All File Changes

v336_preview to v336_preview2 (2016-07-11 to 2016-07-18) v336

• confs/hgwbeta.hg.conf
  • lines changed 3, context: html, text, full: html, text
    3dce1c721fb9a027f06564830bc1f4c2d2fe6b65 Sun Jul 17 01:12:15 2016 -0700
    Installing updated hg.conf files from UCSC servers
    
• confs/hgwdev.hg.conf
  • lines changed 6, context: html, text, full: html, text
    3dce1c721fb9a027f06564830bc1f4c2d2fe6b65 Sun Jul 17 01:12:15 2016 -0700
    Installing updated hg.conf files from UCSC servers
    
• confs/rr.hg.conf
  • lines changed 2, context: html, text, full: html, text
    3dce1c721fb9a027f06564830bc1f4c2d2fe6b65 Sun Jul 17 01:12:15 2016 -0700
    Installing updated hg.conf files from UCSC servers
    
• src/ai/growNet/makefile
  • lines changed 1, context: html, text, full: html, text
    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/ai/letterChain/makefile
  • lines changed 1, context: html, text, full: html, text
    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/ai/pairCompress/makefile
  • lines changed 1, context: html, text, full: html, text
    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/ai/paraFlow/aceTools/makefile
  • lines changed 1, context: html, text, full: html, text
    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/ai/paraFlow/compiler/makefile
  • lines changed 1, context: html, text, full: html, text
    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/ai/paraFlow/makefile
  • lines changed 1, context: html, text, full: html, text
    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/ai/paraFlow/runAsm/makefile
  • lines changed 1, context: html, text, full: html, text
    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/ai/paraFlow/runtime/makefile
  • lines changed 1, context: html, text, full: html, text
    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/ai/paraFlow/testProg/makefile
  • lines changed 1, context: html, text, full: html, text
    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/ai/wordChain/makefile
  • lines changed 1, context: html, text, full: html, text
    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/blat/makefile
  • lines changed 1, context: html, text, full: html, text
    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/blatTheory/makefile
  • lines changed 1, context: html, text, full: html, text
    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/blatz/makefile
  • lines changed 1, context: html, text, full: html, text
    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/cbAli/makefile
  • lines changed 1, context: html, text, full: html, text
    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/cdnaAli/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/fuse/makefile
  • lines changed 1, context: html, text, full: html, text
    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/fuzzyFind/makefile
  • lines changed 1, context: html, text, full: html, text
    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/hg/affyGnf/makefile
  • lines changed 1, context: html, text, full: html, text
    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/hg/affyTransciptome/makefile
  • lines changed 1, context: html, text, full: html, text
    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/hg/agpMergeChromScaf/makefile
  • lines changed 1, context: html, text, full: html, text
    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/hg/agpSangerUnfinished/makefile
  • lines changed 1, context: html, text, full: html, text
    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/hg/agpTweak/makefile
  • lines changed 1, context: html, text, full: html, text
    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/hg/altGraph/makefile
  • lines changed 1, context: html, text, full: html, text
    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/hg/altSplice/affySplice/makefile
  • lines changed 1, context: html, text, full: html, text
    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/hg/altSplice/affySplice/tests/makefile
  • lines changed 1, context: html, text, full: html, text
    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/hg/altSplice/agxToXml/makefile
  • lines changed 1, context: html, text, full: html, text
    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/hg/altSplice/altSplice/makefile
  • lines changed 1, context: html, text, full: html, text
    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/hg/altSplice/altSplice/tests/makefile
  • lines changed 1, context: html, text, full: html, text
    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/hg/altSplice/axtCountBeds/makefile
  • lines changed 1, context: html, text, full: html, text
    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/hg/altSplice/exonWalk/makefile
  • lines changed 1, context: html, text, full: html, text
    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/hg/altSplice/filterEdges/makefile
  • lines changed 1, context: html, text, full: html, text
    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/hg/altSplice/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/hg/autoSql/tests/makefile
  • lines changed 1, context: html, text, full: html, text
    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/hg/autoXml/t/makefile
  • lines changed 1, context: html, text, full: html, text
    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/hg/baseMask/makefile
  • lines changed 1, context: html, text, full: html, text
    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/hg/baseMask/tests/makefile
  • lines changed 1, context: html, text, full: html, text
    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/hg/bedIntersect/tests/input/chrUn_LVXT01056135v1.bed
  • lines changed 1, context: html, text, full: html, text
    ccc04f192749cdcc1e834acf9598d052e5b6783d Wed Jul 13 15:46:35 2016 -0700
    added commutativeTest target refs #17704
    
• src/hg/bedIntersect/tests/input/chrUn_LVXT01056135v1Gaps.bed
  • lines changed 8, context: html, text, full: html, text
    ccc04f192749cdcc1e834acf9598d052e5b6783d Wed Jul 13 15:46:35 2016 -0700
    added commutativeTest target refs #17704
    
• src/hg/bedIntersect/tests/makefile
  • lines changed 1, context: html, text, full: html, text
    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
  • lines changed 6, context: html, text, full: html, text
    ccc04f192749cdcc1e834acf9598d052e5b6783d Wed Jul 13 15:46:35 2016 -0700
    added commutativeTest target refs #17704
    
  • lines changed 2, context: html, text, full: html, text
    4512514645d6913d3c7f5138865365a4a6cb3c2a Wed Jul 13 17:17:54 2016 -0700
    just need better minCoverage, not a bug refs #17704
    
