File Changes for hiram

v281_base to v282_preview (2013-03-25 to 2013-04-02) v282

• src/ameme/makefile
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    testing new makefile organization refs #9104
• src/cdnaAli/ali2alx/makefile
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    testing new makefile organization refs #9104
• src/cdnaAli/aliGlue/makefile
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    using new minimal makefile construction refs #9104
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    correct relative reference to jkOwnLib refs #9104
• src/cdnaAli/binGood/makefile
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    using new minimal makefile construction refs #9104
• src/cdnaAli/cdnaOff/makefile
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    using new minimal makefile construction refs #9104
• src/cdnaAli/cluster/makefile
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    using new minimal makefile construction refs #9104
• src/cdnaAli/exonAli/makefile
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    using new minimal makefile construction refs #9104
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    correct relative reference to jkOwnLib refs #9104
• src/cdnaAli/findCdna/makefile
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    using new minimal makefile construction refs #9104
• src/cdnaAli/g2cCheck/makefile
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    using new minimal makefile construction refs #9104
• src/cdnaAli/introns/makefile
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    using new minimal makefile construction refs #9104
• src/cdnaAli/pairClo/makefile
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    using new minimal makefile construction refs #9104
• src/cdnaAli/patCount/makefile
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    using new minimal makefile construction refs #9104
• src/cdnaAli/patSpace/makefile
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    using new minimal makefile construction refs #9104
• src/cdnaAli/refineAli/makefile
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    using new minimal makefile construction refs #9104
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    correct relative reference to jkOwnLib refs #9104
• src/cdnaAli/sortFilt/makefile
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    using new minimal makefile construction refs #9104
• src/cdnaAli/stitchea/makefile
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    using new minimal makefile construction refs #9104
• src/dnaDust/makefile
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    minimal makefile for kentUtils build refs #9104
• src/hg/featureBits/makefile
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    using new minimal makefile refs #9104
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    eliminate the kludgy flag JKHGAPP from src/hg/ makefiles, can detect that in src/inc/userApp.mk, refs #9104
• src/hg/hgsql/makefile
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    using new minimal makefile refs #9104
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    eliminate the kludgy flag JKHGAPP from src/hg/ makefiles, can detect that in src/inc/userApp.mk, refs #9104
• src/hg/htdocs/images/Amazona_vittata.jpg
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    photo for amaVit1 browser, Tom MacKenzie, U.S. Fish and Wildlife Service www.fws.gov/caribbean/ES/Parrot-Gallery.html refs #10144
• src/hg/makeDb/doc/amaVit1.txt
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    initial browser done, masking in progress, refs #10144
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    done with masking, ready for genbank refs #10144
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    done with genscan and cpgIslandExt refs #10144
• src/hg/makeDb/doc/hg19.txt
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    addes hg19 micMur1 swap for lift over refs #10485
• src/hg/makeDb/doc/mm9.txt
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    per user request refs #10398
• src/hg/makeDb/doc/nomLeu3.txt
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    reset default position slightly and add hg19 chain net swap procedure, refs #9812
• src/hg/makeDb/doc/rn5.txt
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    per user request refs #10398
• src/hg/makeDb/trackDb/birds/amaVit1/description.html
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    initial files from makeGenomeDb.pl refs #10144
• src/hg/makeDb/trackDb/birds/amaVit1/gap.html
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    initial files from makeGenomeDb.pl refs #10144
• src/hg/makeDb/trackDb/birds/amaVit1/gold.html
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    initial files from makeGenomeDb.pl refs #10144
• src/hg/makeDb/trackDb/birds/amaVit1/trackDb.ra
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    initial files from makeGenomeDb.pl refs #10144
• src/hg/makeDb/trackDb/gibbon/nomLeu3/description.html
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    NHGRI is changing their photo links refs #9812
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    add notes about chromosome names refs #9812
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    order the chrM contigs numerically refs #9812
