Commits for braney

v260_preview2 to v260_base (2011-11-22 to 2011-12-06) v260

• treat EOF as a legal end of paragraph. (#586)
  • src/lib/maf.c - lines changed 1, context: html, text, full: html, text
• change blat parameters to find sequences shorter than 30bp (per Jim, #20)
  • src/hg/makeDb/genbank/src/align/gbBlat - lines changed 1, context: html, text, full: html, text
• add sql file that corresponds to bedRnaElements.as,but with "not nulls" added
  • src/hg/encode/autoSql/bedRnaElements.sql - lines changed 20, context: html, text, full: html, text
• add the hubPublic and hubStatus autoSql definitions
  • src/hg/lib/hubPublic.as - lines changed 11, context: html, text, full: html, text
  • src/hg/lib/hubPublic.sql - lines changed 16, context: html, text, full: html, text
  • src/hg/lib/hubStatus.as - lines changed 15, context: html, text, full: html, text
  • src/hg/lib/hubStatus.sql - lines changed 20, context: html, text, full: html, text
• allow specifying different names for the hubPublic and hubStatus tables (#6162)
  • src/hg/hgHubConnect/hgHubConnect.c - lines changed 18, context: html, text, full: html, text
  • src/hg/hgTables/mainPage.c - lines changed 1, context: html, text, full: html, text
  • src/hg/hgTracks/hgTracks.c - lines changed 5, context: html, text, full: html, text
  • src/hg/inc/hgConfig.h - lines changed 4, context: html, text, full: html, text
  • src/hg/inc/hubConnect.h - lines changed 2, context: html, text, full: html, text
  • src/hg/lib/hgConfig.c - lines changed 9, context: html, text, full: html, text
  • src/hg/lib/hubConnect.c - lines changed 30, context: html, text, full: html, text
• fix problems with status field in hubStatus not reflecting the actual state of the hubPublic table. We're no longer using the status field (#5965)
  • src/hg/hgHubConnect/hgHubConnect.c - lines changed 20, context: html, text, full: html, text
  • src/hg/inc/hubConnect.h - lines changed 6, context: html, text, full: html, text
  • src/hg/lib/hubConnect.c - lines changed 16, context: html, text, full: html, text
• make it so it takes an argument that defines the table to use for hubPublic
  • src/hg/utils/hubPublicCheck/hubPublicCheck.c - lines changed 12, context: html, text, full: html, text
• fiddle a bit with the hg.conf variables to change hubPublc and hubStatus (#6162)
  • src/hg/hgHubConnect/hgHubConnect.c - lines changed 1, context: html, text, full: html, text
  • src/hg/inc/hubConnect.h - lines changed 10, context: html, text, full: html, text
  • src/hg/lib/hubConnect.c - lines changed 1, context: html, text, full: html, text
  • src/product/ex.hg.conf - lines changed 4, context: html, text, full: html, text
• add a firstAdded time to the hubStatus table. #5138
  • src/hg/lib/hubConnect.c - lines changed 6, context: html, text, full: html, text
  • src/hg/lib/hubStatus.as - lines changed 1, context: html, text, full: html, text
  • src/hg/lib/hubStatus.sql - lines changed 1, context: html, text, full: html, text
• removed rcsid (#295)
  • src/ai/growNet/growNet.c - lines changed 1, context: html, text, full: html, text
  • src/blat/blat.c - lines changed 1, context: html, text, full: html, text
  • src/fuse/udcFuse/udcFuse.c - lines changed 1, context: html, text, full: html, text
  • src/gfClient/gfClient.c - lines changed 1, context: html, text, full: html, text
  • src/gfServer/gfServer.c - lines changed 1, context: html, text, full: html, text
  • src/hg/affyGnf/affyPslAndAtlasToBed.c - lines changed 1, context: html, text, full: html, text
  • src/hg/affyGnf/affyUclaMergePslData.c - lines changed 11, context: html, text, full: html, text
  • src/hg/affyGnf/pslAffySelect.c - lines changed 1, context: html, text, full: html, text
