All File Changes

v331_preview2 to v331_base (2016-04-04 to 2016-04-11) v331

• confs/hgwdev.hg.conf
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    Installing updated hg.conf files from UCSC servers
    
• confs/preview.hg.conf
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    Installing updated hg.conf files from UCSC servers
    
  • lines changed 238, context: html, text, full: html, text
    Installing updated hg.conf files from UCSC servers
    
• src/hg/cirm/cdw/cdwCheckValidation/cdwCheckValidation.c
  • lines changed 145, context: html, text, full: html, text
    First draft of cdwCheckValidation as suggested by Jim, refs #17100
    
  • lines changed 111, context: html, text, full: html, text
    Put some options and logic checks in the program. Lots of comments and some new stats are printed, refs #17100
    
  • lines changed 205, context: html, text, full: html, text
    Fixing up the program to be more robust and print more accurate stats, refs #17100
    
• src/hg/cirm/cdw/cdwCheckValidation/makefile
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    First draft of cdwCheckValidation as suggested by Jim, refs #17100
    
• src/hg/hgGene/hgGeneData/Human/hg19/links.ra
  • lines changed 8, context: html, text, full: html, text
    new procedure for building knownToWikipedia table on hg19 and hg38 refs #17052
    
• src/hg/hgGene/hgGeneData/Human/hg38/links.ra
  • lines changed 7, context: html, text, full: html, text
    new procedure for building knownToWikipedia table on hg19 and hg38 refs #17052
    
• src/hg/hgGene/hgGeneData/links.ra
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    new procedure for building knownToWikipedia table on hg19 and hg38 refs #17052
    
• src/hg/hgTables/hgTables.c
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    Making bottleneck server check more ubiquitous in hgTables, refs #17113
    
• src/hg/hgTrackUi/hgTrackUi.c
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    Changes after Angie code review (tnx!)
    
• src/hg/hgTracks/gtexTracks.c
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    Fix squish mode problem missing items (falsely 0-length) by using proper scaling function. refs #15645
    
  • lines changed 87, context: html, text, full: html, text
    Fine-tuning map boxes for gene models. Now there is one for the label and one for the gene model, which extends to the end of the item (JK request for this latter). refs #15645
    
  • lines changed 27, context: html, text, full: html, text
    Fix squish mode problem missing items (falsely 0-length) by using proper scaling function. refs #15645
    
  • lines changed 7, context: html, text, full: html, text
    Fix build err.
    
  • lines changed 16, context: html, text, full: html, text
    Fix click box problem -- handling of multi-mapped genes found by QA (Thanks Chris!)
    
  • lines changed 18, context: html, text, full: html, text
    Fixing gtexGene for limitedVis full->pack->squish->dense
    
  • lines changed 40, context: html, text, full: html, text
    resolved merge conflict
    
  • lines changed 2, context: html, text, full: html, text
    Temp fix for build error.
    
  • lines changed 5, context: html, text, full: html, text
    Fixed scope of height variable. Created some separation between height and lineHeight since they are being used differently.
    
  • lines changed 5, context: html, text, full: html, text
    Fix to GTEx limitVis fix, tnx Galt
    
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    Make graph height proportional to font height in large windows to improve viewing with large fonts. refs #15645
    
  • lines changed 14, context: html, text, full: html, text
    trying to clarify and simplify the variables used in gtex totalHeight.
    
  • lines changed 3, context: html, text, full: html, text
    fixing gtex for multi-region. oops needs to search list for matchin ss by vis now since ss is a list.
    
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    Change mouseover on graph to always show raw RPKM. refs #15645
    
• src/hg/hgTracks/hgTracks.h
  • lines changed 5, context: html, text, full: html, text
    Changes after Angie code review (tnx!)
    
  • lines changed 3, context: html, text, full: html, text
    fixing gtex for multi-region. oops needs to search list for matchin ss by vis now since ss is a list.
    
• src/hg/hgTracks/pslTrack.c
  • lines changed 11, context: html, text, full: html, text
    fix a problem with filtering on genbank metadata #11174
    
• src/hg/hgTracks/simpleTracks.c
  • lines changed 1, context: html, text, full: html, text
    Changes after Angie code review (tnx!)
    
  • lines changed 1, context: html, text, full: html, text
    fixing gtex for multi-region. oops needs to search list for matchin ss by vis now since ss is a list.
    