• src/hg/bedOverlap/makefile
  • lines changed 1, context: html, text, full: html, text
    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/hg/bedThickOnly/makefile
  • lines changed 1, context: html, text, full: html, text
    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/hg/bioImage/bioImageLoad/makefile
  • lines changed 1, context: html, text, full: html, text
    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/hg/bioImage/hgBioImage/makefile
  • lines changed 1, context: html, text, full: html, text
    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/hg/bioImage/knownToBioImage/makefile
  • lines changed 1, context: html, text, full: html, text
    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/hg/bioImage/loadMahoney/makefile
  • lines changed 1, context: html, text, full: html, text
    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/hg/blastToPsl/makefile
  • lines changed 1, context: html, text, full: html, text
    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/hg/blastToPsl/tests/makefile
  • lines changed 1, context: html, text, full: html, text
    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/hg/cartDump/makefile
  • lines changed 1, context: html, text, full: html, text
    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/hg/cartReset/makefile
  • lines changed 1, context: html, text, full: html, text
    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/hg/ccTrack/bedToBinDex/makefile
  • lines changed 1, context: html, text, full: html, text
    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/hg/cgiExample/makefile
  • lines changed 1, context: html, text, full: html, text
    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/hg/checkTableCoords/tests/makefile
  • lines changed 1, context: html, text, full: html, text
    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/hg/chimpStuff/chimpChromContigAgp/makefile
  • lines changed 1, context: html, text, full: html, text
    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/hg/chimpStuff/chimpHiQualDiffs/makefile
  • lines changed 1, context: html, text, full: html, text
    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/hg/chimpStuff/chimpSuperQuals/makefile
  • lines changed 1, context: html, text, full: html, text
    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/hg/cirm/cdw/cdwCreateUser/makefile
  • lines changed 1, context: html, text, full: html, text
    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/hg/cirm/cdw/lib/cdwLib.c
  • lines changed 12, context: html, text, full: html, text
    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/hg/cirm/cdw/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/hg/cirm/cdw/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
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• src/hg/encode3/encodeDataWarehouse/lib/makefile
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• src/hg/encode3/encodeDataWarehouse/makefile
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• src/hg/encode3/encodeDataWarehouse/utils/edwBamFilter/edwBamFilter.c
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• src/hg/encode3/encodeDataWarehouse/utils/edwBamRemoveChrom/edwBamRemoveChrom.c
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• src/hg/encode3/encodeDataWarehouse/utils/edwBamStats/edwBamStats.c
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• src/hg/encode3/encodeDataWarehouse/utils/edwSamRepeatAnalysis/edwSamRepeatAnalysis.c
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• src/hg/encode3/encodeDataWarehouse/utils/makefile
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• src/hg/encode3/importEncode2/encode2BedDoctor/makefile
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• src/hg/encode3/importEncode2/encode2BedPlusDoctor/makefile
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• src/hg/encode3/importEncode2/encode2ExpDumpFlat/makefile
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• src/hg/encode3/importEncode2/encode2GffDoctor/makefile
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• src/hg/encode3/importEncode2/encode2MakeEncode3/makefile
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• src/hg/encode3/importEncode2/encodeCvToDb/makefile
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• src/hg/geneBounds/averagExp/makefile
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• src/hg/geneBounds/lib/makefile
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• src/hg/geneBounds/makefile
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• src/hg/geneOverlap/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
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• src/hg/gigAssembler/g2gSeqOverlap/makefile
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• src/hg/gigAssembler/gapper/makefile
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• src/hg/gigAssembler/goldToAgp/makefile
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• src/hg/gigAssembler/makePai/makefile
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• src/hg/gigAssembler/mendMap/makefile
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• src/hg/gigAssembler/mm/checkEnds/makefile
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• src/hg/gigAssembler/mm/mm/makefile
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• src/hg/gigAssembler/mm/mmTestSet/makefile
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• src/hg/gigAssembler/mm/ooMapMend/makefile
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• src/hg/gigAssembler/ntGoldGl/makefile
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• src/hg/gigAssembler/ooChains/makefile
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• src/hg/gigAssembler/ooCloneEnds/makefile
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• src/hg/gigAssembler/ooCloneInfo/makefile
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• src/hg/gigAssembler/ooCloneOverlaps/makefile
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• src/hg/gigAssembler/ooCloneSizes/makefile
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• src/hg/gigAssembler/ooCloneSpan/makefile
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• src/hg/gigAssembler/ooGreedy/bak/makefile
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• src/hg/gigAssembler/ooGreedy/makefile
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• src/hg/gigAssembler/ooLiftSpec/makefile
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• src/hg/gigAssembler/ooNtInput/makefile
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• src/hg/gigAssembler/ooSplitFins/makefile
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• src/hg/gigAssembler/ooTester/makefile
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• src/hg/gigAssembler/ooWeedZero/makefile
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• src/hg/gigAssembler/pairedReads/ppAnalyse/makefile
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• src/hg/gigAssembler/pairedReads/ppSanger/makefile
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• src/hg/gigAssembler/pairedReads/ppStats/makefile
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• src/hg/gigAssembler/pairedReads/ppWashU/makefile
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• src/hg/gigAssembler/pairedReads/ppWhitehead/makefile
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• src/hg/gigAssembler/psLayout/makefile
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• src/hg/gigAssembler/qaGold/makefile
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• src/hg/gisaid/gisaidSample/makefile
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• src/hg/gisaid/gisaidSubj/makefile
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• src/hg/gisaid/gisaidTable/makefile
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• src/hg/gisaid/makefile
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• src/hg/gsid/gsIdXref/makefile
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• src/hg/gsid/gsidAaMsa/makefile
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• src/hg/gsid/gsidGetConsensus/makefile
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• src/hg/gsid/gsidMember/makefile
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• src/hg/gsid/gsidMsa/makefile
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• src/hg/gsid/gsidMsaToTab/makefile
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• src/hg/gsid/gsidPbGateway/makefile
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• src/hg/gsid/gsidPosSelect/makefile
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• src/hg/gsid/gsidSubj/makefile
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• src/hg/gsid/gsidSubj3/makefile
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• src/hg/gsid/gsidTable/makefile
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• src/hg/gsid/makefile
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• src/hg/gsid/pbGsid/makefile
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• src/hg/gsid/pwdtest/makefile
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• src/hg/hgApi/makefile
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• src/hg/hgBatch/makefile
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• src/hg/hgBeacon/makefile
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• src/hg/hgBlat/makefile
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• src/hg/hgBlatTest/makefile
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• src/hg/hgCert/makefile
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• src/hg/hgChooseDb/makefile
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• src/hg/hgConvert/makefile
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• src/hg/hgCoordConv/makefile
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• src/hg/hgCustom/makefile
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• src/hg/hgFileSearch/makefile
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• src/hg/hgFileUi/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/hg/hgGateway/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/hg/hgGene/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/hg/hgGeneBands/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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    pointing to top of the tree.
    
• src/hg/hgGeneList/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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    pointing to top of the tree.
    
• src/hg/hgGeneRing/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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    pointing to top of the tree.
    
• src/hg/hgGenome/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/hg/hgGetAnn/tests/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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    pointing to top of the tree.
    
• src/hg/hgGtexApi/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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    pointing to top of the tree.
    
• src/hg/hgHubConnect/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/hg/hgIntegrator/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/hg/hgLiftOver/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/hg/hgLogin/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/hg/hgMenubar/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/hg/hgMirror/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/hg/hgNotAvail/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/hg/hgNotYet/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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    pointing to top of the tree.
    
• src/hg/hgPal/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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    pointing to top of the tree.
    
• src/hg/hgPcr/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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    pointing to top of the tree.
    
• src/hg/hgPublicSessions/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/hg/hgSession/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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    pointing to top of the tree.
    
• src/hg/hgSuggest/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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    pointing to top of the tree.
    
• src/hg/hgTables/bam.c
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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    pointing to top of the tree.
    
• src/hg/hgTables/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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    pointing to top of the tree.
    
• src/hg/hgTrackUi/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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    pointing to top of the tree.
    
• src/hg/hgTracks/bamTrack.c
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
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    pointing to top of the tree.
    
• src/hg/hgTracks/cds.c
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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    pointing to top of the tree.
    
• src/hg/hgTracks/cds.h
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/hg/hgTracks/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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    pointing to top of the tree.
    
• src/hg/hgTracks/makefile.hgRenderTracks
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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    pointing to top of the tree.
    
• src/hg/hgTracks/simpleTracks.c
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    d89c874346552fbb921d6a1d038a79605f6ce613 Wed Jul 13 11:45:07 2016 -0700
    DECIPHER pipeline now runs on their new file format. Also added more data to the hgc output. refs #14465
    
• src/hg/hgTracks/vcfTrack.c
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/hg/hgUserSuggestion/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/hg/hgVai/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/hg/hgVarAnnogrator/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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    pointing to top of the tree.
    
• src/hg/hgc/bamClick.c
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
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    pointing to top of the tree.
    
• src/hg/hgc/hgc.c
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
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    d89c874346552fbb921d6a1d038a79605f6ce613 Wed Jul 13 11:45:07 2016 -0700
    DECIPHER pipeline now runs on their new file format. Also added more data to the hgc output. refs #14465
    
• src/hg/hgc/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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    pointing to top of the tree.
    
• src/hg/hgc/vcfClick.c
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
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    pointing to top of the tree.
    
• src/hg/hgcentralTidy/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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    pointing to top of the tree.
    
• src/hg/htdocs/goldenPath/help/cram.html
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    5fb1cf60bb8ab27c61e36ed535c2deb0e36d14d3 Wed Jul 13 08:36:59 2016 -0700
    Adding URL section to cram.html that was waiting on v335
    
• src/hg/htdocs/goldenPath/help/mysql.html
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    2f39e2335315cd28bf865c953a6b786f97539585 Fri Jul 15 14:29:40 2016 -0700
    Updating example hg.conf. User noted it wasnt enough to use some utils. refs #17652
    
• src/hg/htdocs/goldenPath/help/trackDb/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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• src/hg/htdocs/images/surveyButton.jpg
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    58b1afb65ce1eba4be5532b354159e26acca94c5 Tue Jul 12 16:34:04 2016 -0700
    Adding button image for 2016 survey from gateway, refs #17622
    
• src/hg/htdocs/index.html
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    49ef5d92148bdf443a5d958a38522a966002dbbd Mon Jul 11 11:07:51 2016 -0700
    Add Cath's survey image to home page, to right of content.
    
