File Changes for braney
switch to commits view, user indexv260_preview2 to v260_base (2011-11-22 to 2011-12-06) v260
- src/ai/growNet/growNet.c
- src/blat/blat.c
- src/fuse/udcFuse/udcFuse.c
- src/gfClient/gfClient.c
- src/gfServer/gfServer.c
- src/hg/affyGnf/affyPslAndAtlasToBed.c
- src/hg/affyGnf/affyUclaMergePslData.c
- src/hg/affyGnf/pslAffySelect.c
- src/hg/affyTransciptome/affyPairsToSample.c
- src/hg/affyTransciptome/affyTransLiftedToSample.c
- src/hg/affyTransciptome/averageZoomLevels.c
- src/hg/affyTransciptome/avgTranscriptomeExps.c
- src/hg/affyTransciptome/bulkChr2XRegression.c
- src/hg/affyTransciptome/groupSamples.c
- src/hg/affyTransciptome/htmlFromBeds.c
- src/hg/affyTransciptome/maxTranscriptomeExps.c
- src/hg/affyTransciptome/mergeAffyFiles.c
- src/hg/affyTransciptome/nmerAlign.c
- src/hg/affyTransciptome/nmerParasolGenome.c
- src/hg/affyTransciptome/normalizeSampleFile.c
- src/hg/affyTransciptome/pickCassettePcrPrimers.c
- src/hg/affyTransciptome/samplesForCoordinates.c
- src/hg/affyTransciptome/scaleSampleFiles.c
- src/hg/affyTransciptome/trackFromLifts.c
- src/hg/agpAllToFaFile/agpAllToFaFile.c
- src/hg/agpCloneCheck/agpCloneCheck.c
- src/hg/agpCloneList/agpCloneList.c
- src/hg/agpMergeChromScaf/agpMergeChromScaf.c
- src/hg/agpSangerUnfinished/agpSangerUnfinished.c
- src/hg/agpToFa/agpToFa.c
- src/hg/agpToGl/agpToGl.c
- src/hg/agpTweak/agpTweak.c
- src/hg/altGraph/altGraph.c
- src/hg/altGraph/test.c
- src/hg/altSplice/altSplice/altAnalysis.c
- src/hg/altSplice/altSplice/altPaths.c
- src/hg/altSplice/altSplice/altSplice.c
- src/hg/altSplice/altSplice/altSummary.c
- src/hg/altSplice/altSplice/correlateWithExpression.c
- src/hg/altSplice/altSplice/geneGraphTest.c
- src/hg/altSplice/altSplice/orthoSplice.c
- src/hg/altSplice/altSplice/spliceStats.c
- src/hg/altSplice/altSplice/testAltGraphXMem.c
- src/hg/altSplice/exonWalk/exonWalk.c
- src/hg/altSplice/lib/affyPres.c
- src/hg/altSplice/lib/affyProbe.c
- src/hg/altSplice/lib/altProbe.c
- src/hg/altSplice/lib/altSpliceSite.c
- src/hg/altSplice/lib/exonGraph.c
- src/hg/altSplice/lib/heap.c
- src/hg/altSplice/lib/heapTest.c
- src/hg/altSplice/lib/mouseAPSetEventMap.c
- src/hg/altSplice/lib/pfamDat.c
- src/hg/altSplice/lib/splice.c
- src/hg/altSplice/lib/spliceGraph.c
- src/hg/altSplice/spliceWalk/spliceWalk.c
- src/hg/autoDtd/autoDtd.c
- src/hg/autoSql/autoSql.c
- src/hg/autoSql/commonSh.c
- src/hg/autoSql/eztok.c
- src/hg/autoSql/tests/dbLinkTest.c
- src/hg/autoSql/tests/makefile
- lines changed 2, context: html, text, full: html, text
oops, missed this rcsid related problem
- src/hg/autoSql/tests/testHarness.c
- src/hg/autoSql/tests/testSymCols.c
- src/hg/autoXml/autoXml.c
- src/hg/autoXml/t/t.c
- src/hg/bedIntersect/bedIntersect.c
- src/hg/bedItemOverlapCount/bedItemOverlapCount.c
- src/hg/bedOrBlocks/bedOrBlocks.c
- src/hg/bedSort/bedSort.c
- src/hg/bedSplitOnChrom/bedSplitOnChrom.c
- src/hg/bedThickOnly/bedThickOnly.c
- src/hg/bedToGenePred/bedToGenePred.c
- src/hg/bioImage/loadMahoney/mahoney.c
- src/hg/blastToPsl/blastToPsl.c
- src/hg/blastToPsl/blastXmlToPsl.c
- src/hg/borfBig/borfBig.c
- src/hg/cartDump/cartDump.c
- src/hg/cartReset/cartReset.c
- src/hg/ccTrack/bedToBinDex/bedToBinDex.c
- src/hg/cgiExample/cgiExample.c
- src/hg/checkCoverageGaps/checkCoverageGaps.c
- src/hg/checkHgFindSpec/checkHgFindSpec.c
- src/hg/checkTableCoords/checkTableCoords.c
- src/hg/chimpStuff/chimpChromContigAgp/chimpChromContigAgp.c
- src/hg/chimpStuff/chimpHiQualDiffs/chimpHiQualDiffs.c
- src/hg/chimpStuff/chimpSuperQuals/chimpSuperQuals.c
- src/hg/ctgFaToFa/ctgFaToFa.c
- src/hg/ctgToChromFa/ctgToChromFa.c
- src/hg/das/das.c
- src/hg/dbTrash/dbTrash.c
- src/hg/embossToPsl/embossToPsl.c
- src/hg/encode/autoSql/bedRnaElements.sql
- lines changed 20, context: html, text, full: html, text
add sql file that corresponds to bedRnaElements.as,but with "not nulls" added
- src/hg/encode/converters/pairedTagToBed12/pairedTagToBed12.c
- src/hg/encode/converters/tagToBed12/tagToBed12.c
- src/hg/encode/docId/docIdReport/docIdReport.c
- src/hg/encode/docId/docIdSubmitDir/docIdSubmitDir.c
- src/hg/encode/docId/docIdView/docIdView.c
- src/hg/encode/encodeMergeReplicates/encodeMergeReplicates.c
- src/hg/encode/encodeMergeReplicatesBatch/encodeMergeReplicatesBatch.c
- src/hg/encode/hgEncodeDataVersions/hgEncodeDataVersions.c
- src/hg/encode/hgEncodeScheduler/hgEncodeScheduler.c
- src/hg/encode/ldGencodeIntron/ldGencodeIntron.c
- src/hg/encode/lib/bedLogR.c
- src/hg/encode/metaCollect/metaCollect.c
- src/hg/encode/metaRename/metaRename.c
- src/hg/encode/regionAgp/regionAgp.c
- src/hg/extractPslForLfs/extractPslForLfs.c
- src/hg/fakeFinContigs/fakeFinContigs.c
- src/hg/fakeOut/fakeOut.c
- src/hg/featureBits/featureBits.c
- src/hg/ffaToFa/ffaToFa.c
- src/hg/fqToQa/fqToQa.c
- src/hg/fqToQac/fqToQac.c
- src/hg/fragPart/fragPart.c
- src/hg/gbGetEntries/gbGetEntries.c
- src/hg/gbOneAcc/gbOneAcc.c
- src/hg/gbToFaRa/gbToFaRa.c
- src/hg/geneBounds/assessLibs/assessLibs.c
- src/hg/geneBounds/averagExp/averagExp.c
- src/hg/geneBounds/axtForEst/axtForEst.c
- src/hg/geneBounds/bedCons/bedCons.c
- src/hg/geneBounds/bedThickToCds/bedThickToCds.c
- src/hg/geneBounds/checkableBorf/checkableBorf.c
- src/hg/geneBounds/clusterGenes/clusterGenes.c
- src/hg/geneBounds/clusterPsl/clusterPsl.c
- src/hg/geneBounds/clusterRna/clusterRna.c
- src/hg/geneBounds/dnaMotifFind/dnaMotifFind.c
- src/hg/geneBounds/eisenInput/eisenInput.c
- src/hg/geneBounds/emblMatrixToMotif/emblMatrixToMotif.c
- src/hg/geneBounds/estLibStats/estLibStats.c
- src/hg/geneBounds/expToRna/expToRna.c
- src/hg/geneBounds/iriToControlTable/iriToControlTable.c
- src/hg/geneBounds/iriToDnaMotif/iriToDnaMotif.c
- src/hg/geneBounds/lib/improbRunInfo.c
- src/hg/geneBounds/liftPromoHits/liftPromoHits.c
- src/hg/geneBounds/motifLogo/motifLogo.c
- src/hg/geneBounds/motifSig/motifSig.c
- src/hg/geneBounds/orf/orf.c
- src/hg/geneBounds/orfCompare/orfCompare.c
- src/hg/geneBounds/orfEnum/orfEnum.c
- src/hg/geneBounds/orfStats/orfStats.c
- src/hg/geneBounds/polyInfo/polyInfo.c
- src/hg/geneBounds/promoSeqFromCluster/promoSeqFromCluster.c
- src/hg/geneBounds/raToCds/raToCds.c
- src/hg/geneBounds/twinOrf/twinOrf.c
- src/hg/geneBounds/twinOrf2/twinOrf2.c