  • lines changed 5, context: html, text, full: html, text
    Fixes problem where altGraphX creates special spaceSavers without setting the window and vis fields
    
• src/hg/hgc/gtexClick.c
  • lines changed 7, context: html, text, full: html, text
    Fix click box problem -- handling of multi-mapped genes found by QA (Thanks Chris!)
    
  • lines changed 5, context: html, text, full: html, text
    Switch details page behavior to always show untransformed values (individual boxplots are already scaled), but include a temp trackDb setting so we can switch behavior back without needing code change for first release if this is requested. refs #15645
    
• src/hg/hgc/hgc.c
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    fixing invalid links in patents track, refs #14486
    
• src/hg/htdocs/FAQ/FAQreleases.html
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    Added macFas5 to list of released assemblies; refs #11174
    
• src/hg/htdocs/goldenPath/credits.html
  • lines changed 45, context: html, text, full: html, text
    Added macFas5 section; refs #11174
    
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 36, context: html, text, full: html, text
    Adding April Fool's joke
    
  • lines changed 5, context: html, text, full: html, text
    Uncommenting announcement for Lens Patents track. Removing a few older news items from the main page. refs #14486
    
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    un-announcing Lens Patents tracks, added back april fools day announcement, refs #14486
    
• src/hg/htdocs/images/joke04012016.png
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    Adding April Fool's joke
    
• src/hg/htdocs/images/session.hg18.stop.png
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    Adding a session image refs #1263
    
• src/hg/htdocs/images/session.hg19.startCodon.png
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    Adding an image for sessions gallery refs #1263
    
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    Replacing an image for sessions gallery refs #1263
    
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    Replacing an image for sessions gallery refs #1263
    
• src/hg/htdocs/images/session.hg19.stopCodons.png
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    Adding an image for sessions gallery refs #1263
    
• src/hg/htdocs/images/training/vidTitle08.jpg
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    changed font to bold on vid08 image text so it's more like the others
    
• src/hg/htdocs/indexNews.html
  • lines changed 55, context: html, text, full: html, text
    Adding April Fool's joke
    
  • lines changed 2, context: html, text, full: html, text
    Fixed broken links
    
  • lines changed 167, context: html, text, full: html, text
    Uncommenting announcement for Lens Patents track. Removing a few older news items from the main page. refs #14486
    
  • lines changed 39, context: html, text, full: html, text
    un-announcing Lens Patents tracks, added back april fools day announcement, refs #14486
    
• src/hg/htdocs/training/index.html
  • lines changed 15, context: html, text, full: html, text
    dropped mention of completed workshops in Kyoto and Kentucky. added missing link to new video
    
  • lines changed 1, context: html, text, full: html, text
    ack. pushed link before testing it. fixed.
    
• src/hg/inc/versionInfo.h
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    New version number v331
    
• src/hg/lib/botDelay.c
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    botDelay now warns with warn() to avoid corrupting HTTP headers, refs #17113
    
• src/hg/lib/hui.c
  • lines changed 10, context: html, text, full: html, text
    fix a problem with filtering on genbank metadata #11174
    
• src/hg/lib/jksql.c
  • lines changed 6, context: html, text, full: html, text
    adding a comment in jksql.c, no redmine
    
• src/hg/makeDb/doc/macFas5/initialBuild.txt
  • lines changed 34, context: html, text, full: html, text
    add search rule for gold/assembly track refs #11174
    
• src/hg/makeDb/doc/rheMac8/initialBuild.txt
  • lines changed 12, context: html, text, full: html, text
    turn on blat server refs #16744
    
• src/hg/makeDb/doc/ucscGenes/hg19.ucscGenes14.csh
  • lines changed 7, context: html, text, full: html, text
    new procedure for building knownToWikipedia table on hg19 and hg38 refs #17052
    
• src/hg/makeDb/doc/ucscGenes/hg38.ucscGenes16.sh
  • lines changed 8, context: html, text, full: html, text
    new procedure for building knownToWikipedia table on hg19 and hg38 refs #17052
    
• src/hg/makeDb/doc/wikipediaScrape.txt
  • lines changed 19, context: html, text, full: html, text
    make doc for scraping wikipedia to get data for knownToWikipedia table
    
• src/hg/makeDb/genbank/etc/hgwbeta.dbs
  • lines changed 1, context: html, text, full: html, text
    Added macFas5 to GenBank on hgwbeta; refs #11174
    
• src/hg/makeDb/genbank/etc/ignore.idx
  • lines changed 1, context: html, text, full: html, text
    change in genbank records
    
  • lines changed 1, context: html, text, full: html, text
    oops, mispelled Genbank
    
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    another pointless recording of a change at genbank
    
• src/hg/makeDb/genbank/etc/metaTables.txt
  • lines changed 24, context: html, text, full: html, text
    checking in first cuts at scripts that enable pushing Genbank tables
    instead of loading them everywhere.
    
