File Changes for hiram

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v282_preview2 to v282_base (2013-04-09 to 2013-04-16) v282

src/blatz/makefile
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  correctly using DESTDIR with BINDIR refs #9104
src/hg/altSplice/altSplice/tests/makefile
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  eliminate BINDIR from tests makefile, refs #9104
src/hg/bedIntersect/tests/makefile
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  eliminate BINDIR from tests makefile, refs #9104
src/hg/bedItemOverlapCount/tests/makefile
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  add makefile for running tests refs #9104
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  add clean target to satisify that from the call above refs #9104
src/hg/blastToPsl/tests/makefile
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  eliminate BINDIR from tests makefile, refs #9104
src/hg/checkTableCoords/tests/makefile
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  do not use BINDIR in the tests makefile to reference the test program
src/hg/chimpStuff/chimpChromContigAgp/tests/makefile
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  eliminate BINDIR from tests makefile, refs #9104
src/hg/encode/regionAgp/tests/makefile
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  eliminate BINDIR from tests makefile, refs #9104
src/hg/genePredToGtf/tests/makefile
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  eliminate BINDIR from tests makefile, refs #9104
src/hg/lib/customFactory.c
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  limit custom track submissions to 1,000 tracks, and add references to Track Hub and Big Wig help when limits prevent custom tracks refs #10599
src/hg/lib/wigAsciiToBinary.c
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  limit custom track submissions to 1,000 tracks, and add references to Track Hub and Big Wig help when limits prevent custom tracks refs #10599
src/hg/liftOver/tests/makefile
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  eliminate BINDIR from tests makefile, refs #9104
src/hg/makeDb/hgLoadMaf/tests/makefile
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  eliminate BINDIR from tests makefile, refs #9104
src/hg/mouseStuff/axtAndBed/makefile
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  implementing minimal makefile userApp.mk refs #9104
src/hg/mouseStuff/axtBest/makefile
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  implementing minimal makefile userApp.mk refs #9104
src/hg/mouseStuff/axtCalcMatrix/makefile
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src/hg/mouseStuff/axtChain/makefile
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src/hg/mouseStuff/axtDropOverlap/makefile
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src/hg/mouseStuff/axtDropSelf/makefile
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src/hg/mouseStuff/axtFilter/makefile
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src/hg/mouseStuff/axtIndex/makefile
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src/hg/mouseStuff/axtPretty/makefile
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src/hg/mouseStuff/axtQueryCount/makefile
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src/hg/mouseStuff/axtRecipBest/makefile
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src/hg/mouseStuff/axtRescore/makefile
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src/hg/mouseStuff/axtSort/makefile
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src/hg/mouseStuff/axtSplitByTarget/makefile
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src/hg/mouseStuff/axtSwap/makefile
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src/hg/mouseStuff/axtToBed/makefile
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src/hg/mouseStuff/axtToChain/makefile
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  implementing minimal makefile userApp.mk refs #9104
src/hg/mouseStuff/axtToMaf/makefile
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src/hg/mouseStuff/axtToMaf/tests/makefile
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  implementing minimal makefile userApp.mk refs #9104
src/hg/mouseStuff/axtToPsl/makefile
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  implementing minimal makefile userApp.mk refs #9104
src/hg/mouseStuff/bedCoverage/makefile
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src/hg/mouseStuff/calcGap/makefile
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src/hg/mouseStuff/chainAntiRepeat/makefile
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src/hg/mouseStuff/chainDbToFile/makefile
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src/hg/mouseStuff/chainFilter/makefile
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src/hg/mouseStuff/chainMergeSort/makefile
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src/hg/mouseStuff/chainNet/makefile
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src/hg/mouseStuff/chainPreNet/makefile
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src/hg/mouseStuff/chainSort/makefile
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src/hg/mouseStuff/chainSplit/makefile
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src/hg/mouseStuff/chainStats/makefile
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src/hg/mouseStuff/chainStitchId/makefile
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src/hg/mouseStuff/chainSwap/makefile
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src/hg/mouseStuff/chainToAxt/makefile
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src/hg/mouseStuff/chainToPsl/makefile
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  implementing minimal makefile userApp.mk refs #9104
src/hg/mouseStuff/gcForBed/makefile
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src/hg/mouseStuff/knownVsBlat/makefile
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  implementing minimal makefile userApp.mk refs #9104
src/hg/mouseStuff/lavToAxt/makefile
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  implementing minimal makefile userApp.mk refs #9104
src/hg/mouseStuff/lavToPsl/makefile