  • src/hg/affyTransciptome/affyPairsToSample.c - lines changed 1, context: html, text, full: html, text
  • src/hg/affyTransciptome/affyTransLiftedToSample.c - lines changed 1, context: html, text, full: html, text
  • src/hg/affyTransciptome/averageZoomLevels.c - lines changed 1, context: html, text, full: html, text
  • src/hg/affyTransciptome/avgTranscriptomeExps.c - lines changed 1, context: html, text, full: html, text
  • src/hg/affyTransciptome/bulkChr2XRegression.c - lines changed 1, context: html, text, full: html, text
  • src/hg/affyTransciptome/groupSamples.c - lines changed 1, context: html, text, full: html, text
  • src/hg/affyTransciptome/htmlFromBeds.c - lines changed 1, context: html, text, full: html, text
  • src/hg/affyTransciptome/maxTranscriptomeExps.c - lines changed 1, context: html, text, full: html, text
  • src/hg/affyTransciptome/mergeAffyFiles.c - lines changed 1, context: html, text, full: html, text
  • src/hg/affyTransciptome/nmerAlign.c - lines changed 1, context: html, text, full: html, text
  • src/hg/affyTransciptome/nmerParasolGenome.c - lines changed 1, context: html, text, full: html, text
  • src/hg/affyTransciptome/normalizeSampleFile.c - lines changed 1, context: html, text, full: html, text
  • src/hg/affyTransciptome/pickCassettePcrPrimers.c - lines changed 1, context: html, text, full: html, text
  • src/hg/affyTransciptome/samplesForCoordinates.c - lines changed 1, context: html, text, full: html, text
  • src/hg/affyTransciptome/scaleSampleFiles.c - lines changed 1, context: html, text, full: html, text
  • src/hg/affyTransciptome/trackFromLifts.c - lines changed 1, context: html, text, full: html, text
  • src/hg/agpAllToFaFile/agpAllToFaFile.c - lines changed 1, context: html, text, full: html, text
  • src/hg/agpCloneCheck/agpCloneCheck.c - lines changed 1, context: html, text, full: html, text
  • src/hg/agpCloneList/agpCloneList.c - lines changed 1, context: html, text, full: html, text
  • src/hg/agpMergeChromScaf/agpMergeChromScaf.c - lines changed 1, context: html, text, full: html, text
  • src/hg/agpSangerUnfinished/agpSangerUnfinished.c - lines changed 1, context: html, text, full: html, text
  • src/hg/agpToFa/agpToFa.c - lines changed 1, context: html, text, full: html, text
  • src/hg/agpToGl/agpToGl.c - lines changed 1, context: html, text, full: html, text
  • src/hg/agpTweak/agpTweak.c - lines changed 1, context: html, text, full: html, text
  • src/hg/altGraph/altGraph.c - lines changed 1, context: html, text, full: html, text
  • src/hg/altGraph/test.c - lines changed 1, context: html, text, full: html, text
  • src/hg/altSplice/altSplice/altAnalysis.c - lines changed 1, context: html, text, full: html, text
  • src/hg/altSplice/altSplice/altPaths.c - lines changed 1, context: html, text, full: html, text
  • src/hg/altSplice/altSplice/altSplice.c - lines changed 1, context: html, text, full: html, text
  • src/hg/altSplice/altSplice/altSummary.c - lines changed 1, context: html, text, full: html, text
  • src/hg/altSplice/altSplice/correlateWithExpression.c - lines changed 1, context: html, text, full: html, text
  • src/hg/altSplice/altSplice/geneGraphTest.c - lines changed 1, context: html, text, full: html, text
  • src/hg/altSplice/altSplice/orthoSplice.c - lines changed 1, context: html, text, full: html, text
  • src/hg/altSplice/altSplice/spliceStats.c - lines changed 1, context: html, text, full: html, text
  • src/hg/altSplice/altSplice/testAltGraphXMem.c - lines changed 1, context: html, text, full: html, text
  • src/hg/altSplice/exonWalk/exonWalk.c - lines changed 1, context: html, text, full: html, text
  • src/hg/altSplice/lib/affyPres.c - lines changed 1, context: html, text, full: html, text
