Commits for hiram

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

• implementing minimal makefile userApp.mk refs #9104
  • src/hg/mouseStuff/axtAndBed/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/mouseStuff/axtBest/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/mouseStuff/axtCalcMatrix/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/mouseStuff/axtChain/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/mouseStuff/axtDropOverlap/makefile - lines changed 18, context: html, text, full: html, text
  • src/hg/mouseStuff/axtDropSelf/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/mouseStuff/axtFilter/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/mouseStuff/axtIndex/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/mouseStuff/axtPretty/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/mouseStuff/axtQueryCount/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/mouseStuff/axtRecipBest/makefile - lines changed 17, context: html, text, full: html, text
  • src/hg/mouseStuff/axtRescore/makefile - lines changed 16, context: html, text, full: html, text
  • src/hg/mouseStuff/axtSort/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/mouseStuff/axtSplitByTarget/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/mouseStuff/axtSwap/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/mouseStuff/axtToBed/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/mouseStuff/axtToChain/makefile - lines changed 18, context: html, text, full: html, text
  • src/hg/mouseStuff/axtToMaf/makefile - lines changed 17, context: html, text, full: html, text
  • src/hg/mouseStuff/axtToMaf/tests/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/mouseStuff/axtToPsl/makefile - lines changed 17, context: html, text, full: html, text
  • src/hg/mouseStuff/bedCoverage/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/mouseStuff/calcGap/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/mouseStuff/chainAntiRepeat/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/mouseStuff/chainDbToFile/makefile - lines changed 18, context: html, text, full: html, text
  • src/hg/mouseStuff/chainFilter/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/mouseStuff/chainMergeSort/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/mouseStuff/chainNet/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/mouseStuff/chainPreNet/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/mouseStuff/chainSort/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/mouseStuff/chainSplit/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/mouseStuff/chainStats/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/mouseStuff/chainStitchId/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/mouseStuff/chainSwap/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/mouseStuff/chainToAxt/makefile - lines changed 15, context: html, text, full: html, text
  • src/hg/mouseStuff/chainToPsl/makefile - lines changed 13, context: html, text, full: html, text
  • src/hg/mouseStuff/gcForBed/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/mouseStuff/knownVsBlat/makefile - lines changed 4, context: html, text, full: html, text
  • src/hg/mouseStuff/lavToAxt/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/mouseStuff/lavToPsl/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/mouseStuff/libScan/makefile - lines changed 13, context: html, text, full: html, text
  • src/hg/mouseStuff/mafCoverage/makefile - lines changed 18, context: html, text, full: html, text
  • src/hg/mouseStuff/mafFetch/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/mouseStuff/mafRanges/makefile - lines changed 19, context: html, text, full: html, text
  • src/hg/mouseStuff/mafToAxt/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/mouseStuff/mafToPsl/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/mouseStuff/mousePoster/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/mouseStuff/netChainSubset/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/mouseStuff/netClass/makefile - lines changed 17, context: html, text, full: html, text
  • src/hg/mouseStuff/netFilter/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/mouseStuff/netSplit/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/mouseStuff/netStats/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/mouseStuff/netSyntenic/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/mouseStuff/netToAxt/makefile - lines changed 17, context: html, text, full: html, text
  • src/hg/mouseStuff/netToAxt/tests/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/mouseStuff/netToBed/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/mouseStuff/netToBedWithId/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/mouseStuff/orthologBySynteny/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/mouseStuff/phToPsl/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/mouseStuff/pslMrnaCover/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/mouseStuff/regionPicker/makefile - lines changed 17, context: html, text, full: html, text