• src/hg/makeDb/genbank/etc/perAss.txt
  • lines changed 27, context: html, text, full: html, text
    checking in first cuts at scripts that enable pushing Genbank tables
    instead of loading them everywhere.
    
• src/hg/makeDb/genbank/etc/rr.dbs
  • lines changed 1, context: html, text, full: html, text
    Turned on GenBank updates for macFas5 on the RR; refs #11174
    
• src/hg/makeDb/genbank/src/copy/checkUpdate.sh
  • lines changed 15, context: html, text, full: html, text
    checking in first cuts at scripts that enable pushing Genbank tables
    instead of loading them everywhere.
    
• src/hg/makeDb/genbank/src/copy/updateDb.sh
  • lines changed 95, context: html, text, full: html, text
    checking in first cuts at scripts that enable pushing Genbank tables
    instead of loading them everywhere.
    
• src/hg/makeDb/genbank/src/copy/updateMeta.sh
  • lines changed 1, context: html, text, full: html, text
    checking in first cuts at scripts that enable pushing Genbank tables
    instead of loading them everywhere.
    
• src/hg/makeDb/genbank/src/dbload/checkUpdate.sh
  • lines changed 22, context: html, text, full: html, text
    checking in first cuts at scripts that enable pushing Genbank tables
    instead of loading them everywhere.
    
• src/hg/makeDb/genbank/src/dbload/updateMetaDev.sh
  • lines changed 70, context: html, text, full: html, text
    checking in first cuts at scripts that enable pushing Genbank tables
    instead of loading them everywhere.
    
• src/hg/makeDb/schema/all.joiner
  • lines changed 106, context: html, text, full: html, text
    add all.joiner rules for gbMeta database
    
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    Allowing duplicate entries in gtex tables, refs #15645
    
• src/hg/makeDb/trackDb/alpaca/vicPac1/gap.html
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    Fixing redirect urls, refs #17144
    
• src/hg/makeDb/trackDb/alpaca/vicPac1/gold.html
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    Fixing redirect urls, refs #17144
    
• src/hg/makeDb/trackDb/alpaca/vicPac2/gap.html
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    Fixing redirect urls, refs #17144
    
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/alpaca/vicPac2/gold.html
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    Fixing redirect urls, refs #17144
    
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/armadillo/dasNov3/gap.html
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    Fixing redirect urls, refs #17144
    
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/armadillo/dasNov3/gold.html
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    Fixing redirect urls, refs #17144
    
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/augustusGene.html
  • lines changed 4, context: html, text, full: html, text
    Made corrections to macFas5 description pages; refs #11174
    
  • lines changed 4, context: html, text, full: html, text
    Made corrections to macFas5 description pages; refs #11174
    
• src/hg/makeDb/trackDb/baboon/papAnu2/gap.html
  • lines changed 1, context: html, text, full: html, text
    Fixing redirect urls, refs #17144
    
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/baboon/papAnu2/gold.html
  • lines changed 1, context: html, text, full: html, text
    Fixing redirect urls, refs #17144
    
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/baboon/papHam1/gap.html
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    Fixing redirect urls, refs #17144
    
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/baboon/papHam1/gold.html
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    Fixing redirect urls, refs #17144
    
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/balAcu/balAcu1/gap.html
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    Fixing redirect urls, refs #17144
    
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/balAcu/balAcu1/gold.html
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    Fixing redirect urls, refs #17144
    
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/birds/amaVit1/gap.html
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    Fixing redirect urls, refs #17144
    
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/birds/amaVit1/gold.html
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    Fixing redirect urls, refs #17144
    
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/birds/aptMan1/gap.html
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    Fixing redirect urls, refs #17144
    
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/birds/aptMan1/gold.html
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    Fixing redirect urls, refs #17144
    
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/birds/aquChr2/gap.html
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    Fixing redirect urls, refs #17144
    
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/birds/aquChr2/gold.html
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    Fixing redirect urls, refs #17144
    
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/birds/geoFor1/gap.html
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    Fixing redirect urls, refs #17144
    
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/birds/geoFor1/gold.html
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    Fixing redirect urls, refs #17144
    
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/birds/melUnd1/gap.html
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    Fixing redirect urls, refs #17144
    