- src/hg/geneBounds/twinOrf3/twinOrf3.c
- src/hg/geneBounds/twinOrfStats/twinOrfStats.c
- src/hg/geneBounds/twinOrfStats2/twinOrfStats2.c
- src/hg/geneBounds/twinOrfStats3/twinOrfStats3.c
- src/hg/genePredCheck/genePredCheck.c
- src/hg/genePredHisto/genePredHisto.c
- src/hg/genePredSingleCover/genePredSingleCover.c
- src/hg/genePredSingleCover/geneScore.c
- src/hg/genePredToFakePsl/genePredToFakePsl.c
- src/hg/genePredToGtf/genePredToGtf.c
- src/hg/genePredToMafFrames/genePredToMafFrames.c
- src/hg/genoPheno/gpFakeData/gpFakeData.c
- src/hg/genoPheno/gpShuffleData/gpShuffleData.c
- src/hg/getFeatDna/getFeatDna.c
- src/hg/getRna/getRna.c
- src/hg/getRnaPred/getRnaPred.c
- src/hg/gigAssembler/barger/barger.c
- src/hg/gigAssembler/checkAgpAndFa/checkAgpAndFa.c
- src/hg/gigAssembler/checkDbSync/checkDbSync.c
- src/hg/gigAssembler/checkGoldDupes/checkGoldDupes.c
- src/hg/gigAssembler/checkN/checkN.c
- src/hg/gigAssembler/checkNt/checkNt.c
- src/hg/gigAssembler/checkOut/checkOut.c
- src/hg/gigAssembler/checkPsl/checkPsl.c
- src/hg/gigAssembler/checkQa/checkQa.c
- src/hg/gigAssembler/checkYbr/checkYbr.c
- src/hg/gigAssembler/cmParse/cmParse.c
- src/hg/gigAssembler/cmParse/imreClone.c
- src/hg/gigAssembler/cmpMap/cmpMap.c
- src/hg/gigAssembler/codJobs/jabba/jabba.c
- src/hg/gigAssembler/codJobs/jabba/jobDb.c
- src/hg/gigAssembler/conJobs/cdnaOnOoJobs/cdnaOnOoJobs.c
- src/hg/gigAssembler/conJobs/patJobs/opatJobs.c
- src/hg/gigAssembler/conJobs/patJobs/patJobs.c
- src/hg/gigAssembler/conJobs/pslGenoJobs/makeFix.c
- src/hg/gigAssembler/conJobs/pslGenoJobs/pslGenoJobs.c
- src/hg/gigAssembler/conJobs/pslGenoJobs/test.c
- src/hg/gigAssembler/conJobs/pslOoJobs/pslOoJobs.c
- src/hg/gigAssembler/conJobs/pslSelfJobs/pslSelfJobs.c
- src/hg/gigAssembler/conJobs/repMaskJobs/repMaskJobs.c
- src/hg/gigAssembler/conJobs/rmskOoJobs/rmskOoJobs.c
- src/hg/gigAssembler/g2gOverlap/g2gOverlap.c
- src/hg/gigAssembler/g2gSeqOverlap/g2gSeqOverlap.c
- src/hg/gigAssembler/gapper/gapper.c
- src/hg/gigAssembler/goldToAgp/goldToAgp.c
- src/hg/gigAssembler/makePai/makePai.c
- src/hg/gigAssembler/mendMap/mendMap.c
- src/hg/gigAssembler/mm/checkEnds/checkEnds.c
- src/hg/gigAssembler/mm/mm/mm.c
- src/hg/gigAssembler/mm/mmTestSet/mmTestSet.c
- src/hg/gigAssembler/mm/ooMapMend/ooMapMend.c
- src/hg/gigAssembler/ntGoldGl/ntGoldGl.c
- src/hg/gigAssembler/ooChains/ooChains.c
- src/hg/gigAssembler/ooCloneEnds/ooCloneEnds.c
- src/hg/gigAssembler/ooCloneInfo/ooCloneInfo.c
- src/hg/gigAssembler/ooCloneOverlaps/ooCloneOverlaps.c
- src/hg/gigAssembler/ooCloneSizes/ooCloneSizes.c
- src/hg/gigAssembler/ooCloneSpan/ooCloneSpan.c
- src/hg/gigAssembler/ooGreedy/bak/ooGreedy.39.c
- src/hg/gigAssembler/ooGreedy/bak/ooGreedy.c
- src/hg/gigAssembler/ooGreedy/getgene/getgene.c
- src/hg/gigAssembler/ooGreedy/ooGreedy.c
- src/hg/gigAssembler/ooGreedy/primeMate/primeMate.c
- src/hg/gigAssembler/ooGreedy/protDust/protDust.c
- src/hg/gigAssembler/ooGreedy/scanIntrons/scanIntrons.c
- src/hg/gigAssembler/ooLiftSpec/ooLiftSpec.c
- src/hg/gigAssembler/ooNtInput/ooNtInput.c
- src/hg/gigAssembler/ooSplitFins/ooSplitFins.c
- src/hg/gigAssembler/ooTester/ooTester.c
- src/hg/gigAssembler/ooWeedZero/ooWeedZero.c
- src/hg/gigAssembler/pairedReads/ppAnalyse/ppAnalyse.c
- src/hg/gigAssembler/pairedReads/ppSanger/ppSanger.c
- src/hg/gigAssembler/pairedReads/ppSanger/sangInsert.c
- src/hg/gigAssembler/pairedReads/ppSanger/sangRange.c
- src/hg/gigAssembler/pairedReads/ppSanger/sangRead.c
- src/hg/gigAssembler/pairedReads/ppStats/pPair.c
- src/hg/gigAssembler/pairedReads/ppStats/ppStats.c
- src/hg/gigAssembler/pairedReads/ppWashU/ppWashU.c
- src/hg/gigAssembler/pairedReads/ppWhitehead/ppWhitehead.c
- src/hg/gigAssembler/psLayout/cruft/chkSym.c
- src/hg/gigAssembler/psLayout/cruft/psLayHit.c
- src/hg/gigAssembler/psLayout/psLayout.c
- src/hg/gigAssembler/qaGold/qaGold.c
- src/hg/gisaid/gisaidSample/demog.c
- src/hg/gisaid/gisaidSample/gisaidSample.c
- src/hg/gisaid/gisaidSample/sequence.c
- src/hg/gisaid/gisaidSubj/demog.c
- src/hg/gisaid/gisaidSubj/gisaidSubj.c
- src/hg/gisaid/gisaidSubj/sequence.c
- src/hg/gisaid/gisaidTable/advFilter.c
- src/hg/gisaid/gisaidTable/configure.c
- src/hg/gisaid/gisaidTable/getSeq.c
- src/hg/gisaid/gisaidTable/gisaidSubjInfo.c
- src/hg/gisaid/gisaidTable/gisaidTable.c
- src/hg/gpStats/gpStats.c
- src/hg/gpToGtf/gpToGtf.c
- src/hg/gpcrParser/gpcrParser.c
- src/hg/gsBig/gsBig.c
- src/hg/gsid/gsidAaMsa/gsidAaMsa.c
- src/hg/gsid/gsidGetConsensus/gsidGetConsensus.c
- src/hg/gsid/gsidMember/gsidMember.c
- src/hg/gsid/gsidMsa/gsidMsa.c
- src/hg/gsid/gsidMsaToTab/gsidMsaToTab.c
- src/hg/gsid/gsidPosSelect/gsidPosSelect.c
- src/hg/gsid/gsidSubj/clinical.c
- src/hg/gsid/gsidSubj/demog.c
- src/hg/gsid/gsidSubj/gsidSubj.c
- src/hg/gsid/gsidSubj/sequence.c
- src/hg/gsid/gsidSubj/vaccine.c
- src/hg/gsid/gsidSubj3/clinical.c
- src/hg/gsid/gsidSubj3/demog.c
- src/hg/gsid/gsidSubj3/gsidSubj3.c
- src/hg/gsid/gsidSubj3/sequence.c
- src/hg/gsid/gsidSubj3/vaccine.c
- src/hg/gsid/gsidTable/advFilter.c
- src/hg/gsid/gsidTable/configure.c
- src/hg/gsid/gsidTable/getSeq.c
- src/hg/gsid/gsidTable/gsidSubjInfo.c
- src/hg/gsid/gsidTable/gsidTable.c
- src/hg/gsid/pbGsid/pbGsid.c
- src/hg/gsid/pwdtest/pwdtest.c
- src/hg/hgApi/hgApi.c
- src/hg/hgBatch/hgBatch.c
- src/hg/hgBlat/hgBlat.c
- src/hg/hgBlatTest/hgBlatTest.c
- src/hg/hgChroms/hgChroms.c
- src/hg/hgConvert/hgConvert.c
- src/hg/hgCoordConv/hgCoordConv.c
- src/hg/hgCustom/hgCustom.c
- src/hg/hgGateway/hgGateway.c
- src/hg/hgGene/altSplice.c
- src/hg/hgGene/ctd.c
- src/hg/hgGene/domains.c
- src/hg/hgGene/flyBaseInfo.c
- src/hg/hgGene/gad.c
- src/hg/hgGene/go.c
- src/hg/hgGene/hgGene.c
- src/hg/hgGene/info.c
- src/hg/hgGene/links.c
- src/hg/hgGene/localization.c
- src/hg/hgGene/method.c
- src/hg/hgGene/microarray.c
- src/hg/hgGene/mrnaDescriptions.c
- src/hg/hgGene/otherOrgs.c
- src/hg/hgGene/pathways.c
- src/hg/hgGene/pseudoGene.c
- src/hg/hgGene/rnaStructure.c
- src/hg/hgGene/sequence.c
- src/hg/hgGene/swissProtComments.c
- src/hg/hgGene/synonym.c
- src/hg/hgGene/wikiTrack.c
- src/hg/hgGeneBands/hgGeneBands.c
- src/hg/hgGeneRing/hgGeneRing.c
- src/hg/hgGeneRing/interaction.c
- src/hg/hgGenome/bedList.c
- src/hg/hgGenome/browseRegions.c
- src/hg/hgGenome/chromGraph.c
