Commits for hiram

v234_preview to v234_base (2010-06-15 to 2010-06-22) v234

• need to have -lz on this link
  • src/utils/wigCorrelate/makefile - lines changed 1, context: html, text, full: html, text
• Merge branch 'master' of hiram@hgwdev.cse.ucsc.edu:/data/git/kent
• reload genomicSuperDups;
  • src/hg/makeDb/doc/hg18.txt - lines changed 25, context: html, text, full: html, text
• last bunch of makefiles that need a clean target
  • src/ai/paraFlow/aceTools/makefile - lines changed 2, context: html, text, full: html, text
  • src/ai/paraFlow/compiler/makefile - lines changed 3, context: html, text, full: html, text
  • src/ai/paraFlow/runAsm/makefile - lines changed 2, context: html, text, full: html, text
  • src/ai/paraFlow/runtime/makefile - lines changed 2, context: html, text, full: html, text
  • src/cbAli/makefile - lines changed 2, context: html, text, full: html, text
  • src/cdnaAli/ali2alx/makefile - lines changed 2, context: html, text, full: html, text
  • src/cdnaAli/aliGlue/makefile - lines changed 3, context: html, text, full: html, text
  • src/cdnaAli/binGood/makefile - lines changed 2, context: html, text, full: html, text
  • src/cdnaAli/cdnaOff/makefile - lines changed 2, context: html, text, full: html, text
  • src/cdnaAli/cluster/makefile - lines changed 2, context: html, text, full: html, text
  • src/cdnaAli/exonAli/makefile - lines changed 2, context: html, text, full: html, text
  • src/cdnaAli/findCdna/makefile - lines changed 3, context: html, text, full: html, text
  • src/cdnaAli/lib/makefile - lines changed 2, context: html, text, full: html, text
  • src/cdnaAli/pairClo/makefile - lines changed 2, context: html, text, full: html, text
  • src/cdnaAli/patCount/makefile - lines changed 3, context: html, text, full: html, text
  • src/cdnaAli/patSpace/makefile - lines changed 2, context: html, text, full: html, text
  • src/cdnaAli/refineAli/makefile - lines changed 2, context: html, text, full: html, text
  • src/cdnaAli/sortFilt/makefile - lines changed 2, context: html, text, full: html, text
  • src/cdnaAli/stitchea/makefile - lines changed 2, context: html, text, full: html, text
  • src/gfClient/makefile - lines changed 3, context: html, text, full: html, text
  • src/gfServer/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/altSplice/affySplice/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/altSplice/axtCountBeds/makefile - lines changed 4, context: html, text, full: html, text
  • src/hg/altSplice/spliceWalk/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/autoXml/t/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/bedOverlap/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/bioImage/hgBioImage/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/encode/hgEncodeDataVersions/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/encode/hgEncodeVocab/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/gigAssembler/barger/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/gigAssembler/checkDbSync/makefile - lines changed 2, context: html, text, full: html, text
  • src/hg/gigAssembler/checkGoldDupes/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/gigAssembler/checkN/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/gigAssembler/checkNt/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/gigAssembler/checkOut/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/gigAssembler/checkPsl/makefile - lines changed 4, context: html, text, full: html, text
  • src/hg/gigAssembler/checkQa/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/gigAssembler/checkYbr/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/gigAssembler/cmParse/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/gigAssembler/cmpMap/makefile - lines changed 4, context: html, text, full: html, text
  • src/hg/gigAssembler/codJobs/jabba/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/gigAssembler/conJobs/cdnaOnOoJobs/makefile - lines changed 2, context: html, text, full: html, text
  • src/hg/gigAssembler/conJobs/patJobs/makefile - lines changed 2, context: html, text, full: html, text
  • src/hg/gigAssembler/conJobs/pslGenoJobs/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/gigAssembler/conJobs/pslOoJobs/makefile - lines changed 2, context: html, text, full: html, text
  • src/hg/gigAssembler/conJobs/pslSelfJobs/makefile - lines changed 4, context: html, text, full: html, text
  • src/hg/gigAssembler/conJobs/repMaskJobs/makefile - lines changed 2, context: html, text, full: html, text
  • src/hg/gigAssembler/conJobs/rmskOoJobs/makefile - lines changed 2, context: html, text, full: html, text
  • src/hg/gigAssembler/g2gOverlap/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/gigAssembler/g2gSeqOverlap/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/gigAssembler/gapper/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/gigAssembler/goldToAgp/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/gigAssembler/makePai/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/gigAssembler/mendMap/makefile - lines changed 2, context: html, text, full: html, text