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    df11e0380d1b2013005fb489dcaa9e0728eaf769 Tue Jul 12 17:01:12 2016 -0700
    Editing index to show survey link, refs #17622
    
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    b55db177d6e01ae45ac415b0b47d026951876a00 Wed Jul 13 12:05:09 2016 -0700
    Commenting out survey link on index - errors, refs #17622
    
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    eb0103a07673259d4d15425e62016fe34ef82c26 Wed Jul 13 14:08:00 2016 -0700
    Adding survey link on index again, refs #17622
    
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    36195abbdbaea498e3c9fd7a13358f62a7f3960c Wed Jul 13 14:12:50 2016 -0700
    Wrap a div around the inclusion of hgMenubar so that if there is an error, it doesn't push page contents to the right.
    
• src/hg/htdocs/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
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    324c1151dbc0092a3960c64add9213743afc66d6 Wed Jul 13 12:07:09 2016 -0700
    Initial stab at having htdocs makefile also run pandoc, refs #14399
    
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    3551bbff6ebaf880f5af27b75349ba52bea074a6 Wed Jul 13 14:22:48 2016 -0700
    Adding pandoc directory for properly configuring markdown documents to html, fixing makefiles to support new directory, refs #14399
    
• src/hg/htdocs/pandoc/installer/README.md
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    3551bbff6ebaf880f5af27b75349ba52bea074a6 Wed Jul 13 14:22:48 2016 -0700
    Adding pandoc directory for properly configuring markdown documents to html, fixing makefiles to support new directory, refs #14399
    
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    994c1c1f15b580c7008527de869bfe8201340911 Wed Jul 13 16:06:44 2016 -0700
    Removing README.md from htdocs, refs #14399
    
• src/hg/htdocs/pandoc/installer/makefile
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    3551bbff6ebaf880f5af27b75349ba52bea074a6 Wed Jul 13 14:22:48 2016 -0700
    Adding pandoc directory for properly configuring markdown documents to html, fixing makefiles to support new directory, refs #14399
    
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    dcf13015ffe4dc3afcf1c7782927483632963252 Wed Jul 13 15:28:27 2016 -0700
    Modifying pandoc makefile to convert from src/product/installer, not from htdocs/pandoc. refs #14399
    
• src/hg/htdocs/pandoc/installer/staticPage.html
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    3551bbff6ebaf880f5af27b75349ba52bea074a6 Wed Jul 13 14:22:48 2016 -0700
    Adding pandoc directory for properly configuring markdown documents to html, fixing makefiles to support new directory, refs #14399
    
• src/hg/htdocs/pandoc/mirrorDocs/makefile
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    3551bbff6ebaf880f5af27b75349ba52bea074a6 Wed Jul 13 14:22:48 2016 -0700
    Adding pandoc directory for properly configuring markdown documents to html, fixing makefiles to support new directory, refs #14399
    
• src/hg/htdocs/pandoc/mirrorDocs/staticPage.html
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    3551bbff6ebaf880f5af27b75349ba52bea074a6 Wed Jul 13 14:22:48 2016 -0700
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• src/hg/htdocs/pandoc/mirrorDocs/staticPage.lua
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    3551bbff6ebaf880f5af27b75349ba52bea074a6 Wed Jul 13 14:22:48 2016 -0700
    Adding pandoc directory for properly configuring markdown documents to html, fixing makefiles to support new directory, refs #14399
    
• src/hg/htdocs/style/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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    pointing to top of the tree.
    
• src/hg/inc/hgBam.h
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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    pointing to top of the tree.
    
• src/hg/intronSizes/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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    pointing to top of the tree.
    
• src/hg/js/external/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/hg/js/hgTracks.js
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    042d859041f3d41a654f4d5590bbf5f91702d1ca Wed Jul 13 14:19:20 2016 -0700
    Remove code that forces all hgTracks <a> links to POST. Ironically, although this was intended to apply to map area items, those are not <a> elements. Clicking on map items causes a POST because of mapClk, not the lines I'm removing here. Forcing POST can cause downstream problems, e.g. Jonathan had to prevent the genome-store link from being a POST, and posting to index.html caused a strange post to be sent to hgMenubar.
    refs #17703 #17622#note-44
    
• src/hg/js/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/hg/js/model/hgChooseDb/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/hg/js/model/hgIntegrator/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/hg/js/model/lib/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/hg/js/model/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/hg/js/react/hgChooseDb/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/hg/js/react/hgIntegrator/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/hg/js/react/lib/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/hg/js/react/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/hg/js/react/mixins/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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    pointing to top of the tree.
    
• src/hg/lib/customAdjacency.c
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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    pointing to top of the tree.
    
• src/hg/lib/customFactory.c
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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    pointing to top of the tree.
    
• src/hg/lib/decipherRaw.sql
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    d89c874346552fbb921d6a1d038a79605f6ce613 Wed Jul 13 11:45:07 2016 -0700
    DECIPHER pipeline now runs on their new file format. Also added more data to the hgc output. refs #14465
    
• src/hg/lib/encode/tests/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/hg/lib/hgBam.c
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/hg/lib/hui.c
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/hg/lib/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/hg/lib/tests/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/hg/liftAcross/tests/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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    pointing to top of the tree.
    
• src/hg/liftAgp/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/hg/liftOver/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/hg/liftOver/tests/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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• src/hg/liftUp/test/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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• src/hg/logCrawl/accessLogFilter/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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• src/hg/logCrawl/accessLogMerge/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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• src/hg/logCrawl/accessLogSort/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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• src/hg/logCrawl/accessLogWigs/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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    pointing to top of the tree.
    
• src/hg/logCrawl/crawlForHogs/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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• src/hg/logCrawl/crawlForPosAndTime/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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• src/hg/logCrawl/encodeUserDbCrawl/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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• src/hg/logCrawl/hgAccessCrawl/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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• src/hg/logCrawl/sessionDbCrawl/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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• src/hg/logCrawl/ticksToWig/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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• src/hg/makeDb/doc/eboVir3/uniprot.txt
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    3887c3b11338a8ed7de6f5805d09019c25979023 Fri Jul 15 15:14:53 2016 -0700
    removing dependencies for uniprot pipeline, moving it into kent repo,
    for #17716. Also preparing for hg38 uniprot track, #17717
    
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    7d2805bf5709b87d6fa8435f2e580c6075fa01c7 Fri Jul 15 15:54:52 2016 -0700
    adding another line I forgot in the last commit
    
• src/hg/makeDb/doc/hg38/hg38.txt
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    f70417672c7568a9dc43fcd7a18d72f140fc3386 Wed Jul 13 10:07:13 2016 -0700
    Reomving line from makedoc about not releasing to the RR since we are releasing the track, refs #17626
    
• src/hg/makeDb/doc/ucscGenes/hg38.ucscGenes17.sh
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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    pointing to top of the tree.
    
• src/hg/makeDb/genbank/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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    pointing to top of the tree.
    
• src/hg/makeDb/genbank/src/align/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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• src/hg/makeDb/genbank/src/ccds/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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• src/hg/makeDb/genbank/src/copy/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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• src/hg/makeDb/genbank/src/dbload/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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• src/hg/makeDb/genbank/src/download/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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• src/hg/makeDb/genbank/src/extFileUpdate/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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• src/hg/makeDb/genbank/src/gbConf/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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• src/hg/makeDb/genbank/src/gbGetSeqs/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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• src/hg/makeDb/genbank/src/gbSanity/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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    pointing to top of the tree.
    
• src/hg/makeDb/genbank/src/lib/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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    pointing to top of the tree.
    
• src/hg/makeDb/genbank/src/lsSnpPdb/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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    pointing to top of the tree.
    
• src/hg/makeDb/genbank/src/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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    pointing to top of the tree.
    
• src/hg/makeDb/genbank/src/process/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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• src/hg/makeDb/genbank/src/process/tests/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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    pointing to top of the tree.
    
• src/hg/makeDb/genbank/src/refSeqCheck/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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    pointing to top of the tree.
    
• src/hg/makeDb/genbank/src/repair/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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    pointing to top of the tree.
    
• src/hg/makeDb/genbank/src/selectWithPsl/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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    pointing to top of the tree.
    
• src/hg/makeDb/genbank/tests/gbFaCheck/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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    pointing to top of the tree.
    
• src/hg/makeDb/genbank/tests/index/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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    pointing to top of the tree.
    
• src/hg/makeDb/genbank/tests/subset/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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    pointing to top of the tree.
    