- src/hg/hgGenome/clickOnImage.c
- src/hg/hgGenome/configure.c
- src/hg/hgGenome/correlate.c
- src/hg/hgGenome/custom.c
- src/hg/hgGenome/hgGenome.c
- src/hg/hgGenome/import.c
- src/hg/hgGenome/maf.c
- src/hg/hgGenome/mainPage.c
- src/hg/hgGenome/sortGenes.c
- src/hg/hgGenome/upload.c
- src/hg/hgGenome/usage.c
- src/hg/hgGenome/wiggle.c
- src/hg/hgGetAnn/hgGetAnn.c
- src/hg/hgHubConnect/hgHubConnect.c
- lines changed 18, context: html, text, full: html, text
allow specifying different names for the hubPublic and hubStatus tables (#6162)
- lines changed 20, 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)
- lines changed 1, context: html, text, full: html, text
fiddle a bit with the hg.conf variables to change hubPublc and hubStatus (#6162)
- src/hg/hgLiftOver/hgLiftOver.c
- src/hg/hgNotAvail/hgNotAvail.c
- src/hg/hgNotYet/hgNotYet.c
- src/hg/hgPal/hgPal.c
- src/hg/hgPcr/hgPcr.c
- src/hg/hgSelect/hgSelect.c
- src/hg/hgSession/hgSession.c
- src/hg/hgSuggest/hgSuggest.c
- src/hg/hgTables/bedList.c
- src/hg/hgTables/bigBed.c
- src/hg/hgTables/compositeTrack.c
- src/hg/hgTables/correlate.c
- src/hg/hgTables/correlatePlot.c
- src/hg/hgTables/custom.c
- src/hg/hgTables/filterFields.c
- src/hg/hgTables/galaxy.c
- src/hg/hgTables/gffOut.c
- src/hg/hgTables/great.c
- src/hg/hgTables/hgTables.c
- src/hg/hgTables/identifiers.c
- src/hg/hgTables/intersect.c
- src/hg/hgTables/joining.c
- src/hg/hgTables/maf.c
- src/hg/hgTables/mainPage.c
- lines changed 1, context: html, text, full: html, text
allow specifying different names for the hubPublic and hubStatus tables (#6162)
- src/hg/hgTables/pal.c
- src/hg/hgTables/rangeHistogram.c
- src/hg/hgTables/schema.c
- src/hg/hgTables/seqOut.c
- src/hg/hgTables/sumStats.c
- src/hg/hgTables/usage.c
- src/hg/hgTables/userRegions.c
- src/hg/hgTables/wiggle.c
- src/hg/hgTables/wikiTrack.c
- src/hg/hgTablesTest/hgTablesTest.c
- src/hg/hgText/hgText.c
- src/hg/hgTrackUi/hgTrackUi.c
- src/hg/hgTracks/altGraphXTrack.c
- src/hg/hgTracks/bamTrack.c
- src/hg/hgTracks/bedGraph.c
- src/hg/hgTracks/cds.c
- src/hg/hgTracks/chainTrack.c
- src/hg/hgTracks/encode.c
- src/hg/hgTracks/gbrowseTest.c
- src/hg/hgTracks/hapmapTrack.c
- src/hg/hgTracks/hgTracks.c
- lines changed 5, context: html, text, full: html, text
allow specifying different names for the hubPublic and hubStatus tables (#6162)
- src/hg/hgTracks/imageV2.c
- src/hg/hgTracks/mafTrack.c
- src/hg/hgTracks/mainMain.c
- src/hg/hgTracks/makeItemsTrack.c
- src/hg/hgTracks/netTrack.c
- src/hg/hgTracks/oneTrack.c
- src/hg/hgTracks/retroGene.c
- src/hg/hgTracks/rnaFoldTrack.c
- src/hg/hgTracks/simpleTracks.c
- src/hg/hgTracks/transcriptome.c
- src/hg/hgTracks/variation.c
- src/hg/hgTracks/wigMafTrack.c
- src/hg/hgTracks/wigTrack.c
- src/hg/hgTracks/wikiTrack.c
- src/hg/hgc/bamClick.c
- src/hg/hgc/dbRIP.c
- src/hg/hgc/expClick.c
- src/hg/hgc/hgc.c
- src/hg/hgc/hgdpClick.c
- src/hg/hgc/lowelab.c
- src/hg/hgc/mafClick.c
- src/hg/hgc/mgcClick.c
- src/hg/hgc/rnaFoldClick.c
- src/hg/hgc/txCdsInfo.c
- src/hg/hgc/virusClick.c
- src/hg/hgc/wiggleClick.c
- src/hg/hgc/wikiTrack.c
- src/hg/hgsql/hgsql.c
- src/hg/hgsqlLocal/hgsqlLocal.c
- src/hg/hgsqlSwapTables/hgsqlSwapTables.c
- src/hg/hgsqlTableDate/hgsqlTableDate.c
- src/hg/hgsqladmin/hgsqladmin.c
- src/hg/hgsqldump/hgsqldump.c
- src/hg/hgsqldumpLocal/hgsqldumpLocal.c
- src/hg/hgsqlimport/hgsqlimport.c
- src/hg/inc/hgConfig.h
- lines changed 4, context: html, text, full: html, text
allow specifying different names for the hubPublic and hubStatus tables (#6162)
- src/hg/inc/hubConnect.h
- lines changed 2, context: html, text, full: html, text
allow specifying different names for the hubPublic and hubStatus tables (#6162)
- lines changed 6, 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)
- lines changed 10, context: html, text, full: html, text
fiddle a bit with the hg.conf variables to change hubPublc and hubStatus (#6162)
- src/hg/intronEnds/intronEnds.c
- src/hg/intronSizes/intronSizes.c
- src/hg/lfsOverlap/lfsOverlap.c
- src/hg/lib/HInv.c
- src/hg/lib/acemblyClass.c
- src/hg/lib/affy10K.c
- src/hg/lib/affy10KDetails.c
- src/hg/lib/affy120KDetails.c
- src/hg/lib/affyAllExonProbe.c
- src/hg/lib/affyAtlas.c
- src/hg/lib/affyGenoDetails.c
- src/hg/lib/affyOffset.c
- src/hg/lib/affyPairs.c
- src/hg/lib/affyTransLifted.c
- src/hg/lib/affyTranscriptome.c
- src/hg/lib/agp.c
- src/hg/lib/agpFrag.c
- src/hg/lib/agpGap.c
- src/hg/lib/alignInfo.c
- src/hg/lib/alleleFreqs.c
- src/hg/lib/allpredictions.c
- src/hg/lib/altGraph.c
- src/hg/lib/altGraphX.c
- src/hg/lib/ancientRref.c
- src/hg/lib/arCOGs.c
- src/hg/lib/arcogdesc.c
- src/hg/lib/atomDb.c
- src/hg/lib/axtInfo.c
- src/hg/lib/axtLib.c
- src/hg/lib/bacCloneAlias.c
- src/hg/lib/bacCloneXRef.c
- src/hg/lib/bacEndAlias.c
- src/hg/lib/bactigPos.c
- src/hg/lib/baseMaskCommon.c
- src/hg/lib/bdgpExprLink.c
- src/hg/lib/bdgpGeneInfo.c
- src/hg/lib/bdgpSwissProt.c
- src/hg/lib/bed.c
- src/hg/lib/bed12Source.c
- src/hg/lib/bed12wSeq.c
- src/hg/lib/bed5FloatScore.c
- src/hg/lib/bed5Pval.c
- src/hg/lib/bed6FloatScore.c
- src/hg/lib/bed8Attrs.c
- src/hg/lib/bedCart.c
- src/hg/lib/bedDetail.c
- src/hg/lib/bgiGeneInfo.c
- src/hg/lib/bgiGeneSnp.c
- src/hg/lib/bgiSnp.c
- src/hg/lib/blastTab.c
- src/hg/lib/blastzNet.c
- src/hg/lib/blatServers.c
- src/hg/lib/borf.c
- src/hg/lib/borkPseudoHom.c
- src/hg/lib/botDelay.c
- src/hg/lib/cartDb.c
- src/hg/lib/ccdsGeneMap.c
- src/hg/lib/ccdsInfo.c
- src/hg/lib/ccdsNotes.c
- src/hg/lib/cddDesc.c
- src/hg/lib/cddInfo.c
- src/hg/lib/cdsEvidence.c
- src/hg/lib/cdsOrtho.c
- src/hg/lib/cdsPick.c
- src/hg/lib/cdsSpec.c
- src/hg/lib/celeraCoverage.c
- src/hg/lib/celeraDupPositive.c
- src/hg/lib/cgapSage/cgapSage.c
- src/hg/lib/cgapSage/cgapSageLib.c
- src/hg/lib/cgh.c
- src/hg/lib/chainCart.c
- src/hg/lib/chainDb.c
- src/hg/lib/chainGap.c
- src/hg/lib/chainLink.c
- src/hg/lib/chainNet.c
- src/hg/lib/chainNetDbLoad.c
- src/hg/lib/chicken13kInfo.c
- src/hg/lib/chr18deletions.c
- src/hg/lib/chromBins.c
- src/hg/lib/chromGraph.c
- src/hg/lib/chromGraphFactory.c
- src/hg/lib/chromInfo.c
- src/hg/lib/chromInserts.c
- src/hg/lib/clonePos.c
- src/hg/lib/cnpIafrate.c
- src/hg/lib/cnpIafrate2.c
- src/hg/lib/cnpLocke.c
- src/hg/lib/cnpRedon.c