  • src/hg/mouseStuff/rikenBestInCluster/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/mouseStuff/simpleChain/makefile - lines changed 17, context: html, text, full: html, text
  • src/hg/mouseStuff/splitSim/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/mouseStuff/subsetAxt/makefile - lines changed 15, context: html, text, full: html, text
  • src/hg/mouseStuff/subsetTraces/makefile - lines changed 13, context: html, text, full: html, text
  • src/hg/mouseStuff/whyConserved/makefile - lines changed 4, context: html, text, full: html, text
  • src/hg/ratStuff/mafAddIRows/makefile - lines changed 15, context: html, text, full: html, text
  • src/hg/ratStuff/mafAddQRows/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/ratStuff/mafFilter/makefile - lines changed 17, context: html, text, full: html, text
  • src/hg/ratStuff/mafFrag/makefile - lines changed 16, context: html, text, full: html, text
  • src/hg/ratStuff/mafFrags/expected/hg16.maf - lines changed 272, context: html, text, full: html, text
  • src/hg/ratStuff/mafFrags/makefile - lines changed 18, context: html, text, full: html, text
  • src/hg/ratStuff/mafGene/makefile - lines changed 16, context: html, text, full: html, text
  • src/hg/ratStuff/mafMeFirst/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/ratStuff/mafOrder/makefile - lines changed 17, context: html, text, full: html, text
  • src/hg/ratStuff/mafSpeciesList/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/ratStuff/mafSpeciesSubset/makefile - lines changed 16, context: html, text, full: html, text
  • src/hg/ratStuff/mafSplit/makefile - lines changed 19, context: html, text, full: html, text
  • src/hg/ratStuff/mafSplitPos/makefile - lines changed 16, context: html, text, full: html, text
  • src/hg/ratStuff/mafsInRegion/makefile - lines changed 16, context: html, text, full: html, text
  • src/hg/ratStuff/makefile - lines changed 8, context: html, text, full: html, text
  • src/hg/ratStuff/stageMultiz/makefile - lines changed 17, context: html, text, full: html, text
• perhaps last lot of makefiles converted to new minimal style refs #9104
  • src/hg/txCds/txCdsBadBed/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/txCds/txCdsCluster/makefile - lines changed 17, context: html, text, full: html, text
  • src/hg/txCds/txCdsEvFromBed/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/txCds/txCdsEvFromBorf/makefile - lines changed 17, context: html, text, full: html, text
  • src/hg/txCds/txCdsEvFromProtein/makefile - lines changed 17, context: html, text, full: html, text
  • src/hg/txCds/txCdsEvFromRna/makefile - lines changed 17, context: html, text, full: html, text
  • src/hg/txCds/txCdsGoodBed/makefile - lines changed 15, context: html, text, full: html, text
  • src/hg/txCds/txCdsOrfInfo/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/txCds/txCdsOrtho/makefile - lines changed 17, context: html, text, full: html, text
  • src/hg/txCds/txCdsPick/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/txCds/txCdsPredict/makefile - lines changed 17, context: html, text, full: html, text
  • src/hg/txCds/txCdsRaExceptions/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/txCds/txCdsRefBestEvOnly/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/txCds/txCdsRepick/makefile - lines changed 18, context: html, text, full: html, text
  • src/hg/txCds/txCdsSuspect/makefile - lines changed 17, context: html, text, full: html, text
  • src/hg/txCds/txCdsSvmInput/makefile - lines changed 17, context: html, text, full: html, text
  • src/hg/txCds/txCdsToGene/makefile - lines changed 17, context: html, text, full: html, text
  • src/hg/txCds/txCdsWeed/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/txCds/txInfoAssemble/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/txGene/txGeneAccession/makefile - lines changed 17, context: html, text, full: html, text
  • src/hg/txGene/txGeneAlias/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/txGene/txGeneAltProt/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/txGene/txGeneCanonical/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/txGene/txGeneCdsMap/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/txGene/txGeneColor/makefile - lines changed 15, context: html, text, full: html, text
  • src/hg/txGene/txGeneExplainUpdate1/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/txGene/txGeneFromBed/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/txGene/txGeneProtAndRna/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/txGene/txGeneSeparateNoncoding/makefile - lines changed 15, context: html, text, full: html, text
  • src/hg/txGene/txGeneXref/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/txGraph/agxToTxg/makefile - lines changed 18, context: html, text, full: html, text
  • src/hg/txGraph/bedToTxEdges/makefile - lines changed 17, context: html, text, full: html, text
  • src/hg/txGraph/txAbFragFind/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/txGraph/txBedToGraph/makefile - lines changed 17, context: html, text, full: html, text
