  • lines changed 5, context: html, text, full: html, text
    In getAlignments function, added code for the Retrposed Genes track that gets only the qName equal to an id not like an id for the table query. Otherwise multiple results are returned rather than the single result required for this track details page.
• src/hg/htdocs/ebola/ebolaPortal.html
  • lines changed 177, context: html, text, full: html, text
    A basic webpage that contains links and useful information about Ebola
  • lines changed 177, context: html, text, full: html, text
    A .png screen shot of the ebola browser
• src/hg/htdocs/ebola/index.html
  • lines changed 66, context: html, text, full: html, text
    First version of Ebola portal from Chris Eisenhart
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    trying to fix broken inks
• src/hg/htdocs/ebolaPortal/ebolaBrowserSS.png
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    A .png screen shot of the ebola browser
• src/hg/htdocs/ebolaPortal/ebolaPortal.html
  • lines changed 177, context: html, text, full: html, text
    A .png screen shot of the ebola browser
  • lines changed 37, context: html, text, full: html, text
    Added a new block, related links, which has Ebola related links (non academic)
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    Updating reference links
  • lines changed 205, context: html, text, full: html, text
    changing file name
• src/hg/htdocs/ebolaPortal/index.html
  • lines changed 205, context: html, text, full: html, text
    changing file name
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    fixing some links in a different version of the same file...
  • lines changed 3, context: html, text, full: html, text
    fixing special chars introduced by some weird editor
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    removing hgsid from link
  • lines changed 1, context: html, text, full: html, text
    removing a link
  • lines changed 21, context: html, text, full: html, text
    Reformatted the Scientific Links section to include article titles(linked to PubMed) following each article's summary, and PDF links
    to full PDF at journals. Corrected some spelling errors.
    Removed hostname, position and hgsid from links to browser.
    
  • lines changed 2, context: html, text, full: html, text
    Grammer and spelling fixes, modifiying the Viral Life Cycle section
  • lines changed 38, context: html, text, full: html, text
    Menus fixes to Ebola page
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    Some work on explanatory text for the site -- this is simlar to info I just included in GB NAR 2014 paper
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    perms?
  • lines changed 113, context: html, text, full: html, text
    Add virus image, Antibody section
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    Tweaked
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    Switch 'read about ebola' link to virus info
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    Tweak image sizes
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    Pulling bad link to NOVA piece on youtube
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    Updating Ebola biology section.
  • lines changed 52, context: html, text, full: html, text
    Add 3rd launcher panel: outbreak graph linked to CDC site. And add back youtube NOVA show with new link
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    Disable feature that doesn't work on IE (middle launcher panel to read Wikipedia page, no biggie)
  • lines changed 53, context: html, text, full: html, text
    Fill out Antibody Resources section with pubs from IEDB B-cell track and IEDB.org site (Table 2)
  • lines changed 89, context: html, text, full: html, text
    Edits to tidy up some of the content format.
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    Removed a pub, per Jim.
  • lines changed 61, context: html, text, full: html, text
    Fix layout for all browsers. Try cleaner style (no borders on panels)
  • lines changed 3, context: html, text, full: html, text
    Added paper to Antibody section
  • lines changed 59, context: html, text, full: html, text
    Add Vaccines panel
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    Adding blank targets to links
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    add target=_blank to screenshot launchers
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    Made a few edits to Vaccine section.
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    One more edit.
• 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/htdocs/images/Graph_Diseased_Ebola_2014.png
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    Graph of cases, from Wikipedia
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    Fix layout for all browsers. Try cleaner style (no borders on panels)
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    Trim graph a bit
• src/hg/htdocs/images/Zaire_ebolavirus_vertical.jpg
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    Fix layout for all browsers. Try cleaner style (no borders on panels)
• src/hg/htdocs/images/ebolaBrowser.png
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    Fix layout for all browsers. Try cleaner style (no borders on panels)
  • lines changed 0, context: html, text, full: html, text
    Update ebola browser screenshot with eboVir2
• src/hg/htdocs/inc/ebola.topbar.html
  • lines changed 15, context: html, text, full: html, text
    Menus fixes to Ebola page
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    Add Vaccines panel
• src/hg/htdocs/indexIntro.html
  • lines changed 1, context: html, text, full: html, text
    Adding to indexIntro 2003 to 2012 dates to a refernce of ENCODE
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    Small changes to wording about ENCODE portal refs #13616
• src/hg/htdocs/license/gblicense.pdf
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    Adding new version of GB license agreement, per Ann.
• src/hg/htdocs/license/index.html
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    changing Wil's address to the more general 'technology' address
• 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
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    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/gire.txt
  • lines changed 67, context: html, text, full: html, text
    Added Missense-only VCF tracks from Gire et al.
  • lines changed 77, context: html, text, full: html, text
    Added track from Gire et al: SNPs specific to 2014 outbreak, withannotated coding changes.
    