• src/hg/makeDb/hgAar/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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    pointing to top of the tree.
    
• src/hg/makeDb/hgBedsToBedExps/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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• src/hg/makeDb/hgCalStat/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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• src/hg/makeDb/hgCgiData/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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    pointing to top of the tree.
    
• src/hg/makeDb/hgCutters/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/hg/makeDb/hgGcPercent/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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• src/hg/makeDb/hgGetKgUrls/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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    pointing to top of the tree.
    
• src/hg/makeDb/hgGetNrOmimGene/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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    pointing to top of the tree.
    
• src/hg/makeDb/hgGoldGapGl/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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    pointing to top of the tree.
    
• src/hg/makeDb/hgLoadAxt/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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    pointing to top of the tree.
    
• src/hg/makeDb/hgLoadBed/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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    pointing to top of the tree.
    
• src/hg/makeDb/hgLoadCdsEvidence/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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    pointing to top of the tree.
    
• src/hg/makeDb/hgLoadMaf/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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    pointing to top of the tree.
    
• src/hg/makeDb/hgLoadMaf/tests/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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    pointing to top of the tree.
    
• src/hg/makeDb/hgLoadWiggle/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/hg/makeDb/hgPar/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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    pointing to top of the tree.
    
• src/hg/makeDb/hgPar/tests/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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    pointing to top of the tree.
    
• src/hg/makeDb/hgRgdParsePathwayObo/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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    pointing to top of the tree.
    
• src/hg/makeDb/hgTomRough/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/hg/makeDb/htTpf/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/hg/makeDb/makeLoChain/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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    pointing to top of the tree.
    
• src/hg/makeDb/mdbUpdate/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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• src/hg/makeDb/mdbUpdate/tests/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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    pointing to top of the tree.
    
• src/hg/makeDb/outside/ensembl/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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    pointing to top of the tree.
    
• src/hg/makeDb/outside/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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• src/hg/makeDb/schema/all.joiner
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    a08ae07aa4dac2ed4abdeeea29622a8b3553de23 Wed Jul 13 10:01:51 2016 -0700
    Adjusting minCheck levels for two gencode tracks, refs #17626
    
• src/hg/makeDb/schema/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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• src/hg/makeDb/simpleGap/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV20.html
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    d60f6f78bfcd61b7dfcd8852d8a040649239b471 Thu Jul 14 11:43:29 2016 -0700
    Minor link and whitespace changes to APPRIS section. Change version number link for v24 page. Other White space changes. mostly refs #17626
    
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV21.html
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    d60f6f78bfcd61b7dfcd8852d8a040649239b471 Thu Jul 14 11:43:29 2016 -0700
    Minor link and whitespace changes to APPRIS section. Change version number link for v24 page. Other White space changes. mostly refs #17626
    
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV22.html
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    d60f6f78bfcd61b7dfcd8852d8a040649239b471 Thu Jul 14 11:43:29 2016 -0700
    Minor link and whitespace changes to APPRIS section. Change version number link for v24 page. Other White space changes. mostly refs #17626
    
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV23.html
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    d60f6f78bfcd61b7dfcd8852d8a040649239b471 Thu Jul 14 11:43:29 2016 -0700
    Minor link and whitespace changes to APPRIS section. Change version number link for v24 page. Other White space changes. mostly refs #17626
    
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV23.ra
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    657177218ce0458c211e9a800bf98e7abe9763de Thu Jul 14 14:37:39 2016 -0700
    Hiding old GENCODE track, refs #17626
    
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV24.html
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    d60f6f78bfcd61b7dfcd8852d8a040649239b471 Thu Jul 14 11:43:29 2016 -0700
    Minor link and whitespace changes to APPRIS section. Change version number link for v24 page. Other White space changes. mostly refs #17626
    
• src/hg/makeDb/trackDb/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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• src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
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    670857293f0380213d401db9bb36b85350508037 Thu Jul 14 11:44:58 2016 -0700
    Removing Patch 1 track after release of patch 4 track, refs #16414
    
• src/hg/makeDb/trackDb/trackDb.ra
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    4f4b670a53ab613f254bd5b2da088490bcbacbf0 Thu Jul 14 15:31:05 2016 -0700
    Changing longLabels for NCBI RefSeq tracks, refs #13673
    
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    42d324f8c666f5f7188c4ef8ca97c78140f9a595 Fri Jul 15 15:20:42 2016 -0700
    try displaying refSeqAli table as a PSL track in refSeqComposite refs #13673
    
• src/hg/makeDb/trackDbPatch/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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• src/hg/makeSeqs/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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• src/hg/monitor/cacti/cactiSine/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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• src/hg/mouseStuff/afsCombine/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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• src/hg/mouseStuff/aliFragScore/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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• src/hg/mouseStuff/axtBestNear/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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• src/hg/mouseStuff/axtChain/tests/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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• src/hg/mouseStuff/axtSomeRecords/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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• src/hg/mouseStuff/axtToMaf/tests/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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    pointing to top of the tree.
    
• src/hg/mouseStuff/axtToPsl/tests/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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• src/hg/mouseStuff/blastzPaper/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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• src/hg/mouseStuff/blastzScripts/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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    pointing to top of the tree.
    
• src/hg/mouseStuff/chainIndex/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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    pointing to top of the tree.
    
• src/hg/mouseStuff/chainInfo/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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    pointing to top of the tree.
    
• src/hg/mouseStuff/chainOverlap/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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    pointing to top of the tree.
    
• src/hg/mouseStuff/chainScore/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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• src/hg/mouseStuff/chainStitch/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/hg/mouseStuff/chainToPsl/tests/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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    pointing to top of the tree.
    
• src/hg/mouseStuff/correctEst/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/hg/mouseStuff/exonMap/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/hg/mouseStuff/ggcPic/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/hg/mouseStuff/knownVsBlat/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/hg/mouseStuff/lavToAxt/tests/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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    pointing to top of the tree.
    
• src/hg/mouseStuff/lavToPsl/tests/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/hg/mouseStuff/mafRanges/tests/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/hg/mouseStuff/mafToClustalw/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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    pointing to top of the tree.
    
• src/hg/mouseStuff/mafToFa/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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• src/hg/mouseStuff/mafToXmfa/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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    pointing to top of the tree.
    