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/birds/melUnd1/gold.html
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    Fixing redirect urls, refs #17144
    
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/bison/bisBis1/gap.html
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    Fixing redirect urls, refs #17144
    
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/bison/bisBis1/gold.html
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    Fixing redirect urls, refs #17144
    
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/bonobo/panPan1/gap.html
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    Fixing redirect urls, refs #17144
    
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/bonobo/panPan1/gold.html
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    Fixing redirect urls, refs #17144
    
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/bushbaby/otoGar3/gap.html
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    Fixing redirect urls, refs #17144
    
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/bushbaby/otoGar3/gold.html
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    Fixing redirect urls, refs #17144
    
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/calMil/calMil1/gap.html
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    Fixing redirect urls, refs #17144
    
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/calMil/calMil1/gold.html
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    Fixing redirect urls, refs #17144
    
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/cat/felCat4/ctgPos2.html
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/cat/felCat4/gap.html
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/cat/felCat4/gold.html
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/cat/felCat5/gap.html
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    Fixing redirect urls, refs #17144
    
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/cat/felCat5/gold.html
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    Fixing redirect urls, refs #17144
    
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/cat/felCat8/gap.html
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    Fixing redirect urls, refs #17144
    
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/cat/felCat8/gold.html
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    Fixing redirect urls, refs #17144
    
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/chimp/panTro4/gap.html
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    Fixing redirect urls, refs #17144
    
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/chimp/panTro4/gold.html
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    Fixing redirect urls, refs #17144
    
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/chinchilla/chiLan1/gap.html
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    Fixing redirect urls, refs #17144
    
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/chinchilla/chiLan1/gold.html
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    Fixing redirect urls, refs #17144
    
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/chlorocebus/chlSab2/gap.html
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    Fixing redirect urls, refs #17144
    
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/chlorocebus/chlSab2/gold.html
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    Fixing redirect urls, refs #17144
    
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/ciliate/oxyTri2/gap.html
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    Fixing redirect urls, refs #17144
    
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• src/hg/makeDb/trackDb/ciliate/oxyTri2/gold.html
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    Fixing redirect urls, refs #17144
    
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/cow/bosTau6/ctgPos2.html
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/cow/bosTau6/gap.html
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/cow/bosTau7/ctgPos2.html
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/cow/bosTau7/gap.html
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/cow/bosTau8/gap.html
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    Fixing redirect urls, refs #17144
    
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/cow/bosTau8/gold.html
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    Fixing redirect urls, refs #17144
    
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/criGri/criGri1/gap.html
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    Fixing redirect urls, refs #17144
    
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/criGri/criGri1/gold.html
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    Fixing redirect urls, refs #17144
    
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/dolphin/turTru2/gap.html
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    Fixing redirect urls, refs #17144
    
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/dolphin/turTru2/gold.html
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    Fixing redirect urls, refs #17144
    
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/drosophila/dm6/gap.html
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    Fixing redirect urls, refs #17144
    
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/drosophila/dm6/gold.html
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    Fixing redirect urls, refs #17144
    
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/ebola/bunEbo1/gap.html
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    Fixing redirect urls, refs #17144
    
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/ebola/bunEbo1/gold.html
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    Fixing redirect urls, refs #17144
    
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/ebola/eboVir1/gap.html
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    Fixing redirect urls, refs #17144
    
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/ebola/eboVir1/gold.html
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    Fixing redirect urls, refs #17144
    
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/ebola/eboVir2/gap.html
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    Fixing redirect urls, refs #17144
    
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/ebola/eboVir2/gold.html
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    Fixing redirect urls, refs #17144
    
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/ebola/eboVir3/gap.html
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    Fixing redirect urls, refs #17144
    
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/ebola/eboVir3/gold.html
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    Fixing redirect urls, refs #17144
    
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/ebola/marVir1/gap.html
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    Fixing redirect urls, refs #17144
    
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/ebola/marVir1/gold.html
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    Fixing redirect urls, refs #17144
    
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/ebola/resEbo1/gap.html
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    Fixing redirect urls, refs #17144
    
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/ebola/resEbo1/gold.html
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    Fixing redirect urls, refs #17144
    
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/ebola/sudEbo1/gap.html
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    Fixing redirect urls, refs #17144
    
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/ebola/sudEbo1/gold.html
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    Fixing redirect urls, refs #17144
    
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/ebola/taiEbo1/gap.html
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    Fixing redirect urls, refs #17144
    
