All File Changes

v323_base to v324_preview (2015-10-05 to 2015-10-12) v324

• src/browserbox/root/updateBrowser.sh
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    tolerate non-virtualbox VMs better in gbib, refs #16186
    
• src/hg/cirm/cdw/utils/cdwVcfStats/tests/expected.out
  • lines changed 15, context: html, text, full: html, text
    adding a test for cdwVcfStats
    
• src/hg/cirm/cdw/utils/cdwVcfStats/tests/indelTrim.vcf
  • lines changed 17, context: html, text, full: html, text
    adding a test for cdwVcfStats
    
• src/hg/cirm/cdw/utils/cdwVcfStats/tests/makefile
  • lines changed 4, context: html, text, full: html, text
    adding a test for cdwVcfStats
    
• src/hg/hgIntegrator/hgIntegrator.c
  • lines changed 6, context: html, text, full: html, text
    In f66bc993 & 6bf69bab, I mistakenly used the top-level track's name
    as the annoStreamer name, which was incorrect for subtracks. Now,
    use tdb->track so if leafTrack is found, we use that.
    fixes #16177
    
• src/hg/hgLogin/hgLogin.c
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    trying to make hgLogin work as a non-root htdocs, refs #16187
    
• src/hg/hgMirror/hgMirror
  • lines changed 40, context: html, text, full: html, text
    use cookie to save last db in hgMirror, refs #16185.
    Also remove the workaround in makefile for hgwdev as it's not needed
    anymore.
    
• src/hg/hgMirror/makefile
  • lines changed 2, context: html, text, full: html, text
    use cookie to save last db in hgMirror, refs #16185.
    Also remove the workaround in makefile for hgwdev as it's not needed
    anymore.
    
• src/hg/hgTables/hgTables.c
  • lines changed 10, context: html, text, full: html, text
    handle table names that include the database
    
• src/hg/hgTracks/extTools.ra
  • lines changed 9, context: html, text, full: html, text
    Commenting out a stanza in extTools.ra to remove CRISPOR tool refs #16160
    
• src/hg/hgc/hgcData/links.ra
  • lines changed 10, context: html, text, full: html, text
    Adding two new external link options for hgc (NCBI and Ensembl via ID)
    
• src/hg/htdocs/ENCODE/pubsEncode.html
  • lines changed 5, context: html, text, full: html, text
    Update author's list (corrected by Consortium at PubMed), per request by Mike Pazin.
    
• src/hg/htdocs/goldenPath/help/customTrackText.html
  • lines changed 1, context: html, text, full: html, text
    fixing link after code review, refs #16106, refs #16145
    
• src/hg/htdocs/license/index.html
  • lines changed 2, context: html, text, full: html, text
    Added 2 more directories to the list of source code that doesn't require a license: kent/src/inc and kent/src/tagStorm.
    
• src/hg/htdocs/training/index.html
  • lines changed 25, context: html, text, full: html, text
    dropped two completed workshops. added next two
    
• src/hg/lib/tests/annoGratorTester.c
  • lines changed 298, context: html, text, full: html, text
    Refactoring: split each test into its own function instead of god-awful long main;
    make structured definition of tests so that adding a new test doesn't require
    so many repetitive edits. Require the testName command line arg.
    
• src/hg/makeDb/trackDb/alpaca/vicPac1/description.html
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    Changing links to images directory to be relative, refs #16099
    
• src/hg/makeDb/trackDb/alpaca/vicPac2/description.html
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    Changing links to images directory to be relative, refs #16099
    
• src/hg/makeDb/trackDb/alpaca/vicVic1/description.html
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    Changing links to images directory to be relative, refs #16099
    
• src/hg/makeDb/trackDb/ancestor/homIni20/description.html
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    Changing links to images directory to be relative, refs #16099
    
• src/hg/makeDb/trackDb/ancestor/homPan20/description.html
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    Changing links to images directory to be relative, refs #16099
    