• src/hg/mouseStuff/netContigs/makefile
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• src/hg/mouseStuff/netToAxt/tests/makefile
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• src/hg/mouseStuff/whyConserved/makefile
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• src/hg/mouseStuff/xmfaToMaf/makefile
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• src/hg/mrnaToGene/tests/makefile
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• src/hg/nci60/makefile
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• src/hg/near/hgExpDistance/makefile
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• src/hg/near/hgNear/makefile
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• src/hg/near/hgNetDist/makefile
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• src/hg/near/hgZfishEnsXRef/makefile
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• src/hg/oneShot/addChrPsl/makefile
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• src/hg/oneShot/addMhcClones/makefile
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• src/hg/oneShot/addTopoToPrimers/makefile
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• src/hg/oneShot/affyAllExonGSColumn/makefile
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• src/hg/oneShot/agpAddCtgNamesAndGaps/makefile
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• src/hg/oneShot/agpNotInf/makefile
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• src/hg/oneShot/agpVsMap/makefile
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• src/hg/oneShot/bargeVsMap/makefile
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• src/hg/oneShot/bed15To3Col/makefile
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• src/hg/oneShot/bedFirstCodingExonSize/makefile
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• src/hg/oneShot/blatFilter/makefile
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• src/hg/oneShot/bridgeDif/makefile
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• src/hg/oneShot/bwTestRead/makefile
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• src/hg/oneShot/cJoinX/makefile
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• src/hg/oneShot/cacheMergedRanges/makefile
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• src/hg/oneShot/cartSim/makefile
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• src/hg/oneShot/cartSimNoInsert/makefile
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• src/hg/oneShot/chromPosLookup/makefile
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• src/hg/oneShot/chromToPos/makefile
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• src/hg/oneShot/clonePos/makefile
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• src/hg/oneShot/clonesInAgp/makefile
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• src/hg/oneShot/clumpEst3/makefile
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• src/hg/oneShot/cmpOverlaps/makefile
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• src/hg/oneShot/codAbsAffyQuery/makefile
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• src/hg/oneShot/compilerError/makefile
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• src/hg/oneShot/createScaffoldsAgp/makefile
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• src/hg/oneShot/doEvoFold/makefile
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• src/hg/oneShot/doEvoFoldV2/makefile
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• src/hg/oneShot/doOmimDisorders/makefile
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• src/hg/oneShot/doRgdGene2/makefile
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• src/hg/oneShot/doRgdGene2UniProt/makefile
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• src/hg/oneShot/doRgdGene2Xref/makefile
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• src/hg/oneShot/dupeFoo/makefile
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• src/hg/oneShot/dupedInTable/makefile
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• src/hg/oneShot/evalEndOverlaps/makefile
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• src/hg/oneShot/evalEnds/makefile
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• src/hg/oneShot/faFiltMasked/makefile
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• src/hg/oneShot/faTest/makefile
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• src/hg/oneShot/fakeBedGraph/makefile
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• src/hg/oneShot/fakeChromGraph/makefile
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• src/hg/oneShot/fakeHomozygousity/makefile
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• src/hg/oneShot/fakeLinkage/makefile
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• src/hg/oneShot/fakeSeqDiffs/makefile
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• src/hg/oneShot/findContigsWithClones/makefile
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• src/hg/oneShot/findToFixBedGraphLimits/makefile
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• src/hg/oneShot/findToFixBedGraphViewLimits/makefile
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• src/hg/oneShot/fixBlastTrack/makefile
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• src/hg/oneShot/fixEnsGtf/makefile
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• src/hg/oneShot/fixGdup/makefile
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• src/hg/oneShot/flagMhcClones/makefile
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• src/hg/oneShot/freen/makefile
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• src/hg/oneShot/getHumanBrainRna/makefile
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• src/hg/oneShot/getRgdGeneCds/makefile
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• src/hg/oneShot/hgFreen/makefile
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• src/hg/oneShot/howBadNt/makefile
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• src/hg/oneShot/jingTestFoo/makefile
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• src/hg/oneShot/joinToPatch/makefile
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• src/hg/oneShot/kgName/makefile
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• src/hg/oneShot/labSheet/makefile
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• src/hg/oneShot/makeOrthoAtgTable/makefile
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• src/hg/oneShot/makeTrackDbTagVals/makefile
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• src/hg/oneShot/makeTrackDbTypeTags/makefile
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• src/hg/oneShot/makefile
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• src/hg/oneShot/mhcToNt/makefile
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• src/hg/oneShot/missingTable/makefile
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• src/hg/oneShot/musAliAt/makefile
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• src/hg/oneShot/newClones/makefile
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• src/hg/oneShot/oo21Nts/makefile
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• src/hg/oneShot/padFile/makefile
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• src/hg/oneShot/parseOmimDisorder/makefile
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• src/hg/oneShot/patchDir/makefile
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• src/hg/oneShot/patchNtAgp/makefile
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• src/hg/oneShot/patchToAgp/makefile
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• src/hg/oneShot/protDat/makefile
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• src/hg/oneShot/pslCut/makefile
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• src/hg/oneShot/raPriority/makefile
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• src/hg/oneShot/randomEst/makefile
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• src/hg/oneShot/rangeGraph/makefile
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• src/hg/oneShot/rcvs/makefile
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• src/hg/oneShot/rmDupCol1/makefile
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• src/hg/oneShot/rmFromFinf/makefile
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• src/hg/oneShot/roundNewViewLimitsInRa/makefile
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• src/hg/oneShot/sangPairs/makefile
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• src/hg/oneShot/seqFromPsl/makefile
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• src/hg/oneShot/somePsls/makefile
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• src/hg/oneShot/spSize/makefile
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• src/hg/oneShot/spanRaft/makefile
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• src/hg/oneShot/splitNcbiFa/makefile
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• src/hg/oneShot/tdbRewriteAddReplaces/makefile
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• src/hg/oneShot/tdbRewriteReduceReplaces/makefile
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• src/hg/oneShot/tdbRewriteRemoveUnused/makefile
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• src/hg/oneShot/tdbRewriteSortTags/makefile
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• src/hg/oneShot/tdbRewriteSubtrackToParent/makefile
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• src/hg/oneShot/tdbRewriteViewsToSubtracks/makefile
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• src/hg/oneShot/tdbRewriteViewsToSubtracks1/makefile
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• src/hg/oneShot/tempLift/makefile
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• src/hg/oneShot/tempLower/makefile
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• src/hg/oneShot/testBb/makefile
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• src/hg/oneShot/testCart/makefile
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• src/hg/oneShot/testIndex/makefile
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• src/hg/oneShot/testIntersect/makefile
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• src/hg/oneShot/testIxx/makefile
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• src/hg/oneShot/testTableExists/makefile
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• src/hg/oneShot/testXap/makefile
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• src/hg/oneShot/tetDensity/makefile
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• src/hg/oneShot/tetFilter/makefile
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• src/hg/oneShot/timeGifPng/makefile
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• src/hg/oneShot/trimFosmids/makefile
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• src/hg/oneShot/tryNewColorOverlay/makefile
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• src/hg/oneShot/weedKnownBlastTab/makefile
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• src/hg/oneShot/weedTab/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
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• src/hg/oneShot/wgEncodeRegGenRa/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
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    pointing to top of the tree.
    
• src/hg/oneShot/wgEncodeRegTfbsDedupeHelp/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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    pointing to top of the tree.
    
• src/hg/orthoMap/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
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• src/hg/pdbSP/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
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    pointing to top of the tree.
    
• src/hg/perf/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
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• src/hg/phyloGif/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
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    pointing to top of the tree.
    
• src/hg/poster/finPoster/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
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    pointing to top of the tree.
    
• src/hg/poster/foldDb/checkDupe/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/hg/poster/foldDb/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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    pointing to top of the tree.
    
• src/hg/poster/foldGfx/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/hg/protein/blastRecipBest/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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• src/hg/protein/dv2/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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• src/hg/protein/fixAgp/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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    pointing to top of the tree.
    
• src/hg/protein/fixMd/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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    pointing to top of the tree.
    
• src/hg/protein/gadPos/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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• src/hg/protein/getInterProFa/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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• src/hg/protein/hmmPfamToTab/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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• src/hg/protein/kgAliasKgXref/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
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• src/hg/protein/kgAliasM/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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• src/hg/protein/kgAliasP/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
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    pointing to top of the tree.
    
• src/hg/protein/kgAliasRefseq/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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    pointing to top of the tree.
    
• src/hg/protein/kgAttachKegg/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
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• src/hg/protein/kgBestMrna/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
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• src/hg/protein/kgBestMrna2/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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• src/hg/protein/kgBestRef2/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
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• src/hg/protein/kgBioCyc0/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
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• src/hg/protein/kgBioCyc1/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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• src/hg/protein/kgCheck/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
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• src/hg/protein/kgCheck2/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
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• src/hg/protein/kgGetCds/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
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• src/hg/protein/kgGetPep/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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• src/hg/protein/kgPepMrna/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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• src/hg/protein/kgPick/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
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• src/hg/protein/kgPick0/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
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• src/hg/protein/kgProtAlias/makefile
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• src/hg/protein/kgProtAliasNCBI/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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• src/hg/protein/kgPutBack/makefile
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• src/hg/protein/kgSelect/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
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• src/hg/protein/kgUniq/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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    pointing to top of the tree.
    
• src/hg/protein/kgXref/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
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• src/hg/protein/kgXref2/makefile
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• src/hg/protein/lib/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
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• src/hg/protein/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
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• src/hg/protein/omimCheckAv/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
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• src/hg/protein/omimParseAv/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
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• src/hg/protein/omimParseRec/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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• src/hg/protein/pbCalDist/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
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• src/hg/protein/pbCalDistGlobal/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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• src/hg/protein/pbCalPi/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
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• src/hg/protein/pbCalResStd/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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• src/hg/protein/pbCalResStdGlobal/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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• src/hg/protein/pbGateway/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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• src/hg/protein/pbGlobal/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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• src/hg/protein/pbHgnc/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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• src/hg/protein/pbTracks/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
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• src/hg/protein/pfamToGoRdf/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
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    pointing to top of the tree.
    