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/ebola/taiEbo1/gold.html
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    Fixing redirect urls, refs #17144
    
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/ebola/zaiEbo1/gap.html
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    Fixing redirect urls, refs #17144
    
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/ebola/zaiEbo1/gold.html
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    Fixing redirect urls, refs #17144
    
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/ferret/musFur1/gap.html
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    Fixing redirect urls, refs #17144
    
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/ferret/musFur1/gold.html
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    Fixing redirect urls, refs #17144
    
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/frog/nanPar1/gap.html
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    Fixing redirect urls, refs #17144
    
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/frog/nanPar1/gold.html
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    Fixing redirect urls, refs #17144
    
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/gadMor/gadMor1/gap.html
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    Fixing redirect urls, refs #17144
    
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/gadMor/gadMor1/gold.html
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    Fixing redirect urls, refs #17144
    
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/galVar/galVar1/gap.html
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    Fixing redirect urls, refs #17144
    
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/galVar/galVar1/gold.html
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    Fixing redirect urls, refs #17144
    
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/gator/allMis1/gap.html
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    Fixing redirect urls, refs #17144
    
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/gator/allMis1/gold.html
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    Fixing redirect urls, refs #17144
    
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/gibbon/nomLeu2/gap.html
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    Fixing redirect urls, refs #17144
    
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/gibbon/nomLeu2/gold.html
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    Fixing redirect urls, refs #17144
    
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/gibbon/nomLeu3/gap.html
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    Fixing redirect urls, refs #17144
    
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/gibbon/nomLeu3/gold.html
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    Fixing redirect urls, refs #17144
    
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/gorilla/gorGor4/gap.html
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    Fixing redirect urls, refs #17144
    
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/gorilla/gorGor4/gold.html
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    Fixing redirect urls, refs #17144
    
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/gorilla/gorGor4/trackDb.chainNet.ra
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    Fixing chain/net matrix on gorilla/human chain net description page, refs #16220
    
• src/hg/makeDb/trackDb/gorilla/gorGor4/trackDb.ra
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    Fixing chain/net matrix on gorilla/human chain net description page, refs #16220
    
• src/hg/makeDb/trackDb/hedgehog/eriEur1/gap.html
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    Fixing redirect urls, refs #17144
    
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/hedgehog/eriEur1/gold.html
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    Fixing redirect urls, refs #17144
    
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/hedgehog/eriEur2/gap.html
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    Fixing redirect urls, refs #17144
    
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/hedgehog/eriEur2/gold.html
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    Fixing redirect urls, refs #17144
    
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/human/chainNetPrimate.ra
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    Corrected 'Crag' to 'Crab' :); refs #11174
    
• src/hg/makeDb/trackDb/human/hg17/ECgene.html
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    Fixed bad url, no RM
    
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    Fixed bad url, no RM
    
• src/hg/makeDb/trackDb/human/hg19/ctgPos.html
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    Fixing redirect urls, refs #17144
    
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/human/hg19/gap.html
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    Fixing redirect urls, refs #17144
    
• src/hg/makeDb/trackDb/human/hg19/gold.html
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    Fixing redirect urls, refs #17144
    
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
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    Moving patSeq url line from top-level in hg19 trackDb so that url is not used on eboVir3 patSeq track, refs #14486
    
• src/hg/makeDb/trackDb/human/hg19Patch2/gap.html
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    Fixing redirect urls, refs #17144
    
• src/hg/makeDb/trackDb/human/hg19Patch2/gold.html
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    Fixing redirect urls, refs #17144
    
• src/hg/makeDb/trackDb/human/hg19Patch9/gap.html
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    Fixing redirect urls, refs #17144
    
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/human/hg19Patch9/gold.html
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    Fixing redirect urls, refs #17144
    
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/human/hg38/altSequence.html
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    Fixing redirect urls, refs #17144
    
• src/hg/makeDb/trackDb/human/hg38/cons100way.html
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    Fixing bad url, refs #17089
    
• src/hg/makeDb/trackDb/human/hg38/gap.html
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    Fixing redirect urls, refs #17144
    
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/human/hg38/gold.html
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    Fixing redirect urls, refs #17144
    
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/human/trackDb.gtex.ra
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    Limit visibility so track switches to squish if too slow in large windows (e.g. >50MB). refs #15645
    
• src/hg/makeDb/trackDb/kangarooRat/dipOrd1/gap.html
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    Fixing redirect urls, refs #17144
    
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/kangarooRat/dipOrd1/gold.html
  • lines changed 1, context: html, text, full: html, text
    Fixing redirect urls, refs #17144
    