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  implementing minimal makefile userApp.mk refs #9104
src/hg/mouseStuff/libScan/makefile
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  implementing minimal makefile userApp.mk refs #9104
src/hg/mouseStuff/mafCoverage/makefile
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  implementing minimal makefile userApp.mk refs #9104
src/hg/mouseStuff/mafFetch/makefile
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src/hg/mouseStuff/mafRanges/makefile
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  implementing minimal makefile userApp.mk refs #9104
src/hg/mouseStuff/mafRanges/tests/makefile
- lines changed 1, context: html, text, full: html, text
  eliminate BINDIR from tests makefile, refs #9104
src/hg/mouseStuff/mafToAxt/makefile
- lines changed 14, context: html, text, full: html, text
  implementing minimal makefile userApp.mk refs #9104
src/hg/mouseStuff/mafToPsl/makefile
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  implementing minimal makefile userApp.mk refs #9104
src/hg/mouseStuff/mousePoster/makefile
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src/hg/mouseStuff/netChainSubset/makefile
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  implementing minimal makefile userApp.mk refs #9104
src/hg/mouseStuff/netClass/makefile
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src/hg/mouseStuff/netFilter/makefile
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src/hg/mouseStuff/netSplit/makefile
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src/hg/mouseStuff/netStats/makefile
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src/hg/mouseStuff/netSyntenic/makefile
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src/hg/mouseStuff/netToAxt/makefile
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src/hg/mouseStuff/netToAxt/tests/makefile
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  implementing minimal makefile userApp.mk refs #9104
src/hg/mouseStuff/netToBed/makefile
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src/hg/mouseStuff/netToBedWithId/makefile
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src/hg/mouseStuff/orthologBySynteny/makefile
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src/hg/mouseStuff/phToPsl/makefile
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src/hg/mouseStuff/pslMrnaCover/makefile
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src/hg/mouseStuff/regionPicker/makefile
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src/hg/mouseStuff/rikenBestInCluster/makefile
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src/hg/mouseStuff/simpleChain/makefile
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src/hg/mouseStuff/splitSim/makefile
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src/hg/mouseStuff/subsetAxt/makefile
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src/hg/mouseStuff/subsetTraces/makefile
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src/hg/mouseStuff/whyConserved/makefile
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src/hg/phyloGif/makefile
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  correctly use DESTDIR with BINDIR refs #9104
src/hg/pslCDnaFilter/tests/makefile
- lines changed 1, context: html, text, full: html, text
  eliminate BINDIR from tests makefile, refs #9104
src/hg/pslHisto/tests/makefile
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  do not use BINDIR in the tests makefile to reference the test program
src/hg/pslStats/tests/makefile
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  eliminate BINDIR from tests makefile, refs #9104
src/hg/ratStuff/mafAddIRows/makefile
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  implementing minimal makefile userApp.mk refs #9104
src/hg/ratStuff/mafAddQRows/makefile
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src/hg/ratStuff/mafFilter/makefile
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src/hg/ratStuff/mafFrag/makefile
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src/hg/ratStuff/mafFrags/expected/hg16.maf
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src/hg/ratStuff/mafFrags/makefile
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src/hg/ratStuff/mafGene/makefile
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src/hg/ratStuff/mafMeFirst/makefile
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src/hg/ratStuff/mafOrder/makefile
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src/hg/ratStuff/mafSpeciesList/makefile
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src/hg/ratStuff/mafSpeciesSubset/makefile
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src/hg/ratStuff/mafSplit/makefile
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src/hg/ratStuff/mafSplitPos/makefile
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src/hg/ratStuff/mafsInRegion/makefile
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src/hg/ratStuff/makefile
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src/hg/ratStuff/stageMultiz/makefile
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src/hg/txCds/txCdsBadBed/makefile
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src/hg/txCds/txCdsCluster/makefile
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src/hg/txCds/txCdsEvFromBed/makefile
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src/hg/txCds/txCdsEvFromBorf/makefile
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src/hg/txCds/txCdsEvFromProtein/makefile
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src/hg/txCds/txCdsEvFromRna/makefile
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src/hg/txCds/txCdsGoodBed/makefile
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src/hg/txCds/txCdsOrfInfo/makefile
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src/hg/txCds/txCdsOrtho/makefile
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src/hg/txCds/txCdsPick/makefile
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src/hg/txCds/txCdsPredict/makefile
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src/hg/txCds/txCdsRaExceptions/makefile
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src/hg/txCds/txCdsRefBestEvOnly/makefile
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src/hg/txCds/txCdsRepick/makefile