• src/hg/protein/pfamXref/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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• src/hg/protein/rmKGPepMrna/makefile
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    pointing to top of the tree.
    
• src/hg/protein/scopCollapse/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
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    pointing to top of the tree.
    
• src/hg/protein/spDbAddVarSplice/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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• src/hg/protein/spLoadPsiBlast/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
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• src/hg/protein/spLoadRankProp/makefile
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• src/hg/protein/spOrganism/makefile
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• src/hg/protein/spTest/makefile
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• src/hg/protein/spToDb/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
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• src/hg/protein/spToProteins/makefile
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• src/hg/protein/spToProteinsVar/makefile
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• src/hg/protein/spToSpXref2/makefile
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• src/hg/protein/spXref3/makefile
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• src/hg/protein/spm3/makefile
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• src/hg/protein/spm6/makefile
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• src/hg/protein/spm7/makefile
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• src/hg/pslAnal/makefile
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• src/hg/pslCDnaFilter/makefile
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• src/hg/pslCDnaFilter/tests/makefile
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• src/hg/pslCDnaGenomeMatch/makefile
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• src/hg/pslCluster/makefile
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• src/hg/pslCrudeCmp/makefile
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• src/hg/pslDiff/makefile
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• src/hg/pslDiff/tests/makefile
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• src/hg/pslDist/makefile
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• src/hg/pslFilterBadCdna/makefile
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• src/hg/pslHisto/tests/makefile
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• src/hg/pslMaxMap/makefile
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• src/hg/pslOneTwo/makefile
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• src/hg/pslPartition/tests/makefile
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• src/hg/pslPseudo/checkExp/makefile
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• src/hg/pslPseudo/makefile
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• src/hg/pslPseudo/tests/makefile
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• src/hg/pslSelect/tests/makefile
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• src/hg/pslSomeRecords/makefile
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• src/hg/pslSplit/makefile
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• src/hg/pslStats/tests/makefile
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• src/hg/pslSwap/tests/makefile
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• src/hg/pslToBed/tests/makefile
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• src/hg/pslToFa/makefile
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• src/hg/pslToPileup/makefile
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• src/hg/qa/makefile
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• src/hg/qaAgpToQacIdx/makefile
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• src/hg/qaPushQ/makefile
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• src/hg/qacAddGapIdx/makefile
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• src/hg/qacIndex/makefile
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• src/hg/raSort/makefile
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• src/hg/randomPlacement/makefile
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• src/hg/ratStuff/faToMaf/makefile
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• src/hg/ratStuff/mafBedSubset/makefile
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• src/hg/ratStuff/mafBreak/makefile
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• src/hg/ratStuff/mafFastFrags/makefile
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• src/hg/ratStuff/mafIndex/makefile
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• src/hg/ratStuff/mafOrtholog/makefile
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• src/hg/ratStuff/mafSplit/test/makefile
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• src/hg/ratStuff/mafStats/makefile
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• src/hg/ratStuff/mafToAnc/makefile
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• src/hg/ratStuff/mafToProtein/makefile
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• src/hg/ratStuff/multizzy/makefile
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• src/hg/ratStuff/segExpandToAnchors/makefile
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• src/hg/ratStuff/segInfo/makefile
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• src/hg/ratStuff/segSplitPairwise/makefile
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• src/hg/regulate/companion/regCompanion5C/makefile
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• src/hg/regulate/companion/regCompanionCalcBedGraphNorm/makefile
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• src/hg/regulate/companion/regCompanionChia/makefile
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• src/hg/regulate/companion/regCompanionCorrelateEnhancerAndExpression/makefile
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• src/hg/regulate/companion/regCompanionEnhProCellSpecificPairs/makefile
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• src/hg/regulate/companion/regCompanionEntropy/makefile
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• src/hg/regulate/companion/regCompanionGraphVsFixedPoints/makefile
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• src/hg/regulate/companion/regCompanionHistoneBox/makefile
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• src/hg/regulate/regBeadPos/makefile
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• src/hg/regulate/regChromiaMergeWindows/makefile
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    9dcd25d3b353e416897abb26876daaa5fe1c6c51 Tue Jul 12 13:55:54 2016 -0700
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    428d5d7480823b3ccc841dda9a11015f3bb836f0 Sat Jul 16 14:29:24 2016 -0700
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    729090c69502053bffc361ec44830fee22a97fe9 Tue Jul 12 13:56:00 2016 -0700
    this is constructing a minimal assembly hub with assembly gap gc5Base trackes refs #13553
    
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    a6cea0fbd88d7a83fdb3585d9ac010a8b98e9dc3 Thu Jul 14 13:12:57 2016 -0700
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    042c30bf42780cc2fd3cf6a8e1f3bb452820d5a7 Fri Jul 15 09:13:18 2016 -0700
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    c10461bdc16c89b939a01f5389134b10869434df Fri Jul 15 14:32:13 2016 -0700
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    293f3895afcb62515ae62c6383e8c9607ef4a16a Fri Jul 15 14:58:50 2016 -0700
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    ac6b56c4f50c0a47fe98ddf3f488c99f33532f3a Sat Jul 16 18:42:02 2016 -0700
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• src/hg/utils/automation/doRepeatMasker.pl
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    8674ad6258c79ff4e04f46553a2631ec8cfe7501 Thu Jul 14 11:33:31 2016 -0700
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• src/hg/utils/automation/doSimpleRepeat.pl
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    589373cd4495395746e0ddcae562aa483835586c Thu Jul 14 11:33:05 2016 -0700
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    70120cf951e38933e4f19fe774fd9fd9bf98b11a Thu Jul 14 20:54:10 2016 -0700
    creating bigBed during doFilter refs #13553
    
• src/hg/utils/automation/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
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• src/hg/utils/bedExtendRanges/makefile
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• src/hg/utils/bedMergeExpData/makefile
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• src/hg/utils/bedMergeOverlappingBlocks/makefile
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• src/hg/utils/bedRandom/makefile
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• src/hg/utils/bedToPsl/tests/makefile
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• src/hg/utils/cageSingleTrack/makefile
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• src/hg/utils/coloredExonToBed/makefile
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• src/hg/utils/findCutters/makefile
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• src/hg/utils/fiveCToBed/makefile
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• src/hg/utils/genePredFilter/tests/makefile
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• src/hg/utils/geoMirrorNode/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
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• src/hg/utils/gff3ToGenePred/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
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• src/hg/utils/gff3ToGenePred/tests/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
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• src/hg/utils/gff3ToPsl/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
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• src/hg/utils/gff3ToPsl/tests/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
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• src/hg/utils/gffToBed/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
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• src/hg/utils/gtfToGenePred/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
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• src/hg/utils/gtfToGenePred/tests/makefile
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• src/hg/utils/hubCheck/makefile
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• src/hg/utils/liftUpBedFromTable/makefile
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• src/hg/utils/makeTableList/makefile
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• src/hg/utils/makeTrackIndex/makefile
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• src/hg/utils/mdbQuery/makefile
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• src/hg/utils/mutationClassifier/makefile
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• src/hg/utils/oligoMatch/tests/makefile
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• src/hg/utils/otto/decipher/buildDecipher
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    d89c874346552fbb921d6a1d038a79605f6ce613 Wed Jul 13 11:45:07 2016 -0700
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    d89c874346552fbb921d6a1d038a79605f6ce613 Wed Jul 13 11:45:07 2016 -0700
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    d89c874346552fbb921d6a1d038a79605f6ce613 Wed Jul 13 11:45:07 2016 -0700
    DECIPHER pipeline now runs on their new file format. Also added more data to the hgc output. refs #14465
    