  • lines changed 12, context: html, text, full: html, text
    Extracted an nh-like tree from Gire et al. supplemental materials.
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    Added Intra-host variants from Gire et al.
  • lines changed 51, context: html, text, full: html, text
    Added gire2014FixedMissense (Protein Changes That Are Fixed in 2014 Outbreak Strains) from Gire et al supplemental data.
  • lines changed 122, context: html, text, full: html, text
    Added tracks gire2014PolymorphicMissense, gire2014KikwitMissense, gire2014MayingaMissense from Gire et al supplemental data.
• src/hg/makeDb/doc/eboVir2/iedb.txt
  • lines changed 37, context: html, text, full: html, text
    makedoc for iedb track
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    adding another genbank track, plus a few changes to track groupings
• src/hg/makeDb/doc/eboVir2/ordinaryTracks.txt
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    document regular track construction refs #13996
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    document regular track construction refs #13996
• src/hg/makeDb/doc/eboVir2/pfam.txt
  • lines changed 20, context: html, text, full: html, text
    add doc for pfam track
• 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
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    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
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    fetching sequence information refs #14011
• src/hg/makeDb/doc/eboVir3/gire.txt
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    Added Gire at al tracks for eboVir3. Moved trackDb.gire.ra and gire*.html upfrom ebola/eboVir2/ to ebola/ so eboVir2 and eboVir3 will share them.
    Made the track labels a little more consistent and added priorities.
    
• src/hg/makeDb/doc/eboVir3/lastz160way.txt
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    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
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    first view of 160-way refs #14011
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    16-way now showing strain names refs #14011
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    catch up with the stray outcast KJ660347v2 which had the incorrect db name in its pairwise refs #14011
• src/hg/makeDb/doc/eboVir3/ncbiGene.txt
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    NCBI Genes for eboVir3
• src/hg/makeDb/doc/eboVir3/ordinaryTracks.txt
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    initial track building refs #14011
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    first view of 160-way refs #14011
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    add blat servers refs #14011
• src/hg/makeDb/doc/eboVir3/pfam.txt
  • lines changed 20, context: html, text, full: html, text
    add pfam track to eboVir3
• 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/doc/equCab2.txt
  • lines changed 58, context: html, text, full: html, text
    Added animalQtl track to make doc; refs #13957
• src/hg/makeDb/trackDb/animalQtl.html
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    Added horse to the description page; refs #13957
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    Updated link to QTLdb on description page; refs #13957
• src/hg/makeDb/trackDb/drosophila/dm2/picTar.html
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    Small html change seen when doing code review, refs #14004
• src/hg/makeDb/trackDb/ebola/eboVir2/description.html
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    Minor tweaks.
• src/hg/makeDb/trackDb/ebola/eboVir2/gire2014FixedMissense.html
  • lines changed 26, context: html, text, full: html, text
    Added gire2014FixedMissense (Protein Changes That Are Fixed in 2014 Outbreak Strains) from Gire et al supplemental data.
  • lines changed 26, context: html, text, full: html, text
    Added Gire at al tracks for eboVir3. Moved trackDb.gire.ra and gire*.html upfrom ebola/eboVir2/ to ebola/ so eboVir2 and eboVir3 will share them.
    Made the track labels a little more consistent and added priorities.
    