  • src/hg/altSplice/lib/affyProbe.c - lines changed 1, context: html, text, full: html, text
  • src/hg/altSplice/lib/altProbe.c - lines changed 1, context: html, text, full: html, text
  • src/hg/altSplice/lib/altSpliceSite.c - lines changed 1, context: html, text, full: html, text
  • src/hg/altSplice/lib/exonGraph.c - lines changed 1, context: html, text, full: html, text
  • src/hg/altSplice/lib/heap.c - lines changed 1, context: html, text, full: html, text
  • src/hg/altSplice/lib/heapTest.c - lines changed 1, context: html, text, full: html, text
  • src/hg/altSplice/lib/mouseAPSetEventMap.c - lines changed 1, context: html, text, full: html, text
  • src/hg/altSplice/lib/pfamDat.c - lines changed 1, context: html, text, full: html, text
  • src/hg/altSplice/lib/splice.c - lines changed 1, context: html, text, full: html, text
  • src/hg/altSplice/lib/spliceGraph.c - lines changed 1, context: html, text, full: html, text
  • src/hg/altSplice/spliceWalk/spliceWalk.c - lines changed 1, context: html, text, full: html, text
  • src/hg/autoDtd/autoDtd.c - lines changed 1, context: html, text, full: html, text
  • src/hg/autoSql/autoSql.c - lines changed 10, context: html, text, full: html, text
  • src/hg/autoSql/commonSh.c - lines changed 1, context: html, text, full: html, text
  • src/hg/autoSql/eztok.c - lines changed 1, context: html, text, full: html, text
  • src/hg/autoSql/tests/dbLinkTest.c - lines changed 1, context: html, text, full: html, text
  • src/hg/autoSql/tests/testHarness.c - lines changed 1, context: html, text, full: html, text
  • src/hg/autoSql/tests/testSymCols.c - lines changed 1, context: html, text, full: html, text
  • src/hg/autoXml/autoXml.c - lines changed 1, context: html, text, full: html, text
  • src/hg/autoXml/t/t.c - lines changed 1, context: html, text, full: html, text
  • src/hg/bedIntersect/bedIntersect.c - lines changed 1, context: html, text, full: html, text
  • src/hg/bedItemOverlapCount/bedItemOverlapCount.c - lines changed 1, context: html, text, full: html, text
  • src/hg/bedOrBlocks/bedOrBlocks.c - lines changed 1, context: html, text, full: html, text
  • src/hg/bedSort/bedSort.c - lines changed 1, context: html, text, full: html, text
  • src/hg/bedSplitOnChrom/bedSplitOnChrom.c - lines changed 1, context: html, text, full: html, text
  • src/hg/bedThickOnly/bedThickOnly.c - lines changed 1, context: html, text, full: html, text
  • src/hg/bedToGenePred/bedToGenePred.c - lines changed 1, context: html, text, full: html, text
  • src/hg/bioImage/loadMahoney/mahoney.c - lines changed 1, context: html, text, full: html, text
  • src/hg/blastToPsl/blastToPsl.c - lines changed 1, context: html, text, full: html, text
  • src/hg/blastToPsl/blastXmlToPsl.c - lines changed 1, context: html, text, full: html, text
  • src/hg/borfBig/borfBig.c - lines changed 1, context: html, text, full: html, text
  • src/hg/cartDump/cartDump.c - lines changed 1, context: html, text, full: html, text
  • src/hg/cartReset/cartReset.c - lines changed 1, context: html, text, full: html, text
  • src/hg/ccTrack/bedToBinDex/bedToBinDex.c - lines changed 1, context: html, text, full: html, text
  • src/hg/cgiExample/cgiExample.c - lines changed 1, context: html, text, full: html, text
  • src/hg/checkCoverageGaps/checkCoverageGaps.c - lines changed 1, context: html, text, full: html, text
  • src/hg/checkHgFindSpec/checkHgFindSpec.c - lines changed 1, context: html, text, full: html, text
  • src/hg/checkTableCoords/checkTableCoords.c - lines changed 1, context: html, text, full: html, text
  • src/hg/chimpStuff/chimpChromContigAgp/chimpChromContigAgp.c - lines changed 1, context: html, text, full: html, text
