File Changes for hiram

v319_preview2 to v319_base (2015-07-06 to 2015-07-13) v319

• src/hg/htdocs/images/Ascaris_suum.jpg
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    photo from CDC public domain refs #15209
    
• src/hg/htdocs/images/Dirofilaria_immitis.jpg
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    photo from R.E. Pugh parasitology collection refs #15209
    
• src/hg/htdocs/images/Loa_loa.jpg
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    image from CDC public domain refs #15209
    
• src/hg/htdocs/images/Onchocerca_volvulus.jpg
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    adding oncVol1 Onchocerca_volvulus from R.E. Pugh parasitology collection refs #15209
    
• src/hg/htdocs/images/Strongyloides_ratti.jpg
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    photo from Mark Vinney/University of Bristol http://www.bristol.ac.uk/biology/people/mark-e-viney/index.html refs #15209
    
• src/hg/htdocs/images/Trichinella_spiralis.jpg
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    photo from CDC refs #15209
    
• src/hg/htdocs/images/Trichuris_suis.jpg
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    photo from CDC public domain refs #15209
    
• src/hg/inc/versionInfo.h
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    New version number v319
    
• src/hg/makeDb/doc/caeAng1.txt
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    liftOver to caeAng2 refs #15209
    
• src/hg/makeDb/doc/ce11/lastzRuns.txt
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    done with haeCon2 lastz/chain/net refs #15209
    
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    don with caeSp111 bruMal2 caeSp51 refs #15209
    
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    finished with caeSp5 strRat2 strRat1 burXyl1 oncVol1 refs #15209
    
• src/hg/makeDb/doc/haeCon1.txt
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    adding liftOvers haeCon1 and 2 both ways and the build of haeCon2 refs #15209
    
• src/hg/makeDb/doc/melInc1.txt
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    liftOvers from melInc1 and 2 both ways and melInc2 browser building refs #15209
    
• src/hg/makeDb/doc/priPac1.txt
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    liftOvers between priPac3 and priPac1 and 2 both ways and priPac3 browser build refs #15209
    
• src/hg/makeDb/doc/priPac2.txt
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    liftOvers between priPac3 and priPac1 and 2 both ways and priPac3 browser build refs #15209
    
• src/hg/makeDb/doc/worms/bruMal2.txt
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    starting build of bruMal2 refs #15209
    
• src/hg/makeDb/doc/worms/burXyl1.txt
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    running up burXyl1 dirImm1 oncVol1 refs #15209
    
• src/hg/makeDb/doc/worms/caeAng2.txt
  • lines changed 117, context: html, text, full: html, text
    liftOvers from caeAng1 and 2 both ways and caeAng2 browser build refs #15209
    
• src/hg/makeDb/doc/worms/caeSp51.txt
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    running up assemblies for caeSp51 strRat1 strRat2 and strRat2 is an organized assmbly so include scripts used refs #15209
    
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    done with default set of tracks refs #15209
    
• src/hg/makeDb/doc/worms/dirImm1.txt
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    running up burXyl1 dirImm1 oncVol1 refs #15209
    
• src/hg/makeDb/doc/worms/haeCon2.txt
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    adding liftOvers haeCon1 and 2 both ways and the build of haeCon2 refs #15209
    
• src/hg/makeDb/doc/worms/loaLoa1.txt
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    running up assemblies Trichinella spiralis, Trichuris suis, Loa loa refs #15209
    
• src/hg/makeDb/doc/worms/melInc2.txt
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    liftOvers from melInc1 and 2 both ways and melInc2 browser building refs #15209
    
• src/hg/makeDb/doc/worms/oncVol1.txt
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    running up burXyl1 dirImm1 oncVol1 refs #15209
    
• src/hg/makeDb/doc/worms/panRed1.txt
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    done with initial tracks refs #15209
    
• src/hg/makeDb/doc/worms/priPac3.txt
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    liftOvers between priPac3 and priPac1 and 2 both ways and priPac3 browser build refs #15209
    
• src/hg/makeDb/doc/worms/strRat1.txt
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    running up assemblies for caeSp51 strRat1 strRat2 and strRat2 is an organized assmbly so include scripts used refs #15209
    
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    completed most tracks ready for lastz runs refs #15209
    
• src/hg/makeDb/doc/worms/strRat2.txt
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    running up assemblies for caeSp51 strRat1 strRat2 and strRat2 is an organized assmbly so include scripts used refs #15209
    
  • lines changed 59, context: html, text, full: html, text
    completed most tracks ready for lastz runs refs #15209
    
• src/hg/makeDb/doc/worms/triSpi1.txt
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    running up assemblies Trichinella spiralis, Trichuris suis, Loa loa refs #15209
    
