File Changes for galt

v312_preview to v312_preview2 (2015-02-02 to 2015-02-09) v312

• java/src/edu/ucsc/genome/qa/linkCheck/LinkCheck.java
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• src/aladdin/aladdin/aladdin.c
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• src/aladdin/aladdin/makefile
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• src/cdnaAli/ali2alx/makefile
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• src/cdnaAli/aliGlue/makefile
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• src/cdnaAli/binGood/makefile
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• src/cdnaAli/cdnaOff/makefile
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• src/cdnaAli/cluster/makefile
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• src/cdnaAli/exonAli/makefile
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• src/cdnaAli/findCdna/makefile
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• src/cdnaAli/g2cCheck/makefile
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• src/cdnaAli/introns/makefile
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• src/cdnaAli/pairClo/makefile
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• src/cdnaAli/patCount/makefile
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• src/cdnaAli/patSpace/makefile
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• src/cdnaAli/refineAli/makefile
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• src/cdnaAli/sortFilt/makefile
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• src/cdnaAli/stitchea/makefile
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• src/hg/ctgFaToFa/makefile
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• src/hg/encode/encodeValidate/test/input/duke/DukeDNase.PIF
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• src/hg/encode/encodeValidate/test/input/duke/Duke_GM12878_DNase.DDF
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• src/hg/fakeOut/makefile
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• src/hg/ffaToFa/makefile
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• src/hg/gigAssembler/goldToAgp/makefile
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• src/hg/gigAssembler/qaGold/makefile
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• src/hg/hgTracks/expRatioTracks.h
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• src/hg/htdocs/README
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    adding some reminders about htdocsExtra repository.
    
• src/hg/htdocs/geneExtra/lepre1.gif
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• src/hg/htdocs/goldenPath/ftLauderdale.pdf
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• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
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    minor tweaks suggested by Angie in codereview.
    
• src/hg/htdocs/images/dot_clear.gif
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• src/hg/htdocs/images/platypus.jpg
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• src/hg/htdocs/makefile
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    adding some reminders about htdocsExtra repository.
    