- src/hg/lib/cnpSebat.c
- src/hg/lib/cnpSebat2.c
- src/hg/lib/cnpSharp.c
- src/hg/lib/cnpSharp2.c
- src/hg/lib/cnpSharpCutoff.c
- src/hg/lib/cnpSharpSample.c
- src/hg/lib/codeBlast.c
- src/hg/lib/codeBlastScore.c
- src/hg/lib/cogs.c
- src/hg/lib/cogsxra.c
- src/hg/lib/columnInfo.c
- src/hg/lib/contigAcc.c
- src/hg/lib/coordConv.c
- src/hg/lib/cpgIsland.c
- src/hg/lib/cpgIslandExt.c
- src/hg/lib/ctgPos.c
- src/hg/lib/ctgPos2.c
- src/hg/lib/customFactory.c
- src/hg/lib/customPp.c
- src/hg/lib/customTrack.c
- src/hg/lib/cutter.c
- src/hg/lib/cytoBand.c
- src/hg/lib/dbDb.c
- src/hg/lib/dbRIP.c
- src/hg/lib/dbSnpRs.c
- src/hg/lib/defaultDb.c
- src/hg/lib/delConrad2.c
- src/hg/lib/delHinds2.c
- src/hg/lib/dgv.c
- src/hg/lib/dless.c
- src/hg/lib/dnaMotifSql.c
- src/hg/lib/dnaProbe.c
- src/hg/lib/dv.c
- src/hg/lib/dvBed.c
- src/hg/lib/dvXref2.c
- src/hg/lib/easyGene.c
- src/hg/lib/ecAttribute.c
- src/hg/lib/ecAttributeCode.c
- src/hg/lib/ecCode.c
- src/hg/lib/encode/encodeErge.c
- src/hg/lib/encode/encodeErge5race.c
- src/hg/lib/encode/encodeErgeBinding.c
- src/hg/lib/encode/encodeErgeDNAseI.c
- src/hg/lib/encode/encodeErgeExpProm.c
- src/hg/lib/encode/encodeErgeHssCellLines.c
- src/hg/lib/encode/encodeErgeInVitroFoot.c
- src/hg/lib/encode/encodeErgeMethProm.c
- src/hg/lib/encode/encodeErgeStableTransf.c
- src/hg/lib/encode/encodeErgeSummary.c
- src/hg/lib/encode/encodeErgeTransTransf.c
- src/hg/lib/encode/encodeHapMapAlleleFreq.c
- src/hg/lib/encode/encodeIndels.c
- src/hg/lib/encode/encodePeak.c
- src/hg/lib/encode/encodePrimateAlleles.c
- src/hg/lib/encode/encodeRegionInfo.c
- src/hg/lib/encode/encodeRegionInfoCustom.c
- src/hg/lib/encode/encodeRna.c
- src/hg/lib/encode/encodeStanfordPromoters.c
- src/hg/lib/encode/encodeStanfordPromotersAverage.c
- src/hg/lib/encode/pairedTagAlign.c
- src/hg/lib/encode/peptideMapping.c
- src/hg/lib/encode/tagAlign.c
- src/hg/lib/encode/wgEncodeGencodeAnnotationRemark.c
- src/hg/lib/encode/wgEncodeGencodeAttrs.c
- src/hg/lib/encode/wgEncodeGencodeExonSupport.c
- src/hg/lib/encode/wgEncodeGencodeGeneSource.c
- src/hg/lib/encode/wgEncodeGencodePdb.c
- src/hg/lib/encode/wgEncodeGencodePolyAFeature.c
- src/hg/lib/encode/wgEncodeGencodePubMed.c
- src/hg/lib/encode/wgEncodeGencodeRefSeq.c
- src/hg/lib/encode/wgEncodeGencodeTag.c
- src/hg/lib/encode/wgEncodeGencodeTranscriptSource.c
- src/hg/lib/encode/wgEncodeGencodeTranscriptSupport.c
- src/hg/lib/encode/wgEncodeGencodeUniProt.c
- src/hg/lib/ensFace.c
- src/hg/lib/ensInfo.c
- src/hg/lib/ensPhusionBlast.c
- src/hg/lib/ensXRefZfish.c
- src/hg/lib/est3.c
- src/hg/lib/estOrientInfo.c
- src/hg/lib/estPair.c
- src/hg/lib/exoFish.c
- src/hg/lib/expData.c
- src/hg/lib/expRecord.c
- src/hg/lib/exprBed.c
- src/hg/lib/fbTables.c
- src/hg/lib/featureBits.c
- src/hg/lib/fishClones.c
- src/hg/lib/flyBase2004Xref.c
- src/hg/lib/flyBaseSwissProt.c
- src/hg/lib/flyreg.c
- src/hg/lib/flyreg2.c
- src/hg/lib/fosEndPairs.c
- src/hg/lib/gbExtFile.c
- src/hg/lib/gbMiscDiff.c
- src/hg/lib/gbProtAnn.c
- src/hg/lib/gbRNAs.c
- src/hg/lib/gbSeq.c
- src/hg/lib/gbWarn.c
- src/hg/lib/gcPercent.c
- src/hg/lib/genMapDb.c
- src/hg/lib/genbank.c
- src/hg/lib/gencodeGeneClass.c
- src/hg/lib/gencodeIntron.c
- src/hg/lib/geneBands.c
- src/hg/lib/geneCheck.c
- src/hg/lib/geneCheckDetails.c
- src/hg/lib/geneGraph.c
- src/hg/lib/genePix.c
- src/hg/lib/genePred.c
- src/hg/lib/geneTree.c
- src/hg/lib/genoLay.c
- src/hg/lib/genomeRangeTreeFile.c
- src/hg/lib/genomicDups.c
- src/hg/lib/genomicSuperDups.c
- src/hg/lib/genotype.c
- src/hg/lib/genotypeFreqs.c
- src/hg/lib/ggCluster.c
- src/hg/lib/ggDbIo.c
- src/hg/lib/ggDbRep.c
- src/hg/lib/ggDump.c
- src/hg/lib/ggGraph.c
- src/hg/lib/ggMrnaAli.c
- src/hg/lib/ggTypes.c
- src/hg/lib/glDbRep.c
- src/hg/lib/goa.c
- src/hg/lib/goaPart.c
- src/hg/lib/googleAnalytics.c
- src/hg/lib/growthCondition.c
- src/hg/lib/grp.c
- src/hg/lib/gv.c
- src/hg/lib/gvUi.c
- src/hg/lib/gwasCatalog.c
- src/hg/lib/hCommon.c
- src/hg/lib/hCytoBand.c
- src/hg/lib/hPrint.c
- src/hg/lib/hapmapAlleleFreq.c
- src/hg/lib/hapmapAlleles.c
- src/hg/lib/hapmapAllelesCombined.c
- src/hg/lib/hapmapAllelesOrtho.c
- src/hg/lib/hapmapAllelesSummary.c
- src/hg/lib/hapmapLd.c
- src/hg/lib/hapmapPhaseIIISummary.c
- src/hg/lib/hapmapPrimateAlleles.c
- src/hg/lib/hapmapSnps.c
- src/hg/lib/hapmapSnpsCombined.c
- src/hg/lib/hdb.c
- src/hg/lib/hgColors.c
- src/hg/lib/hgConfig.c
- lines changed 9, context: html, text, full: html, text
allow specifying different names for the hubPublic and hubStatus tables (#6162)
- src/hg/lib/hgExp.c
- src/hg/lib/hgFind.c
- src/hg/lib/hgFindSpec.c
- src/hg/lib/hgGene.c
- src/hg/lib/hgMaf.c
- src/hg/lib/hgRelate.c
- src/hg/lib/hgSeq.c
- src/hg/lib/hgdpGeo.c
- src/hg/lib/hubConnect.c
- lines changed 30, context: html, text, full: html, text
allow specifying different names for the hubPublic and hubStatus tables (#6162)
- lines changed 16, 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)
- lines changed 1, context: html, text, full: html, text
fiddle a bit with the hg.conf variables to change hubPublc and hubStatus (#6162)
- lines changed 6, context: html, text, full: html, text
add a firstAdded time to the hubStatus table. #5138
- src/hg/lib/hubPublic.as
- lines changed 11, context: html, text, full: html, text
add the hubPublic and hubStatus autoSql definitions
- src/hg/lib/hubPublic.sql
- lines changed 16, context: html, text, full: html, text
add the hubPublic and hubStatus autoSql definitions
- src/hg/lib/hubStatus.as
- lines changed 15, context: html, text, full: html, text
add the hubPublic and hubStatus autoSql definitions
- lines changed 1, context: html, text, full: html, text
add a firstAdded time to the hubStatus table. #5138
- src/hg/lib/hubStatus.sql
- lines changed 20, context: html, text, full: html, text
add the hubPublic and hubStatus autoSql definitions
- lines changed 1, context: html, text, full: html, text
add a firstAdded time to the hubStatus table. #5138
- src/hg/lib/humanParalog.c
- src/hg/lib/hvGfx.c
- src/hg/lib/imageClone.c
- src/hg/lib/isochores.c
- src/hg/lib/ispyTables.c
- src/hg/lib/itemAttr.c
- src/hg/lib/itemConf.c
- src/hg/lib/jaxOrtholog.c
- src/hg/lib/jaxQTL.c
- src/hg/lib/jaxQTL2.c
- src/hg/lib/jaxQTL3.c
- src/hg/lib/jgiGene.c