• src/hg/makeDb/doc/worms/triSui1.txt
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    running up assemblies Trichinella spiralis, Trichuris suis, Loa loa refs #15209
    
• src/hg/makeDb/doc/worms/ucscCompositeAgp.pl
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    running up assemblies for caeSp51 strRat1 strRat2 and strRat2 is an organized assmbly so include scripts used refs #15209
    
• src/hg/makeDb/doc/worms/unlocalized.pl
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    running up assemblies for caeSp51 strRat1 strRat2 and strRat2 is an organized assmbly so include scripts used refs #15209
    
• src/hg/makeDb/doc/worms/unplaced.pl
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    running up assemblies for caeSp51 strRat1 strRat2 and strRat2 is an organized assmbly so include scripts used refs #15209
    
• src/hg/makeDb/genbank/etc/align.dbs
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    Added priPac3 - Pristionchus pacificus refs #15209
    
• src/hg/makeDb/genbank/etc/hgwdev.dbs
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    Added priPac3 - Pristionchus pacificus refs #15209
    
• src/hg/makeDb/schema/all.joiner
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    adding priPac3 definitions refs #15209
    
• src/hg/makeDb/trackDb/makefile
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    adding bruMal2 to the build refs #15209
    
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    adding strRat1 to the build refs #15209
    
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    adding strRat2 to the build refs #15209
    
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    adding dirImm1 to the build refs #15209
    
  • lines changed 1, context: html, text, full: html, text
    adding burXyl1 to the build refs #15209
    
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    adding Onchocerca volvulus oncVol1 to the build refs #15209
    
  • lines changed 1, context: html, text, full: html, text
    adding caeSp51 to the build refs #15209
    
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    adding Trichinella spiralis triSpi1 to the build refs #15209
    
  • lines changed 1, context: html, text, full: html, text
    adding Trichuris suis triSui1 refs #15209
    
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    addgin Loa loa loaLoa1 to the build refs #15209
    
• src/hg/makeDb/trackDb/worm/bruMal2/description.html
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    adding bruMal2 to the build refs #15209
    
• src/hg/makeDb/trackDb/worm/bruMal2/gap.html
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    adding bruMal2 to the build refs #15209
    
• src/hg/makeDb/trackDb/worm/bruMal2/gold.html
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    adding bruMal2 to the build refs #15209
    
• src/hg/makeDb/trackDb/worm/bruMal2/trackDb.ra
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    adding bruMal2 to the build refs #15209
    
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    add gold table search rule refs #15209
    
• src/hg/makeDb/trackDb/worm/burXyl1/description.html
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    adding burXyl1 to the build refs #15209
    
• src/hg/makeDb/trackDb/worm/burXyl1/gap.html
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    adding burXyl1 to the build refs #15209
    
• src/hg/makeDb/trackDb/worm/burXyl1/gold.html
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    adding burXyl1 to the build refs #15209
    
• src/hg/makeDb/trackDb/worm/burXyl1/trackDb.ra
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    adding burXyl1 to the build refs #15209
    
• src/hg/makeDb/trackDb/worm/caeSp51/description.html
  • lines changed 63, context: html, text, full: html, text
    adding caeSp51 to the build refs #15209
    
• src/hg/makeDb/trackDb/worm/caeSp51/gap.html
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    adding caeSp51 to the build refs #15209
    
• src/hg/makeDb/trackDb/worm/caeSp51/gold.html
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    adding caeSp51 to the build refs #15209
    
• src/hg/makeDb/trackDb/worm/caeSp51/trackDb.ra
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    adding caeSp51 to the build refs #15209
    
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    adding gold table search rule refs #15209
    
• src/hg/makeDb/trackDb/worm/dirImm1/description.html
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    adding dirImm1 to the build refs #15209
    
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    reset assembly info link to WormBase refs #15209
    
• src/hg/makeDb/trackDb/worm/dirImm1/gap.html
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    adding dirImm1 to the build refs #15209
    
• src/hg/makeDb/trackDb/worm/dirImm1/gold.html
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    adding dirImm1 to the build refs #15209
    
• src/hg/makeDb/trackDb/worm/dirImm1/trackDb.ra
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    adding dirImm1 to the build refs #15209
    
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    adding gold table search rule refs #15209
    
• src/hg/makeDb/trackDb/worm/loaLoa1/description.html
  • lines changed 63, context: html, text, full: html, text
    addgin Loa loa loaLoa1 to the build refs #15209
    
• src/hg/makeDb/trackDb/worm/loaLoa1/gap.html
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    addgin Loa loa loaLoa1 to the build refs #15209
    