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• src/hg/utils/otto/omim/doOmimGene2/makefile
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• src/hg/utils/otto/omim/doOmimGeneSymbols/makefile
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• src/hg/utils/overlapSelect/tests/makefile
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• src/hg/utils/pslMap/tests/makefile
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• src/hg/utils/randFrag/makefile
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• src/hg/utils/reTraceUtils/reTraceFixMaf/makefile
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• src/hg/utils/refSeqGet/makefile
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• src/hg/utils/ruby/makefile
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• src/hg/utils/tdbQuery/makefile
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• src/hg/visiGene/gensat/gensatRandomXml/makefile
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• src/hg/visiGene/gensat/makefile
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• src/hg/visiGene/hgVisiGene/makefile
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• src/hg/visiGene/jackson/makefile
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• src/htslib/INSTALL
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• src/htslib/cram/os.h
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• src/htslib/cram/pooled_alloc.c
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
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• src/htslib/cram/pooled_alloc.h
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• src/htslib/cram/rANS_byte.h
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
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• src/htslib/cram/rANS_static.c
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
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• src/htslib/cram/rANS_static.h
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• src/htslib/cram/sam_header.c
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
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• src/htslib/cram/sam_header.h
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• src/htslib/cram/string_alloc.c
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• src/htslib/cram/string_alloc.h
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
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• src/htslib/cram/thread_pool.c
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
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• src/htslib/cram/thread_pool.h
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• src/htslib/cram/vlen.c
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• src/htslib/cram/vlen.h
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• src/htslib/cram/zfio.c
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• src/htslib/cram/zfio.h
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• src/htslib/faidx.5
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• src/htslib/faidx.c
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• src/htslib/hfile.c
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• src/htslib/hfile_internal.h
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• src/htslib/hfile_irods.c
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• src/htslib/hfile_libcurl.c
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• src/htslib/hfile_net.c
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• src/htslib/hts.c
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
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    172c9065c1e6d94aabd25f63b238f17b9a51bffc Tue Jul 12 08:49:47 2016 -0700
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• src/htslib/hts_internal.h
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• src/htslib/htsfile.1
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• src/htslib/htsfile.c
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• src/htslib/htslib.mk
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• src/htslib/htslib.pc.in
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• src/htslib/htslib/bgzf.h
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• src/htslib/htslib/cram.h
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• src/htslib/htslib/faidx.h
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• src/htslib/htslib/hfile.h
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• src/htslib/htslib/hts.h
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• src/htslib/htslib/hts_defs.h
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• src/htslib/htslib/kbitset.h
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• src/htslib/htslib/kfunc.h
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• src/htslib/htslib/khash.h
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• src/htslib/htslib/khash_str2int.h
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• src/htslib/htslib/klist.h
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• src/htslib/htslib/knetfile.h
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• src/htslib/htslib/kseq.h
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• src/htslib/htslib/ksort.h
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• src/htslib/htslib/kstring.h
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• src/htslib/htslib/regidx.h
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• src/htslib/htslib/sam.h
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• src/htslib/htslib/synced_bcf_reader.h
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• src/htslib/htslib/tbx.h
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• src/htslib/htslib/vcf.h
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• src/htslib/htslib/vcf_sweep.h
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• src/htslib/htslib/vcfutils.h
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• src/htslib/htslib_vars.mk
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• src/htslib/kfunc.c
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• src/htslib/knetfile.c
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• src/htslib/kstring.c
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• src/htslib/md5.c
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• src/htslib/plugin.c
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• src/htslib/regidx.c
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• src/htslib/sam.5
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• src/htslib/sam.c
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    172c9065c1e6d94aabd25f63b238f17b9a51bffc Tue Jul 12 08:49:47 2016 -0700
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• src/htslib/synced_bcf_reader.c
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    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/htslib/test/xx.fa.fai
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/htslib/vcf.5
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/htslib/vcf.c
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/htslib/vcf_sweep.c
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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    pointing to top of the tree.
    
• src/htslib/vcfutils.c
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/inc/bamFile.h
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/inc/common.mk
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
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• src/inc/linefile.h
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/isPcr/gfPcr/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/isPcr/isPcr/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/isPcr/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/isPcr/webPcr/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/jkOwnLib/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/jkOwnLib/tests/freen/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/kehayden/alphaChain/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/kehayden/learningLibs/.learningLibs.c.swp
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    2067ad32064522a460482a89792627e0218537a4 Mon Jul 11 16:54:02 2016 -0700
    oops, this kind of temporary editor swap file should not get checked in
    
• src/kehayden/learningLibs/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/kehayden/linearSat/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/kehayden/reverseCenReads/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/kehayden/tokenizerLib/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/lib/bamFile.c
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/lib/knetUdc.c
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/lib/linefile.c
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/lib/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/lib/tests/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/lib/tests/tabixFetch.c
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
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• src/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/meta/metaHoist/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/olly/checkSeed/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/olly/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/olly/ollySlow/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/olly/sampleToWig/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/oneShot/addFinFinf/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/oneShot/balancedTree/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/oneShot/blat2p/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/oneShot/burstClient/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/oneShot/burstServer/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/oneShot/checkLayout/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/oneShot/chkGlue/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/oneShot/clusterBox/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/oneShot/clusterClone/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/oneShot/cntGlue/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/oneShot/commonLines/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/oneShot/countClient/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/oneShot/countServer/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/oneShot/coverage/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/oneShot/dateXmlCgi/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/oneShot/deEns/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/oneShot/dynAlign/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/oneShot/echoServer/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/oneShot/findContigsWithClones/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/oneShot/fixInfo/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/oneShot/foo2/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/oneShot/formatFastaSeq/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/oneShot/grokGff/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/oneShot/invert/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/oneShot/jccTest/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/oneShot/jksql/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/oneShot/killRabbit/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/oneShot/m22dirs/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/oneShot/mafFindZero/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/oneShot/mafTest/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
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• src/oneShot/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
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• src/oneShot/motifConvert/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
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• src/oneShot/mungeAuthors/makefile
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• src/oneShot/newSang6/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
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• src/oneShot/newStitch/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
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• src/oneShot/newStitch2/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
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• src/oneShot/newStitch3/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
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• src/oneShot/newStitch4/makefile
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• src/oneShot/onePassBedToBigBed/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
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• src/oneShot/ooRev/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
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• src/oneShot/opendirTest/makefile
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• src/oneShot/passHi/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
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• src/oneShot/patJobs/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
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• src/oneShot/preProcGgfAndy/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
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• src/oneShot/randDNA/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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• src/oneShot/rbIntTest/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
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• src/oneShot/rbTest/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
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• src/oneShot/rgbaGfxTest/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
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• src/oneShot/rt1dTest/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
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• src/oneShot/scrapeCruzBiotech/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
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• src/oneShot/shorten/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
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• src/oneShot/smoothWindow/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
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• src/oneShot/sources/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
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• src/oneShot/splitSql/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
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• src/oneShot/sqlToAs/makefile
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• src/oneShot/tabTable/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
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• src/oneShot/test/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
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• src/oneShot/testBandExt/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
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• src/oneShot/testCache/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
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• src/oneShot/testGitRename/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
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• src/oneShot/testPoly/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
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• src/oneShot/testScripters/countLines/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
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• src/oneShot/testScripters/wordUse/makefile
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• src/oneShot/threadTime/makefile
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• src/oneShot/uniqSize/makefile
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• src/oneShot/unmasked/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
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• src/oneShot/unwrap/makefile
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• src/oneShot/wordsBySize/makefile
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• src/parasol/dataSim/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
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• src/parasol/gensub2/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
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• src/parasol/lib/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
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• src/parasol/netC/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
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• src/parasol/netS/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
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• src/parasol/para/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
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• src/parasol/paraHub/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
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• src/parasol/paraHubStop/makefile
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• src/parasol/paraNode/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
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• src/parasol/paraNodeStart/makefile
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• src/parasol/paraNodeStatus/makefile
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• src/parasol/paraNodeStop/makefile
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• src/parasol/paraTestJob/makefile
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• src/parasol/parasol/makefile
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• src/parasol/simpleC/makefile
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• src/parasol/simpleS/makefile
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• src/product/installer/README.md
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    b180445dc74ceea3c5e0e80dd66c60e5cf695ccd Thu Jul 14 16:00:00 2016 -0700
    Final fixups of gbic readme, fixing some capitilization errors and the like, refs #14399
    