• src/hg/makeDb/trackDb/gibbon/nomLeu3/trackDb.ra
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    add search rule for gold table refs #9812
• src/hg/makeDb/trackDb/human/hg19/hg19primateChainNet.html
  • lines changed 2, context: html, text, full: html, text
    protect nomLeu1 chain on public with the release tag and add Gibbon to the primate chain net description page
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
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    protect nomLeu1 chain on public with the release tag and add Gibbon to the primate chain net description page
• src/hg/makeDb/trackDb/makefile
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    adding amaVit1 parrot to the build refs #10144
• src/hg/utils/automation/mkConfigRa.sh
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    prototype for new config.ra template creation, refs #10144
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    correct usage message, refs #10144
• src/hg/utils/automation/unplacedScaffolds.pl
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    processing genbank unplaced scaffold assemblies into AGP and UCSC named fasta files, refs #10144
• src/hg/utils/gapToLift/makefile
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    adding src/hg/utils link support with jkhgap and mysql libs libraries on conditional refs #9104
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    eliminate the kludgy flag JKHGAPP from src/hg/ makefiles, can detect that in src/inc/userApp.mk, refs #9104
• src/hg/utils/oligoMatch/makefile
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    using minimal makefile to allow build in kentUtils refs #9104
• src/hg/utils/phyloTrees/97way.commonNames.nh
  • lines changed 77, context: html, text, full: html, text
    restore distances to the same as they were in the mm10 60-way refs #10272
• src/hg/utils/phyloTrees/97way.nh
  • lines changed 3, context: html, text, full: html, text
    jerboa moved closer to mouse rat before squirrel and kangaroo rat refs #10272
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    restore distances to the same as they were in the mm10 60-way refs #10272
• src/hg/utils/phyloTrees/97way.scientificNames.nh
  • lines changed 77, context: html, text, full: html, text
    restore distances to the same as they were in the mm10 60-way refs #10272
• src/hg/utils/phyloTrees/commonNames.sh
  • lines changed 1, context: html, text, full: html, text
    restore distances to the same as they were in the mm10 60-way refs #10272
• src/hg/utils/phyloTrees/scientificNames.sh
  • lines changed 1, context: html, text, full: html, text
    restore distances to the same as they were in the mm10 60-way refs #10272
• src/idbQuery/makefile
  • lines changed 18, context: html, text, full: html, text
    minimal makefile for kentUtils build refs #9104
• src/inc/userApp.mk
  • lines changed 35, context: html, text, full: html, text
    testing new makefile organization refs #9104
  • lines changed 3, context: html, text, full: html, text
    adding src/hg/utils link support with jkhgap and mysql libs libraries on conditional refs #9104
  • lines changed 1, context: html, text, full: html, text
    adding src/hg/utils link support with jkhgap and mysql libs libraries on conditional refs #9104
  • lines changed 2, context: html, text, full: html, text
    eliminate the kludgy flag JKHGAPP from src/hg/ makefiles, can detect that in src/inc/userApp.mk, refs #9104
  • lines changed 2, context: html, text, full: html, text
    minimal makefiles for kentUtils build refs #9104
• src/index/bptForTwoBit/makefile
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    using new minimal makefile construction refs #9104
• src/index/bptLookupStringToBits64/makefile
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    using new minimal makefile construction refs #9104
• src/index/bptMakeStringToBits64/makefile
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    using new minimal makefile construction refs #9104
• src/index/fofFa/makefile
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    using new minimal makefile construction refs #9104
• src/index/indexRa/makefile
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    using new minimal makefile construction refs #9104
• src/index/indexfa/makefile
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    using new minimal makefile construction refs #9104
• src/index/indexgl/makefile
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    using new minimal makefile construction refs #9104
• src/index/ixIxx/makefile
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    using new minimal makefile construction refs #9104
• src/index/ixali/makefile
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    using new minimal makefile construction refs #9104
• src/index/ixword1/makefile
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    using new minimal makefile construction refs #9104
• src/index/ixword3/makefile
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    using new minimal makefile construction refs #9104
• src/index/ixxenost/makefile
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    using new minimal makefile construction refs #9104
• src/index/makefile
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    using new minimal makefile construction refs #9104
• src/index/makepgo/makefile