- src/hg/lib/jksql.c
- src/hg/lib/joiner.c
- src/hg/lib/jsHelper.c
- src/hg/lib/kg1ToKg2.c
- src/hg/lib/kgAlias.c
- src/hg/lib/kgColor.c
- src/hg/lib/kgMapName.c
- src/hg/lib/kgProtAlias.c
- src/hg/lib/kgXref.c
- src/hg/lib/knownInfo.c
- src/hg/lib/knownMore.c
- src/hg/lib/knownToSuper.c
- src/hg/lib/landmark.c
- src/hg/lib/ld.c
- src/hg/lib/ld2.c
- src/hg/lib/lfs.c
- src/hg/lib/liftOver.c
- src/hg/lib/liftOverChain.c
- src/hg/lib/liftUp.c
- src/hg/lib/llaInfo.c
- src/hg/lib/lowelabArkinOperonScore.c
- src/hg/lib/lowelabPfamHit.c
- src/hg/lib/lowelabTIGROperonScore.c
- src/hg/lib/lsSnpPdb.c
- src/hg/lib/mafFrames.c
- src/hg/lib/mafGene.c
- src/hg/lib/mafSummary.c
- src/hg/lib/makeItemsItem.c
- src/hg/lib/mammalPsg.c
- src/hg/lib/mapSts.c
- src/hg/lib/mcnBreakpoints.c
- src/hg/lib/mdb.c
- src/hg/lib/megablastInfo.c
- src/hg/lib/metaChromGraph.c
- src/hg/lib/mgiID.c
- src/hg/lib/minChromSize.c
- src/hg/lib/minGeneInfo.c
- src/hg/lib/mouseOrtho.c
- src/hg/lib/mouseSyn.c
- src/hg/lib/mouseSynWhd.c
- src/hg/lib/mrnaMisMatch.c
- src/hg/lib/mysqlTableStatus.c
- src/hg/lib/ncRna.c
- src/hg/lib/netAlign.c
- src/hg/lib/netCart.c
- src/hg/lib/newfoo/cytoBand.c
- src/hg/lib/nonCodingUi.c
- src/hg/lib/omicia.c
- src/hg/lib/omimTitle.c
- src/hg/lib/ooUtils.c
- src/hg/lib/oreganno.c
- src/hg/lib/oregannoUi.c
- src/hg/lib/orthoAlleles.c
- src/hg/lib/pal.c
- src/hg/lib/pbStamp.c
- src/hg/lib/pcrResult.c
- src/hg/lib/pepPred.c
- src/hg/lib/pgPhenoAssoc.c
- src/hg/lib/pgPolyphenPred.c
- src/hg/lib/pgSiftPred.c
- src/hg/lib/plasEndPairs.c
- src/hg/lib/polyGenotype.c
- src/hg/lib/protFeat.c
- src/hg/lib/protVar.c
- src/hg/lib/pscreen.c
- src/hg/lib/pseudoGeneLink.c
- src/hg/lib/pslWQueryID.c
- src/hg/lib/pslWScore.c
- src/hg/lib/putaInfo.c
- src/hg/lib/qaSeq.c
- src/hg/lib/rangeTreeFile.c
- src/hg/lib/rankProp.c
- src/hg/lib/recombRate.c
- src/hg/lib/recombRateMouse.c
- src/hg/lib/recombRateRat.c
- src/hg/lib/refLink.c
- src/hg/lib/refSeqStatus.c
- src/hg/lib/retroMrnaInfo.c
- src/hg/lib/rgdQtl.c
- src/hg/lib/rhMapInfo.c
- src/hg/lib/rhMapZfishInfo.c
- src/hg/lib/riken.c
- src/hg/lib/rikenBest.c
- src/hg/lib/rikenCluster.c
- src/hg/lib/rmskOut.c
- src/hg/lib/rnaFold.c
- src/hg/lib/rnaGene.c
- src/hg/lib/rnaGenes.c
- src/hg/lib/rnaGroup.c
- src/hg/lib/rnaHybridization.c
- src/hg/lib/rnaPLFold.c
- src/hg/lib/rnaSecStr.c
- src/hg/lib/roughAli.c
- src/hg/lib/sage.c
- src/hg/lib/sageCounts.c
- src/hg/lib/sageExp.c
- src/hg/lib/samAlignment.c
- src/hg/lib/sample.c
- src/hg/lib/sanger22extra.c
- src/hg/lib/sangerGene.c
- src/hg/lib/sangerGeneToWBGeneID.c
- src/hg/lib/sargassoSeaXra.c
- src/hg/lib/scopDes.c
- src/hg/lib/scoredRef.c
- src/hg/lib/sgdAbundance.c
- src/hg/lib/sgdClone.c
- src/hg/lib/sgdDescription.c
- src/hg/lib/sgdOther.c
- src/hg/lib/simpleNucDiff.c
- src/hg/lib/simpleRepeat.c
- src/hg/lib/snoRNAs.c
- src/hg/lib/snp.c
- src/hg/lib/snp125.c
- src/hg/lib/snp125CodingCoordless.c
- src/hg/lib/snp125Exceptions.c
- src/hg/lib/snpExceptions.c
- src/hg/lib/snpExtFile.c
- src/hg/lib/snpFasta.c
- src/hg/lib/snpMap.c
- src/hg/lib/snpSeq.c
- src/hg/lib/snpTmp.c
- src/hg/lib/softPromoter.c
- src/hg/lib/softberryHom.c
- src/hg/lib/spDb.c
- src/hg/lib/splignAlign.c
- src/hg/lib/stanMad.c
- src/hg/lib/stsAlias.c
- src/hg/lib/stsInfo.c
- src/hg/lib/stsInfo2.c
- src/hg/lib/stsInfoMouse.c
- src/hg/lib/stsInfoMouseNew.c
- src/hg/lib/stsInfoRat.c
- src/hg/lib/stsMap.c
- src/hg/lib/stsMapMouse.c
- src/hg/lib/stsMapMouseNew.c
- src/hg/lib/stsMapRat.c
- src/hg/lib/stsMarker.c
- src/hg/lib/suggest.c
- src/hg/lib/switchDbTss.c
- src/hg/lib/synMap.c
- src/hg/lib/synteny100000.c
- src/hg/lib/syntenyBerk.c
- src/hg/lib/syntenySanger.c
- src/hg/lib/tRNAs.c
- src/hg/lib/tableDescriptions.c
- src/hg/lib/tableStatus.c
- src/hg/lib/targetDb.c
- src/hg/lib/taxonDivision.c
- src/hg/lib/taxonGeneticCode.c
- src/hg/lib/taxonName.c
- src/hg/lib/taxonNode.c
- src/hg/lib/taxonXref.c
- src/hg/lib/tests/binTest.c
- src/hg/lib/tests/customTrackTester.c
- src/hg/lib/tests/genePredTester.c
- src/hg/lib/tests/pslReaderTester.c
- src/hg/lib/tests/spDbTest.c
- src/hg/lib/tfbsCons.c
- src/hg/lib/tfbsConsFactors.c
- src/hg/lib/tfbsConsMap.c
- src/hg/lib/tfbsConsSites.c
- src/hg/lib/tigrCmrGene.c
- src/hg/lib/tigrOperon.c
- src/hg/lib/tilingPath.c
- src/hg/lib/traceInfo.c
- src/hg/lib/trackDb.c
- src/hg/lib/trackDbCustom.c
- src/hg/lib/trackLayout.c
- src/hg/lib/trackTable.c
- src/hg/lib/trackVersion.c
- src/hg/lib/transMapGene.c
- src/hg/lib/transMapInfo.c
- src/hg/lib/transMapSrc.c
- src/hg/lib/transRegCode.c
- src/hg/lib/transRegCodeCondition.c
- src/hg/lib/transRegCodeProbe.c
- src/hg/lib/trashDir.c
- src/hg/lib/txCluster.c
- src/hg/lib/txCommon.c
- src/hg/lib/txEdgeBed.c
- src/hg/lib/txEdgeOrtho.c
- src/hg/lib/txGraph.c
- src/hg/lib/txInfo.c
- src/hg/lib/txRnaAccs.c
- src/hg/lib/ucscRetroInfo.c
- src/hg/lib/ucscRetroOrtho.c
- src/hg/lib/variome.c
- src/hg/lib/vegaInfo.c
- src/hg/lib/vegaInfoZfish.c
- src/hg/lib/visiGene.c
- src/hg/lib/vntr.c
- src/hg/lib/wabAli.c
- src/hg/lib/web.c
- src/hg/lib/wgRna.c
- src/hg/lib/wigAsciiToBinary.c
- src/hg/lib/wigDataStream.c
- src/hg/lib/wiggle.c
- src/hg/lib/wiggleCart.c
- src/hg/lib/wiggleUtils.c
- src/hg/lib/wikiLink.c
- src/hg/lib/wikiTrack.c
- src/hg/lib/yaleGencodeAssoc.c
- src/hg/lib/zdobnovSynt.c
- src/hg/liftAcross/liftAcross.c
- src/hg/liftAgp/liftAgp.c
- src/hg/liftFrags/liftFrags.c
- src/hg/liftOver/liftOver.c
- src/hg/liftOver/liftOverMerge.c
- src/hg/liftUp/liftUp.c
- src/hg/logCrawl/accessLogFilter/accessLogFilter.c
- src/hg/logCrawl/accessLogMerge/accessLogMerge.c
- src/hg/logCrawl/accessLogSort/accessLogSort.c
- src/hg/logCrawl/accessLogWigs/accessLogWigs.c
- src/hg/logCrawl/crawlForHogs/crawlForHogs.c
- src/hg/logCrawl/crawlForPosAndTime/crawlForPosAndTime.c
- src/hg/logCrawl/hgAccessCrawl/hgAccessCrawl.c
- src/hg/logCrawl/sessionDbCrawl/sessionDbCrawl.c
- src/hg/logCrawl/ticksToWig/ticksToWig.c
- src/hg/makeDb/genbank/src/align/gbAlignCommon.c
- src/hg/makeDb/genbank/src/align/gbAlignGet.c
- src/hg/makeDb/genbank/src/align/gbAlignInstall.c
- src/hg/makeDb/genbank/src/align/gbBlat
- 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/ccds/ccdsImport.c
- src/hg/makeDb/genbank/src/ccds/ccdsLocationsJoin.c