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    93c119f05d282a1fcd5239fd7759a42fd576ffd7 Fri Jul 15 16:11:41 2016 -0700
    small changes to gbic readme
    
• src/product/installer/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
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    6676762506a76c136fe679c33c084143d10ccc8d Tue Jul 12 09:50:02 2016 -0700
    Adding command to make readme executable for ssi, refs #14399
    
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    a78f820ae00104d892ce55cc26a7e2b1922f1464 Tue Jul 12 10:43:24 2016 -0700
    Fixing pathname in makefile, refs #14399
    
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    fe6c534fe170003a7a1b7785a642b18ec6f73c7c Tue Jul 12 15:03:25 2016 -0700
    Makefile changes: switching target all to user, adding rsync command for beta target, refs #14399
    
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    a821c381fb59842e7c623114b68fa146a65735b6 Tue Jul 12 15:21:26 2016 -0700
    Hopefully last makefile change, account for case where user has never made this doc before, refs #14399
    
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    324c1151dbc0092a3960c64add9213743afc66d6 Wed Jul 13 12:07:09 2016 -0700
    Initial stab at having htdocs makefile also run pandoc, refs #14399
    
• src/product/mirrorDocs/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
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• src/product/mirrorManual.txt
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    bed4d8e78b087fea84b6b44a7835793a3b16fedb Fri Jul 15 15:15:52 2016 -0700
    adding instructions on how to modify our code, after discussion with
    david hoover
    
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    cb01f6022f1c69cbafede682ad4d7f6b63064ae3 Fri Jul 15 16:07:20 2016 -0700
    adding cram to the mirror manual
    
• src/product/scripts/fetchMinimalGbdb.sh
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    888a33b88aa0a243dfce9ca459a97d8bc9d5e760 Tue Jul 12 11:29:01 2016 -0700
    eliminate warning messages when no nib directory refs #17676
    
• src/reformat/fa4blast/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/reformat/fsg/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/reformat/gbToFaRa/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/reformat/makeOrf2gene/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/reformat/makec2c/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/shortReads/bfastMafFix/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/shortReads/bwtFind/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/shortReads/bwtMake/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/shortReads/bwtReverse/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/shortReads/elandToSplat/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/shortReads/i16Find/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/shortReads/i16Make/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/shortReads/itsaDump/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/shortReads/itsaFind/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/shortReads/itsaMake/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/shortReads/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/shortReads/shortRepeatFind/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/shortReads/shortRepeatMerge/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/shortReads/splat/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/shortReads/splatCheck1/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/shortReads/splatCheck2/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/shortReads/splatMerge/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/shortReads/splatTestSet/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/shortReads/splatToEland/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/shortReads/splixMake/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/shortReads/streamer/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/shortReads/sufaFind/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/shortReads/sufaMake/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/shortReads/sufaRepeatFind/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/shortReads/sufxDump/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/shortReads/sufxFind/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/shortReads/sufxMake/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/tagStorm/tagStormDeleteTags/tests/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/tagStorm/tagStormInfo/tests/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/tagStorm/tagStormJoinTab/tests/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/test/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/tracks/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/userApps/Makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/userApps/fetchKentSource.sh
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/utils/asCompare/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/utils/bbTest/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/utils/bdfToGem/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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    pointing to top of the tree.
    
• src/utils/bedInvert.pl
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    9b4e3092e23d37d97634b3f09002bec996bd633e Thu Jul 14 16:21:14 2016 -0700
    bed inversion, show gaps between elements refs #13553
    
• src/utils/bedScore/tests/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/utils/bedToBigBed/tests/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/utils/bigWigCat/tests/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/utils/bigWigMerge/tests/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/utils/callGraph/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/utils/ccCpLock/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/utils/chainDist/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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• src/utils/colCount/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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    pointing to top of the tree.
    
• src/utils/colorConv/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/utils/combineFiles/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/utils/correlate/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/utils/dnsInfo/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/utils/est2genomeToPsl/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/utils/est2genomeToPsl/tests/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/utils/faFilter/tests/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/utils/faLowerToN/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/utils/faRandomize/tests/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/utils/faRenameRecords/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/utils/fastaToPsl/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/utils/fileExists/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/utils/genFedTableDef/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/utils/geneStarts/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/utils/gitTools/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/utils/greedyPack/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/utils/lineFileSplit/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/utils/lineRange/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/utils/linesInAllFiles/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/utils/makeRgbRainbow/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/utils/makefile
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    3887c3b11338a8ed7de6f5805d09019c25979023 Fri Jul 15 15:14:53 2016 -0700
    removing dependencies for uniprot pipeline, moving it into kent repo,
    for #17716. Also preparing for hg38 uniprot track, #17717
    
• src/utils/mapViewerToGenePred/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/utils/maxEachRow/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/utils/minEachRow/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/utils/newProg/newProg.c
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    5903bc9d1be545a1cc9e1cdf1875ef452c9ca9fb Fri Jul 15 09:52:52 2016 -0700
    Need to set up udc before calling cartEmptyShell, otherwise hubs don't work right, refs #17686
    
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    a8fbc07ba5a7a0b99f9b736ecf4a4d1a79d8c6ae Fri Jul 15 17:09:39 2016 -0700
    Additional changes to newProg requested by Angie: set up udcTimeout, knetUdc, and initialize genbank, refs #17686
    
• src/utils/nibCheck/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/utils/plotDataMatrix/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/utils/pslLiftSubrangeBlat/tests/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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    pointing to top of the tree.
    
• src/utils/pslScore/tests/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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• src/utils/qa/bigPush.sh
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    f898118e25b9d795f31f1839c87f0ed57fc44a3c Fri Jul 15 15:16:33 2016 -0700
    Changes to argument structure. Database and tables are now required positional arugments, rather than options. Re-did usage message to reflect this. Changed verbose option, no longer outputs to file, just stdout. Added quotes around variables in different placesat Jonathan's recommendation, no redmine
    
• src/utils/qa/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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    pointing to top of the tree.
    
• src/utils/qa/weeklybld/buildEnv.csh
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    d096495c88c94d8f1da8b9aba04203b99ffd87f4 Mon Jul 18 11:14:29 2016 -0700
    v336 preview2
    
• src/utils/raFromTab/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/utils/raMerge/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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    pointing to top of the tree.
    
• src/utils/raToSvmLight/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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    pointing to top of the tree.
    
• src/utils/replaceTextBetween/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/utils/sets/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
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• src/utils/shuffleLines/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/utils/sortFa/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/utils/tTestTwo/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/utils/textBetween/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
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    pointing to top of the tree.
    
• src/utils/uniprotLift
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    3887c3b11338a8ed7de6f5805d09019c25979023 Fri Jul 15 15:14:53 2016 -0700
    removing dependencies for uniprot pipeline, moving it into kent repo,
    for #17716. Also preparing for hg38 uniprot track, #17717
    
• src/utils/uniprotToTab
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    3887c3b11338a8ed7de6f5805d09019c25979023 Fri Jul 15 15:14:53 2016 -0700
    removing dependencies for uniprot pipeline, moving it into kent repo,
    for #17716. Also preparing for hg38 uniprot track, #17717
    
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    4e5e5c77cb6bac09f0da5ae36a19e4677c65a0e3 Fri Jul 15 15:38:12 2016 -0700
    forgot a line in last commit
    
• src/utils/vennIds/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/utils/vulgarToPsl/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/utils/wgetMd5/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/utils/wigAsciiCrunch/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/utils/wigAsciiToBinary/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/utils/wigSetSpanOrStep/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/utils/wigSort/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/utils/wigToBed/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/utils/wigToBedGraph/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/utils/wigToBigWig/tests/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/utils/wordsInEachLine/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/webBlat/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/xenoAli/aliStats/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/xenoAli/blastStats/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/xenoAli/cbAli/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/xenoAli/newIntron/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/xenoAli/smithWat/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/xenoAli/waba/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/xenoAli/xaShow/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.
    
• src/xenoAli/xenWorm/makefile
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    11e45667d4e291b3038ccda729a1cdf5bcaf004a Mon Jul 11 15:46:54 2016 -0700
    incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
    defines, modify a bunch of makefiles to include kentSrc variable
    pointing to top of the tree.