• src/hg/makeDb/trackDb/worm/loaLoa1/gold.html
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    addgin Loa loa loaLoa1 to the build refs #15209
    
• src/hg/makeDb/trackDb/worm/loaLoa1/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    addgin Loa loa loaLoa1 to the build refs #15209
    
  • lines changed 5, context: html, text, full: html, text
    add gold table search rule refs #15209
    
• src/hg/makeDb/trackDb/worm/oncVol1/description.html
  • lines changed 63, context: html, text, full: html, text
    adding Onchocerca volvulus oncVol1 to the build refs #15209
    
• src/hg/makeDb/trackDb/worm/oncVol1/gap.html
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    adding Onchocerca volvulus oncVol1 to the build refs #15209
    
• src/hg/makeDb/trackDb/worm/oncVol1/gold.html
  • lines changed 34, context: html, text, full: html, text
    adding Onchocerca volvulus oncVol1 to the build refs #15209
    
• src/hg/makeDb/trackDb/worm/oncVol1/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    adding Onchocerca volvulus oncVol1 to the build refs #15209
    
  • lines changed 5, context: html, text, full: html, text
    add gold table search rule refs #15209
    
• src/hg/makeDb/trackDb/worm/strRat1/description.html
  • lines changed 63, context: html, text, full: html, text
    adding strRat1 to the build refs #15209
    
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    correct note of reference for photo refs #15209
    
• src/hg/makeDb/trackDb/worm/strRat1/gap.html
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    adding strRat1 to the build refs #15209
    
• src/hg/makeDb/trackDb/worm/strRat1/gold.html
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    adding strRat1 to the build refs #15209
    
• src/hg/makeDb/trackDb/worm/strRat1/trackDb.ra
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    adding strRat1 to the build refs #15209
    
• src/hg/makeDb/trackDb/worm/strRat2/description.html
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    adding strRat2 to the build refs #15209
    
  • lines changed 1, context: html, text, full: html, text
    correct note of reference for photo refs #15209
    
• src/hg/makeDb/trackDb/worm/strRat2/gap.html
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    adding strRat2 to the build refs #15209
    
• src/hg/makeDb/trackDb/worm/strRat2/gold.html
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    adding strRat2 to the build refs #15209
    
• src/hg/makeDb/trackDb/worm/strRat2/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    adding strRat2 to the build refs #15209
    
  • lines changed 5, context: html, text, full: html, text
    adding gold table search rule refs #15209
    
• src/hg/makeDb/trackDb/worm/trackDb.chainNet.ra
  • lines changed 338, context: html, text, full: html, text
    adding definitions for caeAng2 melInc2 priPac3 haeCon2 haeCon1 bruMal2 refs #15209
    
  • lines changed 392, context: html, text, full: html, text
    adding caeSp51 panRed1 burXyl1 melHap1 strRat1 strRat2 oncVol1 refs #15209
    
• src/hg/makeDb/trackDb/worm/triSpi1/description.html
  • lines changed 63, context: html, text, full: html, text
    adding Trichinella spiralis triSpi1 to the build refs #15209
    
• src/hg/makeDb/trackDb/worm/triSpi1/gap.html
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    adding Trichinella spiralis triSpi1 to the build refs #15209
    
• src/hg/makeDb/trackDb/worm/triSpi1/gold.html
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    adding Trichinella spiralis triSpi1 to the build refs #15209
    
• src/hg/makeDb/trackDb/worm/triSpi1/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    adding Trichinella spiralis triSpi1 to the build refs #15209
    
  • lines changed 5, context: html, text, full: html, text
    adding gold table search rule refs #15209
    
• src/hg/makeDb/trackDb/worm/triSui1/description.html
  • lines changed 63, context: html, text, full: html, text
    adding Trichuris suis triSui1 refs #15209
    
• src/hg/makeDb/trackDb/worm/triSui1/gap.html
  • lines changed 30, context: html, text, full: html, text
    adding Trichuris suis triSui1 refs #15209
    
• src/hg/makeDb/trackDb/worm/triSui1/gold.html
  • lines changed 34, context: html, text, full: html, text
    adding Trichuris suis triSui1 refs #15209
    
• src/hg/makeDb/trackDb/worm/triSui1/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    adding Trichuris suis triSui1 refs #15209
    
  • lines changed 5, context: html, text, full: html, text
    adding gold table search rule refs #15209
    
• src/utils/pslScore/pslScore.c
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    add information about column meanings in output in usage message refs #15635
    
• src/utils/qa/weeklybld/buildEnv.csh
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    v319 final build refs #15624