  • src/hg/chimpStuff/chimpHiQualDiffs/chimpHiQualDiffs.c - lines changed 1, context: html, text, full: html, text
  • src/hg/chimpStuff/chimpSuperQuals/chimpSuperQuals.c - lines changed 1, context: html, text, full: html, text
  • src/hg/ctgFaToFa/ctgFaToFa.c - lines changed 1, context: html, text, full: html, text
  • src/hg/ctgToChromFa/ctgToChromFa.c - lines changed 1, context: html, text, full: html, text
  • src/hg/das/das.c - lines changed 1, context: html, text, full: html, text
  • src/hg/dbTrash/dbTrash.c - lines changed 1, context: html, text, full: html, text
  • src/hg/embossToPsl/embossToPsl.c - lines changed 1, context: html, text, full: html, text
  • src/hg/encode/converters/pairedTagToBed12/pairedTagToBed12.c - lines changed 1, context: html, text, full: html, text
  • src/hg/encode/converters/tagToBed12/tagToBed12.c - lines changed 1, context: html, text, full: html, text
  • src/hg/encode/docId/docIdReport/docIdReport.c - lines changed 1, context: html, text, full: html, text
  • src/hg/encode/docId/docIdSubmitDir/docIdSubmitDir.c - lines changed 1, context: html, text, full: html, text
  • src/hg/encode/docId/docIdView/docIdView.c - lines changed 1, context: html, text, full: html, text
  • src/hg/encode/encodeMergeReplicates/encodeMergeReplicates.c - lines changed 1, context: html, text, full: html, text
  • src/hg/encode/encodeMergeReplicatesBatch/encodeMergeReplicatesBatch.c - lines changed 1, context: html, text, full: html, text
  • src/hg/encode/hgEncodeDataVersions/hgEncodeDataVersions.c - lines changed 1, context: html, text, full: html, text
  • src/hg/encode/hgEncodeScheduler/hgEncodeScheduler.c - lines changed 1, context: html, text, full: html, text
  • src/hg/encode/ldGencodeIntron/ldGencodeIntron.c - lines changed 1, context: html, text, full: html, text
  • src/hg/encode/lib/bedLogR.c - lines changed 1, context: html, text, full: html, text
  • src/hg/encode/metaCollect/metaCollect.c - lines changed 1, context: html, text, full: html, text
  • src/hg/encode/metaRename/metaRename.c - lines changed 1, context: html, text, full: html, text
  • src/hg/encode/regionAgp/regionAgp.c - lines changed 1, context: html, text, full: html, text
  • src/hg/extractPslForLfs/extractPslForLfs.c - lines changed 1, context: html, text, full: html, text
  • src/hg/fakeFinContigs/fakeFinContigs.c - lines changed 1, context: html, text, full: html, text
  • src/hg/fakeOut/fakeOut.c - lines changed 1, context: html, text, full: html, text
  • src/hg/featureBits/featureBits.c - lines changed 1, context: html, text, full: html, text
  • src/hg/ffaToFa/ffaToFa.c - lines changed 1, context: html, text, full: html, text
  • src/hg/fqToQa/fqToQa.c - lines changed 1, context: html, text, full: html, text
  • src/hg/fqToQac/fqToQac.c - lines changed 1, context: html, text, full: html, text
  • src/hg/fragPart/fragPart.c - lines changed 1, context: html, text, full: html, text
  • src/hg/gbGetEntries/gbGetEntries.c - lines changed 1, context: html, text, full: html, text
  • src/hg/gbOneAcc/gbOneAcc.c - lines changed 1, context: html, text, full: html, text
  • src/hg/gbToFaRa/gbToFaRa.c - lines changed 1, context: html, text, full: html, text
  • src/hg/geneBounds/assessLibs/assessLibs.c - lines changed 1, context: html, text, full: html, text
  • src/hg/geneBounds/averagExp/averagExp.c - lines changed 1, context: html, text, full: html, text
  • src/hg/geneBounds/axtForEst/axtForEst.c - lines changed 1, context: html, text, full: html, text
  • src/hg/geneBounds/bedCons/bedCons.c - lines changed 1, context: html, text, full: html, text
  • src/hg/geneBounds/bedThickToCds/bedThickToCds.c - lines changed 1, context: html, text, full: html, text