• src/hg/lib/codeBlastScore.as
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• src/hg/lib/codeBlastScore.sql
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• src/hg/lib/gbRNAs.as
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• src/hg/lib/protHomolog.as
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• src/hg/lib/rnaGenes.as
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• src/hg/lib/rnaHybridization.as
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• src/hg/lib/samSubdir.as
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• src/hg/lib/snoRNAs.as
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• src/hg/lib/tRNAs.as
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• src/hg/makeDb/doc/proteins/090821.txt
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• src/hg/makeDb/doc/proteins/101005.txt
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• src/hg/makeDb/doc/proteins/111004.txt
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• src/hg/makeDb/doc/proteins/120806.txt
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• src/hg/makeDb/doc/proteins/121210.txt
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• src/hg/makeDb/doc/proteins/140122.txt
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• src/hg/makeDb/doc/proteins/150115.txt
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• src/hg/makeDb/doc/uniProt/sp080707.txt
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• src/hg/makeDb/doc/uniProt/sp090821.txt
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• src/hg/makeDb/doc/uniProt/sp100331.txt
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• src/hg/makeDb/doc/uniProt/sp101005.txt
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• src/hg/makeDb/doc/uniProt/sp110315.txt
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• src/hg/makeDb/doc/uniProt/sp111004.txt
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• src/hg/makeDb/doc/uniProt/sp120323.txt
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• src/hg/makeDb/doc/uniProt/sp121210.txt
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• src/hg/makeDb/doc/uniProt/sp140122.txt
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• src/hg/makeDb/doc/uniProt/sp150115.txt
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• src/hg/makeDb/outside/ensembl/makefile
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• src/hg/makeDb/tfbsConsLoc/makefile
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• src/hg/oneShot/doEvoFold/doEvoFold.c
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• src/hg/oneShot/doEvoFoldV2/doEvoFoldV2.c
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• src/hg/oneShot/doOmimDisorders/doOmimDisorders.c
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• src/hg/oneShot/missingTable/makefile
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• src/hg/oneShot/rmDupCol1/rmDupCol1.c
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• src/hg/oneShot/spanRaft/makefile
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• src/hg/qaToQac/makefile
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• src/hg/qacAgpLift/makefile
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• src/hg/qacToQa/makefile
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• src/hg/qacToWig/makefile
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• src/hg/splitFa/makefile
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• src/hg/uniqSize/makefile
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• src/hg/zoo/analyze4d/Makefile
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• src/hg/zoo/transitivityCheck/Makefile
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• src/index/fofFa/fofFa.c
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• src/index/fofFa/makefile
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• src/index/indexRa/indexRa.c
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• src/index/indexRa/makefile
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• src/index/indexfa/indexfa.c
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• src/index/indexfa/makefile
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• src/index/indexgl/indexgl.c
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• src/index/indexgl/makefile
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• src/index/ixali/makefile
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• src/index/ixword1/ixword1.c
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• src/index/ixword1/makefile
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• src/index/ixword3/ixword3.c
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• src/index/ixword3/makefile
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• src/index/ixxenost/ixxenost.c
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• src/index/ixxenost/makefile
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• src/index/makepgo/makefile
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• src/index/makepgo/makepgo.c
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• src/index/stToXao/makefile
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• src/index/stToXao/stToXao.c
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• src/intronerator/idb/makefile
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• src/lib/alpha/placeHolder.c
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• src/lib/i386/placeHolder.c
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• src/lib/ppc/placeHolder.c
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• src/lib/sparc/placeHolder.c
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• src/lib/x86_64/placeHolder.c
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• src/oneShot/badbad/badbad.c
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• src/oneShot/cbCountOver/cbCountOver.c
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• src/oneShot/cdnalen/cdnalen.c
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• src/oneShot/chkGlue/forChuck.c
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• src/oneShot/chkGlue/makefile
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• src/oneShot/ck3and5/ck3and5.c
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• src/oneShot/cmpfa/cmpfa.c
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• src/oneShot/cntGlue/cntGlue.c
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• src/oneShot/cntGlue/makefile
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• src/oneShot/conrand/conrand.c
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• src/oneShot/conrand/foo.c
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• src/oneShot/cosmoCtr/cosmoCtr.c
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• src/oneShot/coverage/makefile
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• src/oneShot/deEns/makefile
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• src/oneShot/debog/debog.c
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• src/oneShot/doublea/doublea.c
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• src/oneShot/dynAlign/makefile
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• src/oneShot/faends/faends.c
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• src/oneShot/filterdb/filterdb.c
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• src/oneShot/fixInfo/makefile
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• src/oneShot/foo/foo.c
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• src/oneShot/forChuck/forChuck.c
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• src/oneShot/geneFreq/geneFreq.c
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• src/oneShot/grokGff/makefile
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• src/oneShot/intersect/intersect.c
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• src/oneShot/invert/invert.c
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• src/oneShot/invert/makefile
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• src/oneShot/jimgrep/jimgrep.c
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• src/oneShot/killRabbit/makefile
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• src/oneShot/leaders/leaders.c
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• src/oneShot/m22dirs/makefile
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• src/oneShot/memeint/memeint.c
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• src/oneShot/noali/noali.c
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• src/oneShot/nt4ToFas/nt4ToFas.c
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• src/oneShot/ooRev/makefile
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• src/oneShot/passHi/makefile
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• src/oneShot/passHi/passHi.c
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• src/oneShot/patJobs/makefile
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• src/oneShot/patJobs/patJobs.c
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• src/oneShot/shorten/makefile
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• src/oneShot/shorten/shorten.c
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• src/oneShot/sizeSplitFa/sizeSplitFa.c
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• src/oneShot/sortFoo/sortFoo.c
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• src/oneShot/sources/makefile
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• src/oneShot/sources/sources.c
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• src/oneShot/splitSql/makefile
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• src/oneShot/splitSql/splitSql.c
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• src/oneShot/splitTxt/splitTxt.c
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• src/oneShot/subdyn/subdyn.c
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• src/oneShot/tabTable/makefile
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• src/oneShot/truncat/truncat.c
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• src/oneShot/uniqSize/makefile
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• src/oneShot/unmasked/makefile
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