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    using new minimal makefile construction refs #9104
• src/index/stToXao/makefile
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    using new minimal makefile construction refs #9104
• src/index/trixSearch/makefile
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    using new minimal makefile construction refs #9104
• src/protDust/makefile
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    minimal makefile for kentUtils build refs #9104
• src/reformat/fatont4/makefile
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    minimal makefiles for kentUtils build refs #9104
• src/reformat/gb2cdi/makefile
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    minimal makefiles for kentUtils build refs #9104
• src/reformat/gbtofa/makefile
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    minimal makefiles for kentUtils build refs #9104
• src/reformat/geniegff/makefile
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    minimal makefiles for kentUtils build refs #9104
• src/reformat/gffgenes/makefile
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    minimal makefiles for kentUtils build refs #9104
• src/reformat/makefile
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    minimal makefiles for kentUtils build refs #9104
• src/reformat/moresyn/makefile
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    minimal makefiles for kentUtils build refs #9104
• src/reformat/wabToSt/makefile
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    minimal makefiles for kentUtils build refs #9104
• src/scanIntrons/makefile
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    minimal makefile for kentUtils build refs #9104
• src/utils/aNotB/makefile
  • lines changed 7, context: html, text, full: html, text
    adding some sanity to the makefiles with DESTDIR compile and install targets refs #9104
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    testing new makefile organization refs #9104
• src/utils/addCols/makefile
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    adding some sanity to the makefiles with DESTDIR compile and install targets refs #9104
• src/utils/ave/makefile
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    testing new makefile organization refs #9104
• src/utils/aveCols/makefile
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    adding some sanity to the makefiles with DESTDIR compile and install targets refs #9104
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    testing new makefile organization refs #9104
• src/utils/bdfToGem/makefile
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    adding some sanity to the makefiles with DESTDIR compile and install targets refs #9104
• src/utils/bedRemoveOverlap/makefile
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    testing new makefile organization refs #9104
• src/utils/bestThreshold/makefile
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    adding some sanity to the makefiles with DESTDIR compile and install targets refs #9104
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    testing new makefile organization refs #9104
• src/utils/cCp/cCp.c
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    broken compile refs #9104
• src/utils/cCp/makefile
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    adding some sanity to the makefiles with DESTDIR compile and install targets refs #9104
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    testing new makefile organization refs #9104
• src/utils/faCat/makefile
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    cleanup and proper DESTDIR for refs #9104
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    testing new makefile organization refs #9104
• src/utils/newProg/makefile
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    using new style minimal makefile for ordinary programs, not fixing CGI rules yet, removing obsolete CVS business, refs #9104
• src/utils/newProg/newProg.c
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    using new style minimal makefile for ordinary programs, not fixing CGI rules yet, removing obsolete CVS business, refs #9104
• src/utils/twoBitToFa/makefile
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    testing new makefile organization refs #9104
• src/weblet/bottleneck/makefile
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    minimal makefile for kentUtils build refs #9104
• src/weblet/counter/makefile
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    minimal makefile for kentUtils build refs #9104
• src/weblet/hitreport/makefile
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    minimal makefile for kentUtils build refs #9104
• src/weblet/makefile
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    minimal makefile for kentUtils build refs #9104
• src/xenoAli/bwana/makefile
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    minimal makefiles for kentUtils build refs #9104
• src/xenoAli/dynAlign/makefile
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    minimal makefiles for kentUtils build refs #9104
• src/xenoAli/makefile
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    minimal makefiles for kentUtils build refs #9104
• src/xenoAli/stitcher/makefile
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    minimal makefiles for kentUtils build refs #9104