  • src/hg/geneBounds/checkableBorf/checkableBorf.c - lines changed 1, context: html, text, full: html, text
  • src/hg/geneBounds/clusterGenes/clusterGenes.c - lines changed 1, context: html, text, full: html, text
  • src/hg/geneBounds/clusterPsl/clusterPsl.c - lines changed 1, context: html, text, full: html, text
  • src/hg/geneBounds/clusterRna/clusterRna.c - lines changed 1, context: html, text, full: html, text
  • src/hg/geneBounds/dnaMotifFind/dnaMotifFind.c - lines changed 1, context: html, text, full: html, text
  • src/hg/geneBounds/eisenInput/eisenInput.c - lines changed 1, context: html, text, full: html, text
  • src/hg/geneBounds/emblMatrixToMotif/emblMatrixToMotif.c - lines changed 1, context: html, text, full: html, text
  • src/hg/geneBounds/estLibStats/estLibStats.c - lines changed 1, context: html, text, full: html, text
  • src/hg/geneBounds/expToRna/expToRna.c - lines changed 1, context: html, text, full: html, text
  • src/hg/geneBounds/iriToControlTable/iriToControlTable.c - lines changed 1, context: html, text, full: html, text
  • src/hg/geneBounds/iriToDnaMotif/iriToDnaMotif.c - lines changed 1, context: html, text, full: html, text
  • src/hg/geneBounds/lib/improbRunInfo.c - lines changed 1, context: html, text, full: html, text
  • src/hg/geneBounds/liftPromoHits/liftPromoHits.c - lines changed 1, context: html, text, full: html, text
  • src/hg/geneBounds/motifLogo/motifLogo.c - lines changed 1, context: html, text, full: html, text
  • src/hg/geneBounds/motifSig/motifSig.c - lines changed 1, context: html, text, full: html, text
  • src/hg/geneBounds/orf/orf.c - lines changed 1, context: html, text, full: html, text
  • src/hg/geneBounds/orfCompare/orfCompare.c - lines changed 1, context: html, text, full: html, text
  • src/hg/geneBounds/orfEnum/orfEnum.c - lines changed 1, context: html, text, full: html, text
  • src/hg/geneBounds/orfStats/orfStats.c - lines changed 1, context: html, text, full: html, text
  • src/hg/geneBounds/polyInfo/polyInfo.c - lines changed 1, context: html, text, full: html, text
  • src/hg/geneBounds/promoSeqFromCluster/promoSeqFromCluster.c - lines changed 1, context: html, text, full: html, text
  • src/hg/geneBounds/raToCds/raToCds.c - lines changed 1, context: html, text, full: html, text
  • src/hg/geneBounds/twinOrf/twinOrf.c - lines changed 1, context: html, text, full: html, text
  • src/hg/geneBounds/twinOrf2/twinOrf2.c - lines changed 1, context: html, text, full: html, text
  • src/hg/geneBounds/twinOrf3/twinOrf3.c - lines changed 1, context: html, text, full: html, text
  • src/hg/geneBounds/twinOrfStats/twinOrfStats.c - lines changed 1, context: html, text, full: html, text
  • src/hg/geneBounds/twinOrfStats2/twinOrfStats2.c - lines changed 1, context: html, text, full: html, text
  • src/hg/geneBounds/twinOrfStats3/twinOrfStats3.c - lines changed 1, context: html, text, full: html, text
  • src/hg/genePredCheck/genePredCheck.c - lines changed 1, context: html, text, full: html, text
  • src/hg/genePredHisto/genePredHisto.c - lines changed 1, context: html, text, full: html, text
  • src/hg/genePredSingleCover/genePredSingleCover.c - lines changed 1, context: html, text, full: html, text
  • src/hg/genePredSingleCover/geneScore.c - lines changed 1, context: html, text, full: html, text
  • src/hg/genePredToFakePsl/genePredToFakePsl.c - lines changed 1, context: html, text, full: html, text
  • src/hg/genePredToGtf/genePredToGtf.c - lines changed 1, context: html, text, full: html, text
  • src/hg/genePredToMafFrames/genePredToMafFrames.c - lines changed 1, context: html, text, full: html, text
  • src/hg/genoPheno/gpFakeData/gpFakeData.c - lines changed 1, context: html, text, full: html, text