• src/hg/makeDb/trackDb/ebola/eboVir2/gire2014KikwitMissense.html
  • lines changed 24, context: html, text, full: html, text
    Added tracks gire2014PolymorphicMissense, gire2014KikwitMissense, gire2014MayingaMissense from Gire et al supplemental data.
  • lines changed 24, context: html, text, full: html, text
    Added Gire at al tracks for eboVir3. Moved trackDb.gire.ra and gire*.html upfrom ebola/eboVir2/ to ebola/ so eboVir2 and eboVir3 will share them.
    Made the track labels a little more consistent and added priorities.
    
• src/hg/makeDb/trackDb/ebola/eboVir2/gire2014MayingaMissense.html
  • lines changed 24, context: html, text, full: html, text
    Added tracks gire2014PolymorphicMissense, gire2014KikwitMissense, gire2014MayingaMissense from Gire et al supplemental data.
  • lines changed 24, context: html, text, full: html, text
    Added Gire at al tracks for eboVir3. Moved trackDb.gire.ra and gire*.html upfrom ebola/eboVir2/ to ebola/ so eboVir2 and eboVir3 will share them.
    Made the track labels a little more consistent and added priorities.
    
• src/hg/makeDb/trackDb/ebola/eboVir2/gire2014PolymorphicMissense.html
  • lines changed 26, context: html, text, full: html, text
    Added tracks gire2014PolymorphicMissense, gire2014KikwitMissense, gire2014MayingaMissense from Gire et al supplemental data.
  • lines changed 26, context: html, text, full: html, text
    Added Gire at al tracks for eboVir3. Moved trackDb.gire.ra and gire*.html upfrom ebola/eboVir2/ to ebola/ so eboVir2 and eboVir3 will share them.
    Made the track labels a little more consistent and added priorities.
    
• src/hg/makeDb/trackDb/ebola/eboVir2/gire2014SpecificSnps.html
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    Added track from Gire et al: SNPs specific to 2014 outbreak, withannotated coding changes.
    
  • lines changed 19, context: html, text, full: html, text
    Cleaned up reference, etc.
  • lines changed 28, context: html, text, full: html, text
    Added Gire at al tracks for eboVir3. Moved trackDb.gire.ra and gire*.html upfrom ebola/eboVir2/ to ebola/ so eboVir2 and eboVir3 will share them.
    Made the track labels a little more consistent and added priorities.
    
• src/hg/makeDb/trackDb/ebola/eboVir2/gireZebov.html
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    Cleaned up reference, etc.
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    Added Gire at al tracks for eboVir3. Moved trackDb.gire.ra and gire*.html upfrom ebola/eboVir2/ to ebola/ so eboVir2 and eboVir3 will share them.
    Made the track labels a little more consistent and added priorities.
    
• src/hg/makeDb/trackDb/ebola/eboVir2/iedb.html
  • lines changed 12, context: html, text, full: html, text
    description pages for iedb track
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    Cleaned up some links etc.
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    desc pages for iedb split t cell track
• src/hg/makeDb/trackDb/ebola/eboVir2/iedbBcell.html
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    description pages for iedb track
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    Cleaned up some links etc.
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    changes to iedb desc pages
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    iedb desc page update
• src/hg/makeDb/trackDb/ebola/eboVir2/iedbTcellLong.html
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    desc pages for iedb split t cell track
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    changes to iedb desc pages
• src/hg/makeDb/trackDb/ebola/eboVir2/iedbTcellShort.html
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    desc pages for iedb split t cell track
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    changes to iedb desc pages
• src/hg/makeDb/trackDb/ebola/eboVir2/ncbiGenePfam.html
  • lines changed 44, context: html, text, full: html, text
    add description page for Pfam Domains in NCBI Genes on eboVir2
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    Quick editing pass.
• src/hg/makeDb/trackDb/ebola/eboVir2/spAnnotSecond.html
  • lines changed 57, context: html, text, full: html, text
    Changing shortLabels for IEDB tracks. Adding description page for UniProt Structure track
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    Quick editing pass.
• src/hg/makeDb/trackDb/ebola/eboVir2/spMut.html
  • lines changed 66, context: html, text, full: html, text
    moving spMut.html up to global, keeping a modified copy in ebola
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    Quick editing pass.
• 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
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    setting mafDot on refs #13996
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    Fixed some caps, etc. in labels.
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    West Africa instead of Sierra Leone refs #13396
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    Changing visibilities to hide for some tracks
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    add frames table for 102way
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    show SNPs as red if "showSnp on" is set in the trackDb (trackDb changes)
• src/hg/makeDb/trackDb/ebola/eboVir2/trackDb.49way.ra
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    better short label refs #13996
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    better short label refs #13996
  • lines changed 1, context: html, text, full: html, text
    setting mafDot on refs #13996
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    Changing long labels per Jims request
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    Unchanging previous long labels, changing other long labels
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    Fixed some caps, etc. in labels.
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    experiment with name.name maf file spec refs #13996
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    show SNPs as red if "showSnp on" is set in the trackDb (trackDb changes)
• src/hg/makeDb/trackDb/ebola/eboVir2/trackDb.49wayStrainNames.ra
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    better short label refs #13996
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    setting mafDot on refs #13996
  • lines changed 1, context: html, text, full: html, text
    Changing long labels per Jims request
  • lines changed 2, context: html, text, full: html, text
    Unchanging previous long labels, changing other long labels
  • lines changed 5, context: html, text, full: html, text
    Fixed some caps, etc. in labels.
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    fix some 49way strain names in trackDb to correspond to what's in the maf
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    show SNPs as red if "showSnp on" is set in the trackDb (trackDb changes)
• src/hg/makeDb/trackDb/ebola/eboVir2/trackDb.gire.ra
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    Added track from Gire et al: SNPs specific to 2014 outbreak, withannotated coding changes.
    