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/lamprey/petMar2/gap.html
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    Fixing redirect urls, refs #17144
    
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/lamprey/petMar2/gold.html
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    Fixing redirect urls, refs #17144
    
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/lancelet/braFlo2/gap.html
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    Fixing redirect urls, refs #17144
    
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/lancelet/braFlo2/gold.html
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    Fixing redirect urls, refs #17144
    
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/latCha/latCha1/gap.html
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    Fixing redirect urls, refs #17144
    
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/latCha/latCha1/gold.html
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    Fixing redirect urls, refs #17144
    
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/macaca/macFas5/gap.html
  • lines changed 2, context: html, text, full: html, text
    Made corrections to macFas5 description pages; refs #11174
    
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    Made corrections to macFas5 description pages; refs #11174
    
• src/hg/makeDb/trackDb/macaca/macFas5/gold.html
  • lines changed 2, context: html, text, full: html, text
    Made corrections to macFas5 description pages; refs #11174
    
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    Made corrections to macFas5 description pages; refs #11174
    
• src/hg/makeDb/trackDb/macaca/macFas5/trackDb.chainNet.ra
  • lines changed 8, context: html, text, full: html, text
    Updated trackDb.ra and added trackDb.chainNet.ra to correct values in chain/net description pages; refs #11174
    
  • lines changed 8, context: html, text, full: html, text
    Updated trackDb.ra and added trackDb.chainNet.ra to correct values in chain/net description pages; refs #11174
    
• src/hg/makeDb/trackDb/macaca/macFas5/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    Made corrections to macFas5 description pages; refs #11174
    
  • lines changed 2, context: html, text, full: html, text
    Updated trackDb.ra and added trackDb.chainNet.ra to correct values in chain/net description pages; refs #11174
    
  • lines changed 2, context: html, text, full: html, text
    Made corrections to macFas5 description pages; refs #11174
    
  • lines changed 2, context: html, text, full: html, text
    Updated trackDb.ra and added trackDb.chainNet.ra to correct values in chain/net description pages; refs #11174
    
  • lines changed 6, context: html, text, full: html, text
    enable searching for gold/assembly track refs #11174
    
• src/hg/makeDb/trackDb/manatee/triMan1/gap.html
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    Fixing redirect urls, refs #17144
    
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/manatee/triMan1/gold.html
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    Fixing redirect urls, refs #17144
    
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/marmoset/calJac3/ctgPos2.html
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/megabat/pteVam1/gap.html
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    Fixing redirect urls, refs #17144
    
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/megabat/pteVam1/gold.html
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    Fixing redirect urls, refs #17144
    
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/moleRat/hetGla2/gap.html
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    Fixing redirect urls, refs #17144
    
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/moleRat/hetGla2/gold.html
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    Fixing redirect urls, refs #17144
    
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/mouse/mm10Patch1/gap.html
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    Fixing redirect urls, refs #17144
    
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/mouse/mm10Patch1/gold.html
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    Fixing redirect urls, refs #17144
    
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/mouse/mm10Strains1/gap.html
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    Fixing redirect urls, refs #17144
    
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/mouse/mm10Strains1/gold.html
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• src/hg/makeDb/trackDb/mouseLemur/micMur1/gap.html
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• src/hg/makeDb/trackDb/mouseLemur/micMur1/gold.html
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• src/hg/makeDb/trackDb/mouseLemur/micMur2/gap.html
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• src/hg/makeDb/trackDb/mouseLemur/micMur2/gold.html
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• src/hg/makeDb/trackDb/oreNil/oreNil2/gap.html
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• src/hg/makeDb/trackDb/oreNil/oreNil2/gold.html
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• src/hg/makeDb/trackDb/pangolin/manPen1/gap.html
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• src/hg/makeDb/trackDb/pangolin/manPen1/gold.html
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/patSeq.html
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    Adding some text about how patent docs are listed on details page. Rewording odd sentence. refs #14486
    