  • src/hg/genoPheno/gpShuffleData/gpShuffleData.c - lines changed 1, context: html, text, full: html, text
  • src/hg/getFeatDna/getFeatDna.c - lines changed 1, context: html, text, full: html, text
  • src/hg/getRna/getRna.c - lines changed 1, context: html, text, full: html, text
  • src/hg/getRnaPred/getRnaPred.c - lines changed 1, context: html, text, full: html, text
  • src/hg/gigAssembler/barger/barger.c - lines changed 1, context: html, text, full: html, text
  • src/hg/gigAssembler/checkAgpAndFa/checkAgpAndFa.c - lines changed 1, context: html, text, full: html, text
  • src/hg/gigAssembler/checkDbSync/checkDbSync.c - lines changed 1, context: html, text, full: html, text
  • src/hg/gigAssembler/checkGoldDupes/checkGoldDupes.c - lines changed 1, context: html, text, full: html, text
  • src/hg/gigAssembler/checkN/checkN.c - lines changed 1, context: html, text, full: html, text
  • src/hg/gigAssembler/checkNt/checkNt.c - lines changed 1, context: html, text, full: html, text
  • src/hg/gigAssembler/checkOut/checkOut.c - lines changed 1, context: html, text, full: html, text
  • src/hg/gigAssembler/checkPsl/checkPsl.c - lines changed 1, context: html, text, full: html, text
  • src/hg/gigAssembler/checkQa/checkQa.c - lines changed 1, context: html, text, full: html, text
  • src/hg/gigAssembler/checkYbr/checkYbr.c - lines changed 1, context: html, text, full: html, text
  • src/hg/gigAssembler/cmParse/cmParse.c - lines changed 1, context: html, text, full: html, text
  • src/hg/gigAssembler/cmParse/imreClone.c - lines changed 1, context: html, text, full: html, text
  • src/hg/gigAssembler/cmpMap/cmpMap.c - lines changed 1, context: html, text, full: html, text
  • src/hg/gigAssembler/codJobs/jabba/jabba.c - lines changed 1, context: html, text, full: html, text
  • src/hg/gigAssembler/codJobs/jabba/jobDb.c - lines changed 1, context: html, text, full: html, text
  • src/hg/gigAssembler/conJobs/cdnaOnOoJobs/cdnaOnOoJobs.c - lines changed 1, context: html, text, full: html, text
  • src/hg/gigAssembler/conJobs/patJobs/opatJobs.c - lines changed 1, context: html, text, full: html, text
  • src/hg/gigAssembler/conJobs/patJobs/patJobs.c - lines changed 1, context: html, text, full: html, text
  • src/hg/gigAssembler/conJobs/pslGenoJobs/makeFix.c - lines changed 1, context: html, text, full: html, text
  • src/hg/gigAssembler/conJobs/pslGenoJobs/pslGenoJobs.c - lines changed 1, context: html, text, full: html, text
  • src/hg/gigAssembler/conJobs/pslGenoJobs/test.c - lines changed 1, context: html, text, full: html, text
  • src/hg/gigAssembler/conJobs/pslOoJobs/pslOoJobs.c - lines changed 1, context: html, text, full: html, text
  • src/hg/gigAssembler/conJobs/pslSelfJobs/pslSelfJobs.c - lines changed 1, context: html, text, full: html, text
  • src/hg/gigAssembler/conJobs/repMaskJobs/repMaskJobs.c - lines changed 1, context: html, text, full: html, text
  • src/hg/gigAssembler/conJobs/rmskOoJobs/rmskOoJobs.c - lines changed 1, context: html, text, full: html, text
  • src/hg/gigAssembler/g2gOverlap/g2gOverlap.c - lines changed 1, context: html, text, full: html, text
  • src/hg/gigAssembler/g2gSeqOverlap/g2gSeqOverlap.c - lines changed 1, context: html, text, full: html, text
  • src/hg/gigAssembler/gapper/gapper.c - lines changed 1, context: html, text, full: html, text
  • src/hg/gigAssembler/goldToAgp/goldToAgp.c - lines changed 1, context: html, text, full: html, text
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• oops, missed this rcsid related problem
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• always load non-coding, not just when it's part of RefSeq (part of #20)
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