- src/hg/makeDb/genbank/src/ccds/ccdsMkTables.c
- src/hg/makeDb/genbank/src/ccds/mkCcdsGeneMap.c
- src/hg/makeDb/genbank/src/dbload/dbLoadPartitions.c
- lines changed 1, context: html, text, full: html, text
always load non-coding, not just when it's part of RefSeq (part of #20)
- src/hg/makeDb/genbank/src/dbload/gbAlignData.c
- src/hg/makeDb/genbank/src/dbload/gbBuildState.c
- src/hg/makeDb/genbank/src/dbload/gbLoadRna.c
- src/hg/makeDb/genbank/src/dbload/gbMDParse.c
- src/hg/makeDb/genbank/src/dbload/gbMetaData.c
- src/hg/makeDb/genbank/src/extFileUpdate/extFileUpdate.c
- src/hg/makeDb/genbank/src/gbConf/gbConf.c
- src/hg/makeDb/genbank/src/gbGetSeqs/gbGetSeqs.c
- src/hg/makeDb/genbank/src/gbSanity/chkAlignTbls.c
- src/hg/makeDb/genbank/src/gbSanity/chkCommon.c
- src/hg/makeDb/genbank/src/gbSanity/chkGbIndex.c
- src/hg/makeDb/genbank/src/gbSanity/chkMetaDataTbls.c
- src/hg/makeDb/genbank/src/gbSanity/chkSeqTbl.c
- src/hg/makeDb/genbank/src/gbSanity/gbSanity.c
- src/hg/makeDb/genbank/src/gbSanity/metaData.c
- src/hg/makeDb/genbank/src/lib/extFileTbl.c
- src/hg/makeDb/genbank/src/lib/gbAligned.c
- src/hg/makeDb/genbank/src/lib/gbConf.c
- src/hg/makeDb/genbank/src/lib/gbDefs.c
- src/hg/makeDb/genbank/src/lib/gbEntry.c
- src/hg/makeDb/genbank/src/lib/gbFa.c
- src/hg/makeDb/genbank/src/lib/gbFileOps.c
- src/hg/makeDb/genbank/src/lib/gbGenome.c
- src/hg/makeDb/genbank/src/lib/gbIgnore.c
- src/hg/makeDb/genbank/src/lib/gbIndex.c
- src/hg/makeDb/genbank/src/lib/gbLoadedTbl.c
- src/hg/makeDb/genbank/src/lib/gbProcessed.c
- src/hg/makeDb/genbank/src/lib/gbRelease.c
- src/hg/makeDb/genbank/src/lib/gbStatusTbl.c
- src/hg/makeDb/genbank/src/lib/gbUpdate.c
- src/hg/makeDb/genbank/src/lib/gbVerb.c
- src/hg/makeDb/genbank/src/lib/imageCloneTbl.c
- src/hg/makeDb/genbank/src/lib/mgcStatusTbl.c
- src/hg/makeDb/genbank/src/lib/seqTbl.c
- src/hg/makeDb/genbank/src/lib/sqlDeleter.c
- src/hg/makeDb/genbank/src/lib/sqlUpdater.c
- src/hg/makeDb/genbank/src/lib/uniqueStrTbl.c
- src/hg/makeDb/genbank/src/mgc/mgcClone.c
- src/hg/makeDb/genbank/src/mgc/mgcDbLoad.c
- src/hg/makeDb/genbank/src/mgc/mgcFullength.c
- src/hg/makeDb/genbank/src/mgc/mgcImport.c
- src/hg/makeDb/genbank/src/mgc/mgcLibrary.c
- src/hg/makeDb/genbank/src/mgc/mgcStage1.c
- src/hg/makeDb/genbank/src/orfeome/orfeomeDbLoad.c
- src/hg/makeDb/genbank/src/orfeome/orfeomeImageIds.c
- src/hg/makeDb/genbank/src/process/gbParse.c
- src/hg/makeDb/genbank/src/process/gbProcess.c
- src/hg/makeDb/genbank/src/process/gbProcessedCheck.c
- src/hg/makeDb/genbank/src/refSeqCheck/refSeqCheck.c
- src/hg/makeDb/genbank/src/repair/refPepRepair.c
- src/hg/makeDb/genbank/src/repair/repairExtFile.c
- src/hg/makeDb/genbank/src/selectWithPsl/selectWithPsl.c
- src/hg/makeDb/genbank/tests/gbFaCheck/gbFaCheck.c
- src/hg/makeDb/genbank/tests/index/gbIndexTest.c
- src/hg/makeDb/genbank/tests/subset/gbGetTestSubset.c
- src/hg/makeDb/hgAddLiftOverChain/hgAddLiftOverChain.c
- src/hg/makeDb/hgBbiDbLink/hgBbiDbLink.c
- src/hg/makeDb/hgBedsToBedExps/bToBeCfg.c
- src/hg/makeDb/hgBedsToBedExps/hgBedsToBedExps.c
- src/hg/makeDb/hgCalStat/hgCalStat.c
- src/hg/makeDb/hgClonePos/gsSeqInfo.c
- src/hg/makeDb/hgClonePos/hgClonePos.c
- src/hg/makeDb/hgCountAlign/align.c
- src/hg/makeDb/hgCountAlign/hgCountAlign.c
- src/hg/makeDb/hgCountAlign/slidingWin.c
- src/hg/makeDb/hgCountAlign/winCounts.c
- src/hg/makeDb/hgCtgPos/hgCtgPos.c
- src/hg/makeDb/hgCtgPos/liftSpec.c
- src/hg/makeDb/hgDeleteChrom/hgDeleteChrom.c
- src/hg/makeDb/hgExperiment/hgExperiment.c
- src/hg/makeDb/hgExtFileCheck/hgExtFileCheck.c
- src/hg/makeDb/hgFakeAgp/hgFakeAgp.c
- src/hg/makeDb/hgFindSpec/hgFindSpec.c
- src/hg/makeDb/hgGcPercent/hgGcPercent.c
- src/hg/makeDb/hgGeneBands/hgGeneBands.c
- src/hg/makeDb/hgGetNrOmimGene/hgGetNrOmimGene.c
- src/hg/makeDb/hgGoldGapGl/hgGoldGapGl.c
- src/hg/makeDb/hgGoldGapGl/hgLoadGap.c
- src/hg/makeDb/hgGoldGapGl/ntContig.c
- src/hg/makeDb/hgKgGetText/hgKgGetText.c
- src/hg/makeDb/hgKnownMore.oo21/hgKnownMore.c
- src/hg/makeDb/hgKnownMore.oo21/hugoMulti.c
- src/hg/makeDb/hgKnownMore/hgKnownMore.c
- src/hg/makeDb/hgKnownMore/hugoMulti.c
- src/hg/makeDb/hgLoadBed/hgLoadBed.c
- src/hg/makeDb/hgLoadBlastTab/hgLoadBlastTab.c
- src/hg/makeDb/hgLoadChain/hgLoadChain.c
- src/hg/makeDb/hgLoadChromGraph/hgLoadChromGraph.c
- src/hg/makeDb/hgLoadGenePred/hgLoadGenePred.c
- src/hg/makeDb/hgLoadMaf/hgLoadMaf.c
- src/hg/makeDb/hgLoadMaf/hgLoadMafSummary.c
- src/hg/makeDb/hgLoadMafFrames/hgLoadMafFrames.c
- src/hg/makeDb/hgLoadNet/hgLoadNet.c
- src/hg/makeDb/hgLoadOut/hgLoadOut.c
- src/hg/makeDb/hgLoadPsl/hgLoadPsl.c
- src/hg/makeDb/hgLoadSample/hgLoadSample.c
- src/hg/makeDb/hgLoadSeq/hgLoadSeq.c
- src/hg/makeDb/hgLoadSqlTab/hgLoadSqlTab.c
- src/hg/makeDb/hgLoadWiggle/hgDumpWiggle.c
- src/hg/makeDb/hgLoadWiggle/hgLoadWiggle.c
- src/hg/makeDb/hgLoadWiggle/hgWiggle.c
- src/hg/makeDb/hgLoadWiggle/wigEncode.c
- src/hg/makeDb/hgMapMicroarray/hgMapMicroarray.c
- src/hg/makeDb/hgMedianMicroarray/hgMedianMicroarray.c
- src/hg/makeDb/hgNibSeq/hgNibSeq.c
- src/hg/makeDb/hgPar/hgPar.c
- src/hg/makeDb/hgPar/parSpec.c
- src/hg/makeDb/hgPepPred/hgPepPred.c
- src/hg/makeDb/hgRatioMicroarray/hgRatioMicroarray.c
- src/hg/makeDb/hgRgdParsePathwayObo/hgRgdParsePathwayObo.c
- src/hg/makeDb/hgSanger20/hgSanger20.c
- src/hg/makeDb/hgSanger22/hgSanger22.c
- src/hg/makeDb/hgStanfordMicroarray/hgStanfordMicroarray.c
- src/hg/makeDb/hgStsAlias/hgStsAlias.c
- src/hg/makeDb/hgStsMarkers/hgStsMarkers.c
- src/hg/makeDb/hgTomRough/hgTomRough.c
- src/hg/makeDb/hgTomRough/tomRough.c
- src/hg/makeDb/hgTpf/hgTpf.c
- src/hg/makeDb/hgTraceInfo/hgTraceInfo.c
- src/hg/makeDb/hgTrackDb/hgTrackDb.c
- src/hg/makeDb/hgWaba/hgWaba.c
- src/hg/makeDb/htTpf/htTpf.c
- src/hg/makeDb/ldHgGene/ldHgGene.c
- src/hg/makeDb/mdbUpdate/mdbPrint.c
- src/hg/makeDb/mdbUpdate/mdbUpdate.c
- src/hg/makeDb/outside/allenBrain/allenCleanup/allenCleanup.c
- src/hg/makeDb/outside/allenBrain/allenCollectSeq/allenCollectSeq.c
- src/hg/makeDb/outside/hgAvidShortBed/hgAvidShortBed.c
- src/hg/makeDb/outside/hgExonerate/hgExonerate.c
- src/hg/makeDb/outside/hgFiberglass/hgFiberglass.c
- src/hg/makeDb/outside/hgFlyBase/hgFlyBase.c
- src/hg/makeDb/outside/hgGnfMicroarray/hgGnfMicroarray.c
- src/hg/makeDb/outside/hgLoadEranModules/hgLoadEranModules.c