  • lines changed 1, context: html, text, full: html, text
    Changing long labels per Jims request
  • lines changed 5, context: html, text, full: html, text
    Fixed some caps, etc. in labels.
  • lines changed 2, context: html, text, full: html, text
    Changing longLabels for 101 variants tracks
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    Changing visibilities to hide for some tracks
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    Added Intra-host variants from Gire et al.
  • lines changed 8, context: html, text, full: html, text
    Added gire2014FixedMissense (Protein Changes That Are Fixed in 2014 Outbreak Strains) from Gire et al supplemental data.
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    Added tracks gire2014PolymorphicMissense, gire2014KikwitMissense, gire2014MayingaMissense from Gire et al supplemental data.
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    The Kikit and Mayinga diff tracks are only for the GP gene; make that clear in shortLabel.
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    Fixing typos for in shortLabels of Ebola tracks
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    Added Gire at al tracks for eboVir3. Moved trackDb.gire.ra and gire*.html upfrom ebola/eboVir2/ to ebola/ so eboVir2 and eboVir3 will share them.
    Made the track labels a little more consistent and added priorities.
    
• src/hg/makeDb/trackDb/ebola/eboVir2/trackDb.ra
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    adding B-cell epitope track
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    adding a few more linkouts
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    adding one more linkout
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    Added Missense-only VCF tracks from Gire et al.
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    It's 101 not 102.
  • lines changed 29, context: html, text, full: html, text
    Added track from Gire et al: SNPs specific to 2014 outbreak, withannotated coding changes.
    
  • lines changed 1, context: html, text, full: html, text
    adding 102-way multiz alignment refs #13996
  • lines changed 1, context: html, text, full: html, text
    adding uniprot gene descriptions
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    Changing long labels per Jims request
  • lines changed 5, context: html, text, full: html, text
    moving spMut.html up to global, keeping a modified copy in ebola
  • lines changed 1, context: html, text, full: html, text
    fixing urls of iedb tcells
  • lines changed 1, context: html, text, full: html, text
    Fixed cap in longLabel.
  • lines changed 1, context: html, text, full: html, text
    Changing visibilities to hide for some tracks
  • lines changed 5, context: html, text, full: html, text
    forgot what I'm comitting here
  • lines changed 7, context: html, text, full: html, text
    adding iedb predictions
  • lines changed 11, context: html, text, full: html, text
    adding another uniprot track, only structure-based info
  • lines changed 1, context: html, text, full: html, text
    typo
  • lines changed 8, context: html, text, full: html, text
    add pFam track to eboVir2
  • lines changed 3, context: html, text, full: html, text
    moving IEDB tracks into new immunology group
  • lines changed 11, context: html, text, full: html, text
    t pushZZMerge branch 'master' of hgwdev.cse.ucsc.edu:/data/git/kent
    