• src/hg/makeDb/trackDb/apis/apiMel1/description.html
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    Changing links to images directory to be relative, refs #16099
    
• src/hg/makeDb/trackDb/apis/apiMel2/description.html
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    Changing links to images directory to be relative, refs #16099
    
• src/hg/makeDb/trackDb/armadillo/dasNov1/description.html
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    Changing links to images directory to be relative, refs #16099
    
• src/hg/makeDb/trackDb/armadillo/dasNov2/description.html
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    Changing links to images directory to be relative, refs #16099
    
• src/hg/makeDb/trackDb/armadillo/dasNov3/description.html
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    Changing links to images directory to be relative, refs #16099
    
• src/hg/makeDb/trackDb/baboon/papAnu2/description.html
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    Changing links to images directory to be relative, refs #16099
    
• src/hg/makeDb/trackDb/baboon/papHam1/description.html
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    Changing links to images directory to be relative, refs #16099
    
• src/hg/makeDb/trackDb/balAcu/balAcu1/description.html
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    Changing links to images directory to be relative, refs #16099
    
• src/hg/makeDb/trackDb/birds/amaVit1/description.html
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    Changing links to images directory to be relative, refs #16099
    
• src/hg/makeDb/trackDb/birds/aquChr2/description.html
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    Changing links to images directory to be relative, refs #16099
    
• src/hg/makeDb/trackDb/birds/geoFor1/description.html
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    Changing links to images directory to be relative, refs #16099
    
• src/hg/makeDb/trackDb/birds/melUnd1/description.html
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    Changing links to images directory to be relative, refs #16099
    
• src/hg/makeDb/trackDb/bison/bisBis1/description.html
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    Changing links to images directory to be relative, refs #16099
    
• src/hg/makeDb/trackDb/bonobo/panPan1/description.html
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    Changing links to images directory to be relative, refs #16099
    
• src/hg/makeDb/trackDb/bushbaby/otoGar1/description.html
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    Changing links to images directory to be relative, refs #16099
    
• src/hg/makeDb/trackDb/bushbaby/otoGar3/description.html
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    Changing links to images directory to be relative, refs #16099
    
• src/hg/makeDb/trackDb/cactus/cacTus1/description.html
  • lines changed 1, context: html, text, full: html, text
    Changing links to images directory to be relative, refs #16099
    
• src/hg/makeDb/trackDb/cactus/cacTus2/description.html
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    Changing links to images directory to be relative, refs #16099
    
• src/hg/makeDb/trackDb/calMil/calMil1/description.html
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    Changing links to images directory to be relative, refs #16099
    
• src/hg/makeDb/trackDb/cat/felCat3/description.html
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    Changing links to images directory to be relative, refs #16099
    
• src/hg/makeDb/trackDb/cat/felCat5/description.html
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    Changing links to images directory to be relative, refs #16099
    
• src/hg/makeDb/trackDb/cat/felCat8/description.html
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    Changing links to images directory to be relative, refs #16099
    
• src/hg/makeDb/trackDb/chicken/galGal2/description.html
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    Changing links to images directory to be relative, refs #16099
    
• src/hg/makeDb/trackDb/chicken/galGal3/description.html
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    Changing links to images directory to be relative, refs #16099
    
• src/hg/makeDb/trackDb/chicken/galGal4/description.html
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    Changing links to images directory to be relative, refs #16099
    
• src/hg/makeDb/trackDb/chimp/panTro1/description.html
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    Changing links to images directory to be relative, refs #16099
    
• src/hg/makeDb/trackDb/chimp/panTro2/description.html
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    Changing links to images directory to be relative, refs #16099
    
• src/hg/makeDb/trackDb/chimp/panTro3/description.html
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    Changing links to images directory to be relative, refs #16099
    
• src/hg/makeDb/trackDb/chimp/panTro4/description.html
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    Changing links to images directory to be relative, refs #16099
    
• src/hg/makeDb/trackDb/chinchilla/chiLan1/description.html
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    Changing links to images directory to be relative, refs #16099
    