- src/hg/makeDb/outside/hgLsSnpPdbLoad/hgLsSnpPdbLoad.c
- src/hg/makeDb/outside/hgPhMouse/hgPhMouse.c
- src/hg/makeDb/outside/hgRnaGenes/hgRnaGenes.c
- src/hg/makeDb/outside/hgSoftPromoter/hgSoftPromoter.c
- src/hg/makeDb/outside/hgSoftberryHom/hgSoftberryHom.c
- src/hg/makeDb/outside/nibb/nibbImageProbes/nibbImageProbes.c
- src/hg/makeDb/outside/nibb/nibbNameFix/nibbNameFix.c
- src/hg/makeDb/outside/nibb/nibbParseImageDir/nibbParseImageDir.c
- src/hg/makeDb/outside/nibb/nibbPrepImages/nibbPrepImages.c
- src/hg/makeDb/outside/sanger22gtf/sanger22gtf.c
- src/hg/makeDb/outside/vegaBuildInfo/vegaBuildInfo.c
- src/hg/makeDb/outside/yeast/checkSgdSync/checkSgdSync.c
- src/hg/makeDb/outside/yeast/fixHarbisonMotifs/fixHarbisonMotifs.c
- src/hg/makeDb/outside/yeast/hgSgdGff3/hgSgdGff3.c
- src/hg/makeDb/outside/yeast/hgSgdGfp/hgSgdGfp.c
- src/hg/makeDb/outside/yeast/hgSgdPep/hgSgdPep.c
- src/hg/makeDb/outside/yeast/hgYeastRegCode/hgYeastRegCode.c
- src/hg/makeDb/schema/dbFindFieldsWith/dbFindFieldsWith.c
- src/hg/makeDb/schema/dbSnoop/dbSnoop.c
- src/hg/makeDb/schema/joinTwoInfo/joinTwoInfo.c
- src/hg/makeDb/schema/joinableFields/joinableFields.c
- src/hg/makeDb/schema/joinerCheck/joinerCheck.c
- src/hg/makeDb/schema/makeTableDescriptions/makeTableDescriptions.c
- src/hg/makeDb/simpleGap/simpleGap.c
- src/hg/makeDb/tfbsConsLoc/seq.c
- src/hg/makeDb/tfbsConsLoc/util.c
- src/hg/makeDb/trackDbPatch/trackDbPatch.c
- src/hg/makeDb/trackDbRaFormat/trackDbRaFormat.c
- src/hg/makeSeqs/makeSeqs.c
- src/hg/maskOutFa/maskOutFa.c
- src/hg/mdToNcbiLift/mdToNcbiLift.c
- src/hg/monitor/cacti/cactiSine/cactiSine.c
- src/hg/mouseStuff/afsCombine/afsCombine.c
- src/hg/mouseStuff/axtAndBed/axtAndBed.c
- src/hg/mouseStuff/axtBest/axtBest.c
- src/hg/mouseStuff/axtBestNear/axtBestNear.c
- src/hg/mouseStuff/axtCalcMatrix/axtCalcMatrix.c
- src/hg/mouseStuff/axtChain/axtChain.c
- src/hg/mouseStuff/axtDropOverlap/axtDropOverlap.c
- src/hg/mouseStuff/axtDropSelf/axtDropSelf.c
- src/hg/mouseStuff/axtFilter/axtFilter.c
- src/hg/mouseStuff/axtIndex/axtIndex.c
- src/hg/mouseStuff/axtPretty/axtPretty.c
- src/hg/mouseStuff/axtQueryCount/axtQueryCount.c
- src/hg/mouseStuff/axtRecipBest/axtRecipBest.c
- src/hg/mouseStuff/axtRescore/axtRescore.c
- src/hg/mouseStuff/axtSort/axtSort.c
- src/hg/mouseStuff/axtSplitByTarget/axtSplitByTarget.c
- src/hg/mouseStuff/axtSwap/axtSwap.c
- src/hg/mouseStuff/axtToBed/axtToBed.c
- src/hg/mouseStuff/axtToChain/axtToChain.c
- src/hg/mouseStuff/axtToMaf/axtToMaf.c
- src/hg/mouseStuff/axtToPsl/axtToPsl.c
- src/hg/mouseStuff/bedCoverage/bedCoverage.c
- src/hg/mouseStuff/calcGap/calcGap.c
- src/hg/mouseStuff/chainAntiRepeat/chainAntiRepeat.c
- src/hg/mouseStuff/chainDbToFile/chainDbToFile.c
- src/hg/mouseStuff/chainFilter/chainFilter.c
- src/hg/mouseStuff/chainIndex/chainIndex.c
- src/hg/mouseStuff/chainMergeSort/chainMergeSort.c
- src/hg/mouseStuff/chainNet/chainNet.c
- src/hg/mouseStuff/chainPreNet/chainPreNet.c
- src/hg/mouseStuff/chainSort/chainSort.c
- src/hg/mouseStuff/chainSplit/chainSplit.c
- src/hg/mouseStuff/chainSwap/chainSwap.c
- src/hg/mouseStuff/chainToAxt/chainToAxt.c
- src/hg/mouseStuff/chainToPsl/chainToPsl.c
- src/hg/mouseStuff/correctEst/correctEst.c
- src/hg/mouseStuff/gcForBed/gcForBed.c
- src/hg/mouseStuff/ggcPic/ggcPic.c
- src/hg/mouseStuff/knownVsBlat/blatStats.c
- src/hg/mouseStuff/knownVsBlat/knownVsBlat.c
- src/hg/mouseStuff/knownVsBlat/kvsSummary.c
- src/hg/mouseStuff/lavToAxt/lavToAxt.c
- src/hg/mouseStuff/lavToPsl/lavToPsl.c
- src/hg/mouseStuff/libScan/libScan.c
- src/hg/mouseStuff/mafCoverage/mafCoverage.c
- src/hg/mouseStuff/mafFetch/mafFetch.c
- src/hg/mouseStuff/mafToClustalw/mafToClustalw.c
- src/hg/mouseStuff/mafToFa/mafToFa.c
- src/hg/mouseStuff/mafToPsl/mafToPsl.c
- src/hg/mouseStuff/mafToXmfa/mafToXmfa.c
- src/hg/mouseStuff/mousePoster/mousePoster.c
- src/hg/mouseStuff/netChainSubset/netChainSubset.c
- src/hg/mouseStuff/netClass/netClass.c
- src/hg/mouseStuff/netContigs/netContigs.c
- src/hg/mouseStuff/netFilter/netFilter.c
- src/hg/mouseStuff/netSplit/netSplit.c
- src/hg/mouseStuff/netStats/netStats.c
- src/hg/mouseStuff/netSyntenic/netSyntenic.c
- src/hg/mouseStuff/netToAxt/netToAxt.c
- src/hg/mouseStuff/netToBed/netToBed.c
- src/hg/mouseStuff/netToBedWithId/netToBedWithId.c
- src/hg/mouseStuff/orthologBySynteny/orthologBySynteny.c
- src/hg/mouseStuff/phToPsl/phToPsl.c
- src/hg/mouseStuff/pslMrnaCover/pslMrnaCover.c
- src/hg/mouseStuff/regionPicker/regionPicker.c
- src/hg/mouseStuff/rikenBestInCluster/rikenBestInCluster.c
- src/hg/mouseStuff/splitSim/splitSim.c
- src/hg/mouseStuff/subsetAxt/subsetAxt.c
- src/hg/mouseStuff/subsetTraces/subsetTraces.c
- src/hg/mouseStuff/whyConserved/trackOverlap.c
- src/hg/mouseStuff/whyConserved/whyConserved.c
- src/hg/mouseStuff/xmfaToMaf/xmfaToMaf.c
- src/hg/mrnaToGene/mrnaToGene.c
- src/hg/nci60/findStanAlignments.c
- src/hg/nci60/stanToBedAndExpRecs.c
- src/hg/near/hgCeOrfToGene/hgCeOrfToGene.c
- src/hg/near/hgClusterGenes/hgClusterGenes.c
- src/hg/near/hgEmblProtLinks/hgEmblProtLinks.c
- src/hg/near/hgExpDistance/diffDistTables.c
- src/hg/near/hgExpDistance/hgExpDistance.c
- src/hg/near/hgExpDistance/hgExpDistance_fm.c
- src/hg/near/hgExpDistance/hgExpDistance_fm_tm.c
- src/hg/near/hgExpDistance/hgExpDistance_fq.c
- src/hg/near/hgExpDistance/hgExpDistance_fq_tm.c
- src/hg/near/hgExpDistance/hgExpDistance_tm.c
- src/hg/near/hgGoAssociation/hgGoAssociation.c
- src/hg/near/hgKnownToSuper/hgKnownToSuper.c
- src/hg/near/hgMapToGene/hgMapToGene.c
- src/hg/near/hgMapViaSwissProt/hgMapViaSwissProt.c
- src/hg/near/hgNear/advFilter.c
- src/hg/near/hgNear/afiAli.c
- src/hg/near/hgNear/configure.c
- src/hg/near/hgNear/expRatio.c
- src/hg/near/hgNear/flyBase.c
- src/hg/near/hgNear/getSeq.c
- src/hg/near/hgNear/go.c
- src/hg/near/hgNear/hgNear.c
- src/hg/near/hgNear/knownGene.c
- src/hg/near/hgNear/search.c
- src/hg/near/hgNear/userSettings.c
- src/hg/near/hgNearTest/hgNearTest.c
- src/hg/near/hgNetDist/hgLoadNetDist.c
- src/hg/near/hgNetDist/hgNetDist.c
- src/hg/near/hgProtIdToGenePred/hgProtIdToGenePred.c
- src/hg/near/hgWormLinks/hgWormLinks.c
- src/hg/near/hgZfishEnsXRef/hgEnsGeneXRef.c
- src/hg/near/pepPredToFa/pepPredToFa.c
- src/hg/oneShot/addChrPsl/addChrPsl.c