  • 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
  • lines changed 7, context: html, text, full: html, text
    adding genbank alignments
  • lines changed 1, context: html, text, full: html, text
    adding url
  • lines changed 33, context: html, text, full: html, text
    adding another genbank track, plus a few changes to track groupings
  • lines changed 1, context: html, text, full: html, text
    gold to hide
  • lines changed 1, context: html, text, full: html, text
    gold to hide
  • lines changed 14, context: html, text, full: html, text
    track title change
  • lines changed 2, context: html, text, full: html, text
    Fixing typos for in shortLabels of Ebola tracks
  • lines changed 1, context: html, text, full: html, text
    Added Gire at al tracks for eboVir3. Moved trackDb.gire.ra and gire*.html upfrom ebola/eboVir2/ to ebola/ so eboVir2 and eboVir3 will share them.
    Made the track labels a little more consistent and added priorities.
    
  • lines changed 1, context: html, text, full: html, text
    Changing color of IEDB track
  • lines changed 25, context: html, text, full: html, text
    Rearranging Gire et al trackDb entries. Removing some tracks from display. Renaming Max's Blat tracks.
  • lines changed 4, context: html, text, full: html, text
    Changing shortLables for IEDB tracks and UniProt annotations track. Adding include statement for eboVir3 trackDb.gire.ra
  • lines changed 2, context: html, text, full: html, text
    Changing shortLabels for IEDB tracks. Adding description page for UniProt Structure track
  • lines changed 7, context: html, text, full: html, text
    adding arjun's prediction's as a temporary dev track. will need morework on the details page
    
  • lines changed 19, context: html, text, full: html, text
    t pushMerge branch 'master' of hgwdev.cse.ucsc.edu:/data/git/kent
    
  • lines changed 11, context: html, text, full: html, text
    splitting tcell track into two depending on length of peptide
  • lines changed 12, context: html, text, full: html, text
    adding pdb track
  • lines changed 2, context: html, text, full: html, text
    inc weidth
• 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 1, context: html, text, full: html, text
    NCBI Genes for eboVir3
  • 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
  • lines changed 1, context: html, text, full: html, text
    show SNPs as red if "showSnp on" is set in the trackDb (trackDb changes)
• src/hg/makeDb/trackDb/ebola/eboVir3/trackDb.gire.ra
  • lines changed 62, context: html, text, full: html, text
    Rearranging Gire et al trackDb entries. Removing some tracks from display. Renaming Max's Blat tracks.
  • lines changed 1, context: html, text, full: html, text
    Adding description pages for 2 Gire et al tracks. Changing shortLabel of Gire track to fit in 17 chars.
• 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 12, context: html, text, full: html, text
    NCBI Genes for eboVir3
  • lines changed 8, context: html, text, full: html, text
    add pfam track to eboVir3
  • lines changed 1, context: html, text, full: html, text
    Changing shortLables for IEDB tracks and UniProt annotations track. Adding include statement for eboVir3 trackDb.gire.ra
  • 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
  • lines changed 1, context: html, text, full: html, text
    show SNPs as red if "showSnp on" is set in the trackDb (trackDb changes)
• src/hg/makeDb/trackDb/ebola/gire2014FixedMissense.html
  • lines changed 26, context: html, text, full: html, text
    Added Gire at al tracks for eboVir3. Moved trackDb.gire.ra and gire*.html upfrom ebola/eboVir2/ to ebola/ so eboVir2 and eboVir3 will share them.
    Made the track labels a little more consistent and added priorities.
    
  • lines changed 2, context: html, text, full: html, text
    Quick editing pass.
• src/hg/makeDb/trackDb/ebola/gire2014KikwitMissense.html
  • lines changed 24, context: html, text, full: html, text
    Added Gire at al tracks for eboVir3. Moved trackDb.gire.ra and gire*.html upfrom ebola/eboVir2/ to ebola/ so eboVir2 and eboVir3 will share them.
    Made the track labels a little more consistent and added priorities.
    