• src/hg/makeDb/trackDb/chlorocebus/chlSab2/description.html
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    Changing links to images directory to be relative, refs #16099
    
• src/hg/makeDb/trackDb/cow/bosTau1/description.html
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    Changing links to images directory to be relative, refs #16099
    
• src/hg/makeDb/trackDb/cow/bosTau2/description.html
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    Changing links to images directory to be relative, refs #16099
    
• src/hg/makeDb/trackDb/cow/bosTau3/description.html
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    Changing links to images directory to be relative, refs #16099
    
• src/hg/makeDb/trackDb/cow/bosTau4/description.html
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    Changing links to images directory to be relative, refs #16099
    
• src/hg/makeDb/trackDb/cow/bosTau5/description.html
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    Changing links to images directory to be relative, refs #16099
    
• src/hg/makeDb/trackDb/cow/bosTau6/description.html
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    Changing links to images directory to be relative, refs #16099
    
• src/hg/makeDb/trackDb/cow/bosTau7/description.html
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    Changing links to images directory to be relative, refs #16099
    
• src/hg/makeDb/trackDb/cow/bosTau8/description.html
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    Changing links to images directory to be relative, refs #16099
    
• src/hg/makeDb/trackDb/criGri/criGri1/description.html
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    Changing links to images directory to be relative, refs #16099
    
• src/hg/makeDb/trackDb/dog/canFam1/description.html
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    Changing links to images directory to be relative, refs #16099
    
• src/hg/makeDb/trackDb/dog/canFam2/description.html
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    Changing links to images directory to be relative, refs #16099
    
• src/hg/makeDb/trackDb/dog/canFam3/description.html
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    Changing links to images directory to be relative, refs #16099
    
• src/hg/makeDb/trackDb/dog/canFamPoodle1/description.html
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    Changing links to images directory to be relative, refs #16099
    
• src/hg/makeDb/trackDb/dolphin/turTru1/description.html
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    Changing links to images directory to be relative, refs #16099
    
• src/hg/makeDb/trackDb/dolphin/turTru2/description.html
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    Changing links to images directory to be relative, refs #16099
    
• src/hg/makeDb/trackDb/drosophila/dm6/description.html
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    Changing links to images directory to be relative, refs #16099
    
• src/hg/makeDb/trackDb/ebola/bunEbo1/description.html
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    Changing links to images directory to be relative, refs #16099
    
• src/hg/makeDb/trackDb/ebola/eboVir1/description.html
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    Changing links to images directory to be relative, refs #16099
    
• src/hg/makeDb/trackDb/ebola/eboVir2/description.html
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    Changing links to images directory to be relative, refs #16099
    
• src/hg/makeDb/trackDb/ebola/eboVir3/description.html
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    Changing links to images directory to be relative, refs #16099
    
• src/hg/makeDb/trackDb/ebola/marVir1/description.html
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    Changing links to images directory to be relative, refs #16099
    
• src/hg/makeDb/trackDb/ebola/resEbo1/description.html
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    Changing links to images directory to be relative, refs #16099
    
• src/hg/makeDb/trackDb/ebola/sudEbo1/description.html
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    Changing links to images directory to be relative, refs #16099
    
• src/hg/makeDb/trackDb/ebola/taiEbo1/description.html
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    Changing links to images directory to be relative, refs #16099
    
• src/hg/makeDb/trackDb/ebola/zaiEbo1/description.html
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    Changing links to images directory to be relative, refs #16099
    
• src/hg/makeDb/trackDb/elephant/loxAfr1/description.html
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• src/hg/makeDb/trackDb/elephant/loxAfr2/description.html
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• src/hg/makeDb/trackDb/elephant/loxAfr3/description.html
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• src/hg/makeDb/trackDb/ferret/musFur1/description.html
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    Changing links to images directory to be relative, refs #16099
    
• src/hg/makeDb/trackDb/frog/nanPar1/description.html
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    Changing links to images directory to be relative, refs #16099
    