• src/hg/makeDb/trackDb/pig/susScr2/ctgPos2.html
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/pig/susScr2/gap.html
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/pig/susScr2/gold.html
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/pig/susScr3/gap.html
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• src/hg/makeDb/trackDb/pig/susScr3/gold.html
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• src/hg/makeDb/trackDb/pika/ochPri2/gap.html
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• src/hg/makeDb/trackDb/pika/ochPri2/gold.html
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• src/hg/makeDb/trackDb/pika/ochPri3/gap.html
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• src/hg/makeDb/trackDb/pika/ochPri3/gold.html
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• src/hg/makeDb/trackDb/platypus/ornAna2/gap.html
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• src/hg/makeDb/trackDb/platypus/ornAna2/gold.html
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• src/hg/makeDb/trackDb/poeRet/poeRet1/gap.html
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• src/hg/makeDb/trackDb/poeRet/poeRet1/gold.html
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• src/hg/makeDb/trackDb/proboscis/nasLar1/gap.html
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• src/hg/makeDb/trackDb/proboscis/nasLar1/gold.html
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• src/hg/makeDb/trackDb/rat/rn6/gap.html
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• src/hg/makeDb/trackDb/rat/rn6/gold.html
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• src/hg/makeDb/trackDb/reptiles/thaSir1/gap.html
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• src/hg/makeDb/trackDb/reptiles/thaSir1/gold.html
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• src/hg/makeDb/trackDb/rhesus/rheMac3/ctgPos2.html
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/rhesus/rheMac3/gap.html
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• src/hg/makeDb/trackDb/rhesus/rheMac3/gold.html
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• src/hg/makeDb/trackDb/rhesus/rheMac7/gap.html
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• src/hg/makeDb/trackDb/rhesus/rheMac7/gold.html
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• src/hg/makeDb/trackDb/rhesus/rheMac8/gap.html
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• src/hg/makeDb/trackDb/rhesus/rheMac8/gold.html
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• src/hg/makeDb/trackDb/rhino/cerSim1/gap.html
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• src/hg/makeDb/trackDb/rhino/cerSim1/gold.html
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• src/hg/makeDb/trackDb/rhinopithecus/rhiRox1/gap.html
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• src/hg/makeDb/trackDb/rhinopithecus/rhiRox1/gold.html
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• src/hg/makeDb/trackDb/rockHyrax/proCap1/gap.html
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• src/hg/makeDb/trackDb/rockHyrax/proCap1/gold.html
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• src/hg/makeDb/trackDb/saiBol/saiBol1/gap.html
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• src/hg/makeDb/trackDb/saiBol/saiBol1/gold.html
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    Fixing redirect urls, refs #17144
    
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• src/hg/makeDb/trackDb/sheep/oviAri1/ctgPos2.html
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/sheep/oviAri1/gap.html
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• src/hg/makeDb/trackDb/sheep/oviAri1/gold.html
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• src/hg/makeDb/trackDb/sheep/oviAri3/gap.html
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• src/hg/makeDb/trackDb/sheep/oviAri3/gold.html
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• src/hg/makeDb/trackDb/shrew/sorAra1/gap.html
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• src/hg/makeDb/trackDb/shrew/sorAra1/gold.html
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• src/hg/makeDb/trackDb/shrew/sorAra2/gap.html
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• src/hg/makeDb/trackDb/shrew/sorAra2/gold.html
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• src/hg/makeDb/trackDb/sloth/choHof1/gap.html
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• src/hg/makeDb/trackDb/sloth/choHof1/gold.html
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• src/hg/makeDb/trackDb/squirrel/speTri2/gap.html
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• src/hg/makeDb/trackDb/squirrel/speTri2/gold.html
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• src/hg/makeDb/trackDb/squirt/ci3/gap.html
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• src/hg/makeDb/trackDb/squirt/ci3/gold.html
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/tagTypes.tab
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    Tag for gtex details display (for UI flexibility, likely temporary). refs #15645
    
• src/hg/makeDb/trackDb/tarsier/tarSyr1/gap.html
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• src/hg/makeDb/trackDb/tarsier/tarSyr1/gold.html
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• src/hg/makeDb/trackDb/tarsier/tarSyr2/gap.html
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• src/hg/makeDb/trackDb/tarsier/tarSyr2/gold.html
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• src/hg/makeDb/trackDb/tasmanianDevil/sarHar1/gap.html
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• src/hg/makeDb/trackDb/tenrec/echTel2/gap.html
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• src/hg/makeDb/trackDb/tenrec/echTel2/gold.html
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/trackDb.ra
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    Moving patSeq url line from top-level in hg19 trackDb so that url is not used on eboVir3 patSeq track, refs #14486
    
• src/hg/makeDb/trackDb/treeShrew/tupBel1/gap.html
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• src/hg/makeDb/trackDb/treeShrew/tupBel1/gold.html
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• src/hg/makeDb/trackDb/turkey/melGal1/ctgPos2.html
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/turkey/melGal1/gap.html
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    Fixing 2nd redirect url, refs #17114
    