  • lines changed 1, context: html, text, full: html, text
    Quick editing pass.
• src/hg/makeDb/trackDb/ebola/gire2014MayingaMissense.html
  • lines changed 24, context: html, text, full: html, text
    Added Gire at al tracks for eboVir3. Moved trackDb.gire.ra and gire*.html upfrom ebola/eboVir2/ to ebola/ so eboVir2 and eboVir3 will share them.
    Made the track labels a little more consistent and added priorities.
    
  • lines changed 1, context: html, text, full: html, text
    Quick editing pass.
• src/hg/makeDb/trackDb/ebola/gire2014Missense.html
  • lines changed 41, context: html, text, full: html, text
    Adding description pages for 2 Gire et al tracks. Changing shortLabel of Gire track to fit in 17 chars.
• src/hg/makeDb/trackDb/ebola/gire2014PolymorphicMissense.html
  • lines changed 26, context: html, text, full: html, text
    Added Gire at al tracks for eboVir3. Moved trackDb.gire.ra and gire*.html upfrom ebola/eboVir2/ to ebola/ so eboVir2 and eboVir3 will share them.
    Made the track labels a little more consistent and added priorities.
    
  • lines changed 2, context: html, text, full: html, text
    Quick editing pass.
• src/hg/makeDb/trackDb/ebola/gire2014SpecificSnps.html
  • lines changed 28, context: html, text, full: html, text
    Added Gire at al tracks for eboVir3. Moved trackDb.gire.ra and gire*.html upfrom ebola/eboVir2/ to ebola/ so eboVir2 and eboVir3 will share them.
    Made the track labels a little more consistent and added priorities.
    
• src/hg/makeDb/trackDb/ebola/gireMethods.html
  • lines changed 21, context: html, text, full: html, text
    Adding include-files for Methods and References sections of Gire et al. tracks.
• src/hg/makeDb/trackDb/ebola/gireReferences.html
  • lines changed 21, context: html, text, full: html, text
    Adding include-files for Methods and References sections of Gire et al. tracks.
• src/hg/makeDb/trackDb/ebola/gireZebov.html
  • lines changed 16, context: html, text, full: html, text
    Added Gire at al tracks for eboVir3. Moved trackDb.gire.ra and gire*.html upfrom ebola/eboVir2/ to ebola/ so eboVir2 and eboVir3 will share them.
    Made the track labels a little more consistent and added priorities.
    
• src/hg/makeDb/trackDb/ebola/gireZebovMissense.html
  • lines changed 41, context: html, text, full: html, text
    Adding description pages for 2 Gire et al tracks. Changing shortLabel of Gire track to fit in 17 chars.
• src/hg/makeDb/trackDb/ebola/trackDb.gire.ra
  • lines changed 89, context: html, text, full: html, text
    Added Gire at al tracks for eboVir3. Moved trackDb.gire.ra and gire*.html upfrom ebola/eboVir2/ to ebola/ so eboVir2 and eboVir3 will share them.
    Made the track labels a little more consistent and added priorities.
    
  • lines changed 63, context: html, text, full: html, text
    Rearranging Gire et al trackDb entries. Removing some tracks from display. Renaming Max's Blat tracks.
• src/hg/makeDb/trackDb/ebola/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    Added Gire at al tracks for eboVir3. Moved trackDb.gire.ra and gire*.html upfrom ebola/eboVir2/ to ebola/ so eboVir2 and eboVir3 will share them.
    Made the track labels a little more consistent and added priorities.
    