  • src/hg/txGraph/txOrtho/makefile - lines changed 16, context: html, text, full: html, text
  • src/hg/txGraph/txPslFilter/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/txGraph/txPslToBed/makefile - lines changed 16, context: html, text, full: html, text
  • src/hg/txGraph/txReadRa/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/txGraph/txWalk/makefile - lines changed 16, context: html, text, full: html, text
  • src/hg/txGraph/txgAddEvidence/makefile - lines changed 16, context: html, text, full: html, text
  • src/hg/txGraph/txgAnalyze/makefile - lines changed 16, context: html, text, full: html, text
  • src/hg/txGraph/txgGoodEdges/makefile - lines changed 16, context: html, text, full: html, text
  • src/hg/txGraph/txgToAgx/makefile - lines changed 16, context: html, text, full: html, text
  • src/hg/txGraph/txgToXml/makefile - lines changed 16, context: html, text, full: html, text
  • src/hg/txGraph/txgTrim/makefile - lines changed 16, context: html, text, full: html, text
  • src/hg/utils/bedToPsl/makefile - lines changed 27, context: html, text, full: html, text
  • src/hg/utils/bedWeedOverlapping/makefile - lines changed 16, context: html, text, full: html, text
  • src/hg/utils/chromGraphFromBin/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/utils/chromGraphToBin/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/utils/crTreeIndexBed/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/utils/crTreeSearchBed/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/utils/positionalTblCheck/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/utils/pslUniq/makefile - lines changed 17, context: html, text, full: html, text
  • src/hg/utils/refreshNamedSessionCustomTracks/makefile - lines changed 19, context: html, text, full: html, text
  • src/hg/utils/safePush/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/utils/toDev64/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/utils/twoBitMask/makefile - lines changed 16, context: html, text, full: html, text
  • src/hg/utils/wigBedToStep/makefile - lines changed 14, context: html, text, full: html, text
• add makefile for running tests refs #9104
  • src/hg/bedItemOverlapCount/tests/makefile - lines changed 3, context: html, text, full: html, text
• add makefile for running tests refs #9104
  • src/utils/convolve/tests/makefile - lines changed 5, context: html, text, full: html, text
• do not use BINDIR in the tests makefile to reference the test program
  • src/hg/checkTableCoords/tests/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/pslHisto/tests/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/gff3ToGenePred/tests/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/gff3ToPsl/tests/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/overlapSelect/tests/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/pslMap/tests/makefile - lines changed 2, context: html, text, full: html, text
  • src/hg/utils/refSeqGet/tests/makefile - lines changed 1, context: html, text, full: html, text
  • src/utils/bedScore/tests/makefile - lines changed 1, context: html, text, full: html, text
• eliminate BINDIR from tests makefile, refs #9104
  • src/hg/altSplice/altSplice/tests/makefile - lines changed 9, context: html, text, full: html, text
  • src/hg/bedIntersect/tests/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/blastToPsl/tests/makefile - lines changed 4, context: html, text, full: html, text
  • src/hg/chimpStuff/chimpChromContigAgp/tests/makefile - lines changed 2, context: html, text, full: html, text
  • src/hg/encode/regionAgp/tests/makefile - lines changed 7, context: html, text, full: html, text
  • src/hg/genePredToGtf/tests/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/liftOver/tests/makefile - lines changed 17, context: html, text, full: html, text
  • src/hg/makeDb/hgLoadMaf/tests/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/mouseStuff/mafRanges/tests/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/tests/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/pslStats/tests/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/bedToPsl/tests/makefile - lines changed 1, context: html, text, full: html, text
  • src/utils/pslLiftSubrangeBlat/tests/makefile - lines changed 1, context: html, text, full: html, text
• correctly use DESTDIR with BINDIR refs #9104
  • src/hg/phyloGif/makefile - lines changed 2, context: html, text, full: html, text
• correctly using DESTDIR with BINDIR refs #9104
  • src/blatz/makefile - lines changed 6, context: html, text, full: html, text
  • src/isPcr/gfPcr/makefile - lines changed 2, context: html, text, full: html, text
  • src/isPcr/isPcr/makefile - lines changed 2, context: html, text, full: html, text
• 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/customFactory.c - lines changed 2, context: html, text, full: html, text
  • src/hg/lib/wigAsciiToBinary.c - lines changed 2, context: html, text, full: html, text
• add clean target to satisify that from the call above refs #9104
  • src/hg/bedItemOverlapCount/tests/makefile - lines changed 3, context: html, text, full: html, text