  • src/hg/gigAssembler/mm/checkEnds/makefile - lines changed 2, context: html, text, full: html, text
  • src/hg/gigAssembler/mm/mm/makefile - lines changed 2, context: html, text, full: html, text
  • src/hg/gigAssembler/mm/mmTestSet/makefile - lines changed 2, context: html, text, full: html, text
  • src/hg/gigAssembler/mm/ooMapMend/makefile - lines changed 2, context: html, text, full: html, text
  • src/hg/gigAssembler/ntGoldGl/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/gigAssembler/ooChains/makefile - lines changed 4, context: html, text, full: html, text
  • src/hg/gigAssembler/ooCloneEnds/makefile - lines changed 2, context: html, text, full: html, text
  • src/hg/gigAssembler/ooCloneInfo/makefile - lines changed 2, context: html, text, full: html, text
  • src/hg/gigAssembler/ooCloneOverlaps/makefile - lines changed 2, context: html, text, full: html, text
  • src/hg/gigAssembler/ooCloneSizes/makefile - lines changed 2, context: html, text, full: html, text
  • src/hg/gigAssembler/ooCloneSpan/makefile - lines changed 2, context: html, text, full: html, text
  • src/hg/gigAssembler/ooGreedy/bak/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/gigAssembler/ooGreedy/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/gigAssembler/ooLiftSpec/makefile - lines changed 2, context: html, text, full: html, text
  • src/hg/gigAssembler/ooNtInput/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/gigAssembler/ooSplitFins/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/gigAssembler/ooTester/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/gigAssembler/ooWeedZero/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/gigAssembler/pairedReads/makefile - lines changed 6, context: html, text, full: html, text
  • src/hg/gigAssembler/pairedReads/ppAnalyse/makefile - lines changed 2, context: html, text, full: html, text
  • src/hg/gigAssembler/pairedReads/ppSanger/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/gigAssembler/pairedReads/ppStats/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/gigAssembler/pairedReads/ppWashU/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/gigAssembler/pairedReads/ppWhitehead/makefile - lines changed 2, context: html, text, full: html, text
  • src/hg/gigAssembler/psLayout/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/gigAssembler/qaGold/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/gisaid/gisaidSample/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/gisaid/makefile - lines changed 4, context: html, text, full: html, text
  • src/hg/gsid/gsidPbGateway/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/gsid/gsidTable/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/hgApi/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/hgBlat/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/hgGeneRing/makefile - lines changed 4, context: html, text, full: html, text
  • src/hg/hgTracks/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/pbTracksHelpFiles/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/hgAar/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/hgAddLiftOverChain/makefile - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/hgExperiment/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/hgExtFileCheck/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/hgFindSpec/makefile - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/hgGeneBands/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/hgKgMrna/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/hgLoadAxt/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/hgLoadBlastTab/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/hgLoadSample/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/hgLoadSqlTab/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/hgMedianMicroarray/makefile - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/hgMrnaRefseq/makefile - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/hgRatioMicroarray/makefile - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/hgRgdParsePathwayObo/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/hgSanger20/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/hgSanger22/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/hgStanfordMicroarray/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/hgTpf/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/htTpf/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/makeLoChain/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/outside/ensembl/makefile - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/outside/hgAvidShortBed/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/outside/hgBioCyc/makefile - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/outside/hgCGAP/makefile - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/outside/hgExonerate/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/outside/hgFiberglass/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/outside/hgFlyBase/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/outside/hgGnfMicroarray/makefile - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/outside/hgKegg/makefile - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/outside/hgKegg2/makefile - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/outside/hgKegg3/makefile - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/outside/hgLoadEranModules/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/outside/hgPhMouse/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/outside/hgSoftPromoter/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/outside/hgSoftberryHom/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/outside/hgSuperfam/makefile - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/outside/makefile - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/outside/sanger22gtf/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/outside/vegaBuildInfo/makefile - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/outside/yeast/hgSgdGff3/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/outside/yeast/hgSgdGfp/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/outside/yeast/hgSgdPep/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/schema/joinerGraph/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/schema/makefile - lines changed 23, context: html, text, full: html, text
  • src/hg/makeDb/tfbsConsSort/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDbRaFormat/makefile - lines changed 6, context: html, text, full: html, text
  • src/hg/makeSeqs/makefile - lines changed 4, context: html, text, full: html, text
  • src/hg/nci60/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/near/hgZfishEnsXRef/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/phyloGif/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/poster/finPoster/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/pslAnal/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/pslToPileup/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/qaPushQ/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/secure/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/snp/fixedDiffs/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/synMap/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/tutorial/cgiAlign/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/rgdGeneXref2/makefile - lines changed 2, context: html, text, full: html, text
  • src/hg/utils/ruby/makefile - lines changed 2, context: html, text, full: html, text
  • src/hg/visiGene/gensat/makefile - lines changed 25, context: html, text, full: html, text
  • src/hg/visiGene/hgVisiGene/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/visiGene/jackson/makefile - lines changed 25, context: html, text, full: html, text
  • src/hg/visiGene/makefile - lines changed 20, context: html, text, full: html, text
  • src/hg/wikiPlot/makefile - lines changed 3, context: html, text, full: html, text
  • src/shortReads/makefile - lines changed 38, context: html, text, full: html, text
  • src/utils/aNotB/makefile - lines changed 3, context: html, text, full: html, text
  • src/utils/addCols/makefile - lines changed 2, context: html, text, full: html, text
  • src/utils/ave/makefile - lines changed 5, context: html, text, full: html, text
  • src/utils/aveCols/makefile - lines changed 2, context: html, text, full: html, text
  • src/utils/cCp/makefile - lines changed 2, context: html, text, full: html, text
  • src/utils/calc/makefile - lines changed 3, context: html, text, full: html, text
  • src/utils/callGraph/makefile - lines changed 3, context: html, text, full: html, text
  • src/utils/catDir/makefile - lines changed 3, context: html, text, full: html, text
  • src/utils/catUncomment/makefile - lines changed 2, context: html, text, full: html, text
  • src/utils/ccCp/makefile - lines changed 2, context: html, text, full: html, text
  • src/utils/ccCpLock/makefile - lines changed 2, context: html, text, full: html, text
  • src/utils/chopFaLines/makefile - lines changed 2, context: html, text, full: html, text
  • src/utils/colCount/makefile - lines changed 2, context: html, text, full: html, text
  • src/utils/countChars/makefile - lines changed 2, context: html, text, full: html, text
  • src/utils/cvsTools/makefile - lines changed 3, context: html, text, full: html, text
  • src/utils/detab/makefile - lines changed 3, context: html, text, full: html, text
  • src/utils/dnsInfo/makefile - lines changed 3, context: html, text, full: html, text
  • src/utils/endsInLf/makefile - lines changed 3, context: html, text, full: html, text
  • src/utils/faCmp/makefile - lines changed 3, context: html, text, full: html, text
  • src/utils/faFilterN/makefile - lines changed 3, context: html, text, full: html, text
  • src/utils/faFlyBaseToUcsc/makefile - lines changed 3, context: html, text, full: html, text
  • src/utils/faGapLocs/makefile - lines changed 2, context: html, text, full: html, text
  • src/utils/faGapSizes/makefile - lines changed 2, context: html, text, full: html, text
  • src/utils/faNcbiToUcsc/makefile - lines changed 3, context: html, text, full: html, text
  • src/utils/faNoise/makefile - lines changed 2, context: html, text, full: html, text
  • src/utils/faPolyASizes/makefile - lines changed 3, context: html, text, full: html, text