• src/hg/makeDb/trackDb/turtle/chrPic2/gap.html
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• src/hg/makeDb/trackDb/turtle/chrPic2/gold.html
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• src/hg/makeDb/trackDb/worm/ancCey1/gap.html
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• src/hg/makeDb/trackDb/worm/ancCey1/gold.html
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• src/hg/makeDb/trackDb/worm/ascSuu1/gap.html
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• src/hg/makeDb/trackDb/worm/ascSuu1/gold.html
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• src/hg/makeDb/trackDb/worm/bruMal2/gap.html
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• src/hg/makeDb/trackDb/worm/bruMal2/gold.html
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• src/hg/makeDb/trackDb/worm/burXyl1/gap.html
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• src/hg/makeDb/trackDb/worm/burXyl1/gold.html
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• src/hg/makeDb/trackDb/worm/caeAng2/gap.html
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• src/hg/makeDb/trackDb/worm/caeAng2/gold.html
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• src/hg/makeDb/trackDb/worm/caeSp51/gap.html
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• src/hg/makeDb/trackDb/worm/caeSp51/gold.html
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• src/hg/makeDb/trackDb/worm/dirImm1/gap.html
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• src/hg/makeDb/trackDb/worm/dirImm1/gold.html
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• src/hg/makeDb/trackDb/worm/haeCon2/gap.html
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• src/hg/makeDb/trackDb/worm/haeCon2/gold.html
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• src/hg/makeDb/trackDb/worm/hetBac1/gap.html
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    Fixing redirect urls, refs #17144
    
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• src/hg/makeDb/trackDb/worm/hetBac1/gold.html
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• src/hg/makeDb/trackDb/worm/loaLoa1/gap.html
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• src/hg/makeDb/trackDb/worm/loaLoa1/gold.html
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• src/hg/makeDb/trackDb/worm/melInc2/gap.html
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• src/hg/makeDb/trackDb/worm/melInc2/gold.html
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• src/hg/makeDb/trackDb/worm/necAme1/gap.html
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• src/hg/makeDb/trackDb/worm/necAme1/gold.html
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• src/hg/makeDb/trackDb/worm/oncVol1/gap.html
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• src/hg/makeDb/trackDb/worm/oncVol1/gold.html
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• src/hg/makeDb/trackDb/worm/panRed1/gap.html
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• src/hg/makeDb/trackDb/worm/panRed1/gold.html
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• src/hg/makeDb/trackDb/worm/priExs1/gap.html
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• src/hg/makeDb/trackDb/worm/priExs1/gold.html
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• src/hg/makeDb/trackDb/worm/priPac3/gap.html
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• src/hg/makeDb/trackDb/worm/priPac3/gold.html
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• src/hg/makeDb/trackDb/worm/strRat1/gap.html
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• src/hg/makeDb/trackDb/worm/strRat1/gold.html
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• src/hg/makeDb/trackDb/worm/strRat2/gap.html
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• src/hg/makeDb/trackDb/worm/strRat2/gold.html
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• src/hg/makeDb/trackDb/worm/triSpi1/gap.html
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• src/hg/makeDb/trackDb/worm/triSpi1/gold.html
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• src/hg/makeDb/trackDb/worm/triSui1/gap.html
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• src/hg/makeDb/trackDb/worm/triSui1/gold.html
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• src/hg/makeDb/trackDb/xenTro/xenTro7/gap.html
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• src/hg/makeDb/trackDb/xenTro/xenTro7/gold.html
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• src/hg/makeDb/trackDb/zebraFinch/taeGut2/gap.html
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• src/hg/makeDb/trackDb/zebraFinch/taeGut2/gold.html
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    Fixing redirect urls, refs #17144
    
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• src/hg/makeDb/trackDb/zebrafish/danRer10/gap.html
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    Fixing redirect urls, refs #17144
    
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• src/hg/makeDb/trackDb/zebrafish/danRer10/gold.html
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    Fixing redirect urls, refs #17144
    
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• src/hg/utils/automation/makeGenomeDb.pl
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    update NCBI links to assembly information and AGP spec refs #11174
    
• src/hg/utils/otto/clinvar/clinVarToBed
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    clinvar otto is broken again. fixing again
    
• src/lib/common.c
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    adding comment after email from Chris, no redmine
    
• src/lib/obscure.c
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    more comments after email from chris
    
• src/utils/qa/weeklybld/buildEnv.csh
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