• src/hg/makeDb/trackDb/horse/equCab2/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    Added outside link to animalQtl details page; refs #13957
• 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/human/hg19/denisovaMethylation.html
  • lines changed 1, context: html, text, full: html, text
    Making difference between red and green items clearer. Removing release tags, refs #13439
• src/hg/makeDb/trackDb/human/hg19/neandertalMethylation.html
  • lines changed 1, context: html, text, full: html, text
    Making difference between red and green items clearer. Removing release tags, refs #13439
• src/hg/makeDb/trackDb/human/hg19/trackDb.denisova.ra
  • lines changed 1, context: html, text, full: html, text
    Adding release tags for ancient human methylation tracks
  • lines changed 1, context: html, text, full: html, text
    Making difference between red and green items clearer. Removing release tags, refs #13439
• src/hg/makeDb/trackDb/human/snp141.shared.html
  • lines changed 6, context: html, text, full: html, text
    Changing greater/less than signs to html names. Changing link. refs #13309
• src/hg/makeDb/trackDb/human/spMut.html
  • lines changed 75, context: html, text, full: html, text
    moving spMut.html up to global, keeping a modified copy in ebola
• src/hg/makeDb/trackDb/human/trackDb.nt.ra
  • lines changed 1, context: html, text, full: html, text
    Adding release tags for ancient human methylation tracks
  • lines changed 1, context: html, text, full: html, text
    Making difference between red and green items clearer. Removing release tags, refs #13439
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 11, context: html, text, full: html, text
    moving spMut track into global trackDb file
  • lines changed 11, context: html, text, full: html, text
    moving spAnnot up global and adding a description page
• src/hg/makeDb/trackDb/makefile
  • lines changed 1, context: html, text, full: html, text
    adding eboVir3 refs #14011
• src/hg/makeDb/trackDb/spAnnot.html
  • lines changed 65, context: html, text, full: html, text
    moving spAnnot up global and adding a description page
• src/hg/makeDb/trackDb/spMut.html
  • lines changed 75, context: html, text, full: html, text
    moving spMut.html up to global, keeping a modified copy in ebola
• src/hg/makeDb/trackDb/tagTypes.tab
  • lines changed 1, context: html, text, full: html, text
    Added new tag type for Retroposed Genes track to specify parent gene annotation tables.
  • lines changed 10, context: html, text, full: html, text
    ordered by visual similarity and grouped refs #14011
  • lines changed 1, context: html, text, full: html, text
    show SNPs as red if "showSnp on" is set in the trackDb (trackDb changes)
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 11, context: html, text, full: html, text
    moving spMut track into global trackDb file
  • lines changed 11, context: html, text, full: html, text
    moving spAnnot up global and adding a description page
  • lines changed 2, context: html, text, full: html, text
    adding another genbank track, plus a few changes to track groupings
• src/hg/makeDb/trackDb/uniprot.txt
  • lines changed 15, context: html, text, full: html, text
    new uniprot lifting pipeline and makedoc for it for ebola
• src/hg/utils/automation/gireVcfToUcsc.pl
  • lines changed 51, context: html, text, full: html, text
    Added Missense-only VCF tracks from Gire et al.
• 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/inc/maf.h
  • lines changed 6, context: html, text, full: html, text
    show SNPs as red in maf and wigMaf tracks if "showSnp on" is set in the trackDb
• src/lib/hacTree.c
  • lines changed 7, context: html, text, full: html, text
    Missing NULL check that somehow hid for a long time, then reared itsugly head when zoomed in to a small region in eboVir2.
    I should really just switch vcfTrack over to using Jim's improved
    hacTree, when the ebola dust settles.
    
• src/lib/mafScore.c
  • lines changed 6, context: html, text, full: html, text
    color mismatches as red ticks in mafs
  • lines changed 54, context: html, text, full: html, text
    show SNPs as red in maf and wigMaf tracks if "showSnp on" is set in the trackDb
• src/oneShot/bedFixBlockOverlaps/bedFixBlockOverlaps
  • lines changed 54, context: html, text, full: html, text
    little script to fix block overlaps in bed files
• src/oneShot/bedFixBlockOverlaps/makefile
  • lines changed 22, context: html, text, full: html, text
    little script to fix block overlaps in bed files
• 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/bigWigCluster/bigWigCluster.c
  • lines changed 30, context: html, text, full: html, text
    Fixed comments and memory leak
  • lines changed 251, context: html, text, full: html, text
    Working through a merge conflict
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 3, context: html, text, full: html, text
    v306 final build refs #13832
• src/utils/uniprotLift/makefile
  • lines changed 22, context: html, text, full: html, text
    new uniprot lifting pipeline and makedoc for it for ebola
• src/utils/uniprotLift/uniprotLift
  • lines changed 316, context: html, text, full: html, text
    new uniprot lifting pipeline and makedoc for it for ebola

• lines changed: 7571
• files changed: 282