• src/hg/makeDb/trackDb/fugu/fr1/description.html
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    Changing links to images directory to be relative, refs #16099
    
• src/hg/makeDb/trackDb/fugu/fr2/description.html
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    Changing links to images directory to be relative, refs #16099
    
• src/hg/makeDb/trackDb/fugu/fr3/description.html
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• src/hg/makeDb/trackDb/gadMor/gadMor1/description.html
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• src/hg/makeDb/trackDb/gator/allMis1/description.html
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• src/hg/makeDb/trackDb/gibbon/nomLeu1/description.html
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• src/hg/makeDb/trackDb/gibbon/nomLeu2/description.html
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• src/hg/makeDb/trackDb/gibbon/nomLeu3/description.html
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• src/hg/makeDb/trackDb/gorilla/gorGor1/description.html
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• src/hg/makeDb/trackDb/gorilla/gorGor2/description.html
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• src/hg/makeDb/trackDb/gorilla/gorGor3/description.html
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• src/hg/makeDb/trackDb/guineaPig/cavPor3/description.html
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• src/hg/makeDb/trackDb/haplotypes/hg19Haps/description.html
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• src/hg/makeDb/trackDb/hedgehog/eriEur1/description.html
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• src/hg/makeDb/trackDb/hedgehog/eriEur2/description.html
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• src/hg/makeDb/trackDb/horse/equCab1/description.html
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• src/hg/makeDb/trackDb/horse/equCab2/description.html
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• src/hg/makeDb/trackDb/human/bamSLDenisova.html
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• src/hg/makeDb/trackDb/human/encode_MSA2_MLAGAN.html
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• src/hg/makeDb/trackDb/human/gvPosOld.html
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• src/hg/makeDb/trackDb/human/hg16/description.html
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• src/hg/makeDb/trackDb/human/hg16/multizMm3Rn3GalGal2_phyloHMM.html
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• src/hg/makeDb/trackDb/human/hg16/mzPt1Mm3Rn3Gg2_pHMM.html
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• src/hg/makeDb/trackDb/human/hg17/description.html
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• src/hg/makeDb/trackDb/human/hg17/encodeMsaElements.html
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• src/hg/makeDb/trackDb/human/hg17/tfbsConsSites.html
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• src/hg/makeDb/trackDb/human/hg18/description.html
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• src/hg/makeDb/trackDb/human/hg18/tfbsConsSites.html
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• src/hg/makeDb/trackDb/human/hg19/description.html
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• src/hg/makeDb/trackDb/human/hg19/dhcBamDenisova.html
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• src/hg/makeDb/trackDb/human/hg19/dhcVcfDenisovaPinky.html
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• src/hg/makeDb/trackDb/human/hg19/tfbsConsSites.html
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• src/hg/makeDb/trackDb/human/hg19Patch2/description.html
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• src/hg/makeDb/trackDb/human/hg19Patch5/description.html
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• src/hg/makeDb/trackDb/human/hg19Patch9/description.html
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• src/hg/makeDb/trackDb/human/hg38/description.html
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• src/hg/makeDb/trackDb/human/laminB1Super.html
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• src/hg/makeDb/trackDb/kangarooRat/dipOrd1/description.html
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• src/hg/makeDb/trackDb/lamprey/petMar1/description.html
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• src/hg/makeDb/trackDb/lamprey/petMar2/description.html
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• src/hg/makeDb/trackDb/lancelet/braFlo1/description.html
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• src/hg/makeDb/trackDb/lancelet/braFlo2/description.html
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• src/hg/makeDb/trackDb/latCha/latCha1/description.html
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• src/hg/makeDb/trackDb/lizard/anoCar1/description.html
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• src/hg/makeDb/trackDb/lizard/anoCar2/description.html
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• src/hg/makeDb/trackDb/macaca/macFas5/description.html
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• src/hg/makeDb/trackDb/manatee/triMan1/description.html
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