  • src/utils/faRc/makefile - lines changed 3, context: html, text, full: html, text
  • src/utils/faSimplify/makefile - lines changed 3, context: html, text, full: html, text
  • src/utils/faToTab/makefile - lines changed 3, context: html, text, full: html, text
  • src/utils/faTrans/makefile - lines changed 3, context: html, text, full: html, text
  • src/utils/faTrimPolyA/makefile - lines changed 3, context: html, text, full: html, text
  • src/utils/fixCr/makefile - lines changed 2, context: html, text, full: html, text
  • src/utils/genFedTableDef/makefile - lines changed 2, context: html, text, full: html, text
  • src/utils/geneStarts/makefile - lines changed 2, context: html, text, full: html, text
  • src/utils/gffPeek/makefile - lines changed 3, context: html, text, full: html, text
  • src/utils/gitTools/makefile - lines changed 3, context: html, text, full: html, text
  • src/utils/htmlPics/makefile - lines changed 2, context: html, text, full: html, text
  • src/utils/jkUniq/makefile - lines changed 2, context: html, text, full: html, text
  • src/utils/lineCount/makefile - lines changed 3, context: html, text, full: html, text
  • src/utils/nibCheck/makefile - lines changed 3, context: html, text, full: html, text
  • src/utils/nibSize/makefile - lines changed 2, context: html, text, full: html, text
  • src/utils/nt4Frag/makefile - lines changed 3, context: html, text, full: html, text
  • src/utils/pslPosTarget/makefile - lines changed 3, context: html, text, full: html, text
  • src/utils/pslToPslx/makefile - lines changed 3, context: html, text, full: html, text
  • src/utils/pslToXa/makefile - lines changed 3, context: html, text, full: html, text
  • src/utils/qa/makefile - lines changed 3, context: html, text, full: html, text
  • src/utils/raToLines/makefile - lines changed 2, context: html, text, full: html, text
  • src/utils/randomLines/makefile - lines changed 3, context: html, text, full: html, text
  • src/utils/rmFaDups/makefile - lines changed 2, context: html, text, full: html, text
  • src/utils/scrambleFa/makefile - lines changed 2, context: html, text, full: html, text
  • src/utils/sizeof/makefile - lines changed 2, context: html, text, full: html, text
  • src/utils/sortFa/makefile - lines changed 2, context: html, text, full: html, text
  • src/utils/spacedToTab/makefile - lines changed 3, context: html, text, full: html, text
  • src/utils/splitFile/makefile - lines changed 3, context: html, text, full: html, text
  • src/utils/stringify/makefile - lines changed 3, context: html, text, full: html, text
  • src/utils/subChar/makefile - lines changed 2, context: html, text, full: html, text
  • src/utils/subs/makefile - lines changed 2, context: html, text, full: html, text
  • src/utils/tableSum/makefile - lines changed 3, context: html, text, full: html, text
  • src/utils/textHist2/makefile - lines changed 3, context: html, text, full: html, text
  • src/utils/tickToDate/makefile - lines changed 3, context: html, text, full: html, text
  • src/utils/toLower/makefile - lines changed 2, context: html, text, full: html, text
  • src/utils/toUpper/makefile - lines changed 2, context: html, text, full: html, text
  • src/utils/undupFa/makefile - lines changed 2, context: html, text, full: html, text
  • src/utils/upper/makefile - lines changed 2, context: html, text, full: html, text
  • src/utils/venn/makefile - lines changed 3, context: html, text, full: html, text
  • src/utils/wordLine/makefile - lines changed 2, context: html, text, full: html, text
  • src/xenoAli/aliStats/makefile - lines changed 3, context: html, text, full: html, text
  • src/xenoAli/blastStats/makefile - lines changed 3, context: html, text, full: html, text
  • src/xenoAli/cbAli/makefile - lines changed 3, context: html, text, full: html, text
  • src/xenoAli/newIntron/makefile - lines changed 3, context: html, text, full: html, text
  • src/xenoAli/smithWat/makefile - lines changed 3, context: html, text, full: html, text
  • src/xenoAli/waba/makefile - lines changed 3, context: html, text, full: html, text
  • src/xenoAli/xaShow/makefile - lines changed 2, context: html, text, full: html, text
  • src/xenoAli/xenWorm/makefile - lines changed 3, context: html, text, full: html, text
• adding clean targets to makefiles reached via clean_utils
  • src/hg/affyTransciptome/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/agpCloneList/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/agpToGl/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/bedIntersect/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/checkHgFindSpec/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/ctgFaToFa/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/fakeOut/makefile - lines changed 2, context: html, text, full: html, text
  • src/hg/ffaToFa/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/fqToQa/makefile - lines changed 3, context: html, text, full: html, text
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• Merge branch 'master' of hiram@hgwdev.cse.ucsc.edu:/data/git/kent
• fixup bedToBigBed usage message -k2,2n
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