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src/hg/txCds/txCdsSuspect/makefile
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src/hg/txCds/txCdsSvmInput/makefile
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src/hg/txCds/txCdsToGene/makefile
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src/hg/txCds/txCdsWeed/makefile
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src/hg/txCds/txInfoAssemble/makefile
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src/hg/txGene/txGeneAccession/makefile
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src/hg/txGene/txGeneAlias/makefile
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src/hg/txGene/txGeneAltProt/makefile
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src/hg/txGene/txGeneCanonical/makefile
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src/hg/txGene/txGeneCdsMap/makefile
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src/hg/txGene/txGeneColor/makefile
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src/hg/txGene/txGeneExplainUpdate1/makefile
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src/hg/txGene/txGeneFromBed/makefile
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src/hg/txGene/txGeneProtAndRna/makefile
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src/hg/txGene/txGeneSeparateNoncoding/makefile
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src/hg/txGene/txGeneXref/makefile
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src/hg/txGraph/agxToTxg/makefile
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src/hg/txGraph/bedToTxEdges/makefile
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src/hg/txGraph/txAbFragFind/makefile
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src/hg/txGraph/txBedToGraph/makefile
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src/hg/txGraph/txOrtho/makefile
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src/hg/txGraph/txPslFilter/makefile
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src/hg/txGraph/txPslToBed/makefile
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src/hg/txGraph/txReadRa/makefile
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src/hg/txGraph/txWalk/makefile
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src/hg/txGraph/txgAddEvidence/makefile
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src/hg/txGraph/txgAnalyze/makefile
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src/hg/txGraph/txgGoodEdges/makefile
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src/hg/txGraph/txgToAgx/makefile
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src/hg/txGraph/txgToXml/makefile
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src/hg/txGraph/txgTrim/makefile
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src/hg/utils/bedToPsl/makefile
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src/hg/utils/bedToPsl/tests/makefile
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src/hg/utils/bedWeedOverlapping/makefile
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src/hg/utils/chromGraphFromBin/makefile
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src/hg/utils/chromGraphToBin/makefile
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src/hg/utils/crTreeIndexBed/makefile
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src/hg/utils/crTreeSearchBed/makefile
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src/hg/utils/gff3ToGenePred/tests/makefile
- lines changed 1, context: html, text, full: html, text
  do not use BINDIR in the tests makefile to reference the test program
src/hg/utils/gff3ToPsl/tests/makefile
- lines changed 1, context: html, text, full: html, text
  do not use BINDIR in the tests makefile to reference the test program
src/hg/utils/overlapSelect/tests/makefile
- lines changed 1, context: html, text, full: html, text
  do not use BINDIR in the tests makefile to reference the test program
src/hg/utils/positionalTblCheck/makefile
- lines changed 14, context: html, text, full: html, text
  perhaps last lot of makefiles converted to new minimal style refs #9104
src/hg/utils/pslMap/tests/makefile
- lines changed 2, context: html, text, full: html, text
  do not use BINDIR in the tests makefile to reference the test program
src/hg/utils/pslUniq/makefile
- lines changed 17, context: html, text, full: html, text
  perhaps last lot of makefiles converted to new minimal style refs #9104
src/hg/utils/refSeqGet/tests/makefile
- lines changed 1, context: html, text, full: html, text
  do not use BINDIR in the tests makefile to reference the test program
src/hg/utils/refreshNamedSessionCustomTracks/makefile
- lines changed 19, context: html, text, full: html, text
  perhaps last lot of makefiles converted to new minimal style refs #9104
src/hg/utils/safePush/makefile
- lines changed 14, context: html, text, full: html, text
  perhaps last lot of makefiles converted to new minimal style refs #9104
src/hg/utils/toDev64/makefile
- lines changed 14, context: html, text, full: html, text
  perhaps last lot of makefiles converted to new minimal style refs #9104
src/hg/utils/twoBitMask/makefile
- lines changed 16, context: html, text, full: html, text
  perhaps last lot of makefiles converted to new minimal style refs #9104
src/hg/utils/wigBedToStep/makefile
- lines changed 14, context: html, text, full: html, text
  perhaps last lot of makefiles converted to new minimal style refs #9104
src/isPcr/gfPcr/makefile
- lines changed 2, context: html, text, full: html, text
  correctly using DESTDIR with BINDIR refs #9104
src/isPcr/isPcr/makefile
- lines changed 2, context: html, text, full: html, text
  correctly using DESTDIR with BINDIR refs #9104
src/utils/bedScore/tests/makefile
- lines changed 1, context: html, text, full: html, text
  do not use BINDIR in the tests makefile to reference the test program
src/utils/convolve/tests/makefile
- lines changed 5, context: html, text, full: html, text
  add makefile for running tests refs #9104
src/utils/pslLiftSubrangeBlat/tests/makefile
- lines changed 1, context: html, text, full: html, text
  eliminate BINDIR from tests makefile, refs #9104

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