- src/hg/oneShot/addMhcClones/addMhcClones.c
- src/hg/oneShot/addTopoToPrimers/addTopoToPrimers.c
- src/hg/oneShot/agpNotInf/agpNotInf.c
- src/hg/oneShot/agpVsMap/agpVsMap.c
- src/hg/oneShot/bargeVsMap/bargeVsMap.c
- src/hg/oneShot/bedFirstCodingExonSize/bedFirstCodingExonSize.c
- src/hg/oneShot/blatFilter/blatFilter.c
- src/hg/oneShot/bridgeDif/bridgeDif.c
- src/hg/oneShot/bwTest/bwTest.c
- src/hg/oneShot/bwTestRead/bwTestRead.c
- src/hg/oneShot/cJoinX/cJoinX.c
- src/hg/oneShot/cacheMergedRanges/cacheMergedRanges.c
- src/hg/oneShot/cacheMergedRanges/rbmTree.c
- src/hg/oneShot/cartSim/cartSim.c
- src/hg/oneShot/cartSimNoInsert/cartSimNoInsert.c
- src/hg/oneShot/chromPosLookup/chromPosLookup.c
- src/hg/oneShot/chromToPos/chromToPos.c
- src/hg/oneShot/clonePos/clonePos.c
- src/hg/oneShot/clonesInAgp/clonesInAgp.c
- src/hg/oneShot/clumpEst3/clumpEst3.c
- src/hg/oneShot/cmpOverlaps/cmpOverlaps.c
- src/hg/oneShot/codAbsAffyQuery/codAbsAffyQuery.c
- src/hg/oneShot/compilerError/compilerError.c
- src/hg/oneShot/dupeFoo/dupeFoo.c
- src/hg/oneShot/dupedInTable/dupedInTable.c
- src/hg/oneShot/evalEndOverlaps/evalEndOverlaps.c
- src/hg/oneShot/evalEndOverlaps/ocp.c
- src/hg/oneShot/evalEnds/evalEnds.c
- src/hg/oneShot/faFiltMasked/faFiltMasked.c
- src/hg/oneShot/faTest/faTest.c
- src/hg/oneShot/fakeBedGraph/fakeBedGraph.c
- src/hg/oneShot/fakeChromGraph/fakeChromGraph.c
- src/hg/oneShot/fakeHomozygousity/fakeHomozygousity.c
- src/hg/oneShot/fakeLinkage/fakeLinkage.c
- src/hg/oneShot/fakeSeqDiffs/fakeSeqDiffs.c
- src/hg/oneShot/findContigsWithClones/findContigsWithClones.c
- src/hg/oneShot/findToFixBedGraphLimits/findToFixBedGraphLimits.c
- src/hg/oneShot/findToFixBedGraphViewLimits/findToFixBedGraphViewLimits.c
- src/hg/oneShot/fixEnsGtf/fixEnsGtf.c
- src/hg/oneShot/fixGdup/fixGdup.c
- src/hg/oneShot/flagMhcClones/flagMhcClones.c
- src/hg/oneShot/getHumanBrainRna/getHumanBrainRna.c
- src/hg/oneShot/hgFreen/hgFreen.c
- src/hg/oneShot/howBadNt/howBadNt.c
- src/hg/oneShot/jingTestFoo/jingTestFoo.c
- src/hg/oneShot/joinToPatch/joinToPatch.c
- src/hg/oneShot/labSheet/labSheet.c
- src/hg/oneShot/makeOrthoAtgTable/makeOrthoAtgTable.c
- src/hg/oneShot/makeTrackDbTagVals/makeTrackDbTagVals.c
- src/hg/oneShot/makeTrackDbTypeTags/makeTrackDbTypeTags.c
- src/hg/oneShot/mapToSts/mapToSts.c
- src/hg/oneShot/mhcToNt/mhcToNt.c
- src/hg/oneShot/missingTable/missingTable.c
- src/hg/oneShot/musAliAt/musAliAt.c
- src/hg/oneShot/newClones/newClones.c
- src/hg/oneShot/oo21Nts/oo21Nts.c
- src/hg/oneShot/padFile/padFile.c
- src/hg/oneShot/patchDir/patchDir.c
- src/hg/oneShot/patchNtAgp/patchNtAgp.c
- src/hg/oneShot/patchToAgp/patchToAgp.c
- src/hg/oneShot/pslCut/pslCut.c
- src/hg/oneShot/raPriority/raPriority.c
- src/hg/oneShot/randomEst/randomEst.c
- src/hg/oneShot/rangeGraph/rangeGraph.c
- src/hg/oneShot/rangeGraph/rgi.c
- src/hg/oneShot/rcvs/rcvs.c
- src/hg/oneShot/rmFromFinf/rmFromFinf.c
- src/hg/oneShot/roundNewViewLimitsInRa/roundNewViewLimitsInRa.c
- src/hg/oneShot/sangPairs/sangPairs.c
- src/hg/oneShot/seqFromPsl/seqFromPsl.c
- src/hg/oneShot/somePsls/somePsls.c
- src/hg/oneShot/spSize/spSize.c
- src/hg/oneShot/spanRaft/spanRaft.c
- src/hg/oneShot/splitNcbiFa/splitNcbiFa.c
- src/hg/oneShot/tdbRewriteAddReplaces/tdbRewriteAddReplaces.c
- src/hg/oneShot/tdbRewriteReduceReplaces/tdbRewriteReduceReplaces.c
- src/hg/oneShot/tdbRewriteRemoveUnused/tdbRewriteRemoveUnused.c
- src/hg/oneShot/tdbRewriteSortTags/tdbRewriteSortTags.c
- src/hg/oneShot/tdbRewriteSubtrackToParent/tdbRewriteSubtrackToParent.c
- src/hg/oneShot/tdbRewriteViewsToSubtracks/tdbRewriteViewsToSubtracks.c
- src/hg/oneShot/tdbRewriteViewsToSubtracks1/tdbRewriteViewsToSubtracks1.c
- src/hg/oneShot/tempLift/tempLift.c
- src/hg/oneShot/tempLower/tempLower.c
- src/hg/oneShot/testBb/testBb.c
- src/hg/oneShot/testCart/cart.c
- src/hg/oneShot/testCart/testCart.c
- src/hg/oneShot/testIndex/testIndex.c
- src/hg/oneShot/testIntersect/testIntersect.c
- src/hg/oneShot/testIxx/testIxx.c
- src/hg/oneShot/testSearch/testSearch.c
- src/hg/oneShot/testTableExists/testTableExists.c
- src/hg/oneShot/testXap/testXap.c
- src/hg/oneShot/tetDensity/tetDensity.c
- src/hg/oneShot/tetFilter/tetFilter.c
- src/hg/oneShot/timeGifPng/timeGifPng.c
- src/hg/oneShot/trimFosmids/trimFosmids.c
- src/hg/oneShot/tryNewColorOverlay/tryNewColorOverlay.c
- src/hg/oneShot/weedKnownBlastTab/weedKnownBlastTab.c
- src/hg/oneShot/weedTab/weedTab.c
- src/hg/oneShot/wgEncodeRegGenRa/wgEncodeRegGenRa.c
- src/hg/orthoMap/orthoEval.c
- src/hg/orthoMap/orthoEvaluate.c
- src/hg/orthoMap/orthoMap.c
- src/hg/orthoMap/orthoPickIntron.c
- src/hg/patCount/patCount.c
- src/hg/perf/hgTracksRandom.c
- src/hg/perf/rangeQuery.c
- src/hg/phyloGif/phyloGif.c
- src/hg/poster/finPoster/finPoster.c
- src/hg/poster/foldDb/checkDupe/checkDupe.c
- src/hg/poster/foldDb/foldDb.c
- src/hg/poster/foldGfx/foldGfx.c
- src/hg/protein/blastRecipBest/blastRecipBest.c
- src/hg/protein/hmmPfamToTab/hmmPfamToTab.c
- src/hg/protein/kgAttachKegg/kgAttachKegg.c
- src/hg/protein/kgBioCyc1/kgBioCyc1.c
- src/hg/protein/kgGetCds/kgGetCds.c
- src/hg/protein/lib/doSam.c
- src/hg/protein/lib/doStamps.c
- src/hg/protein/lib/doTracks.c
- src/hg/protein/lib/domains.c
- src/hg/protein/lib/pbUtil.c
- src/hg/protein/lib/spKgMap.c
- src/hg/protein/lib/spMapper.c
- src/hg/protein/lib/uniref.c
- src/hg/protein/lib/unirefTbl.c
- src/hg/protein/omimParseAv/omimParseAv.c
- src/hg/protein/omimParseRec/omimParseRec.c
- src/hg/protein/pbGlobal/pbGlobal.c
- src/hg/protein/pbTracks/pbTracks.c
- src/hg/protein/scopCollapse/scopCollapse.c
- src/hg/protein/spDbAddVarSplice/spDbAddVarSplice.c
- src/hg/protein/spLoadPsiBlast/spLoadPsiBlast.c
- src/hg/protein/spLoadRankProp/rankPropProt.c
- src/hg/protein/spLoadRankProp/spLoadRankProp.c
- src/hg/protein/spTest/spTest.c
- src/hg/protein/spToDb/spToDb.c
- src/hg/pslCDnaFilter/polyASize.c
- src/hg/pslCDnaGenomeMatch/pslCDnaGenomeMatch.c
- src/hg/pslCat/pslCat.c
- src/hg/pslCheck/pslCheck.c
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- src/hg/pslCrudeCmp/pslCrudeCmp.c
- src/hg/pslDropOverlap/pslDropOverlap.c
- src/hg/pslFilter/pslFilter.c
- src/hg/pslFilterBadCdna/pslFilterBadCdna.c
- src/hg/pslGlue/pslGlue.c
- src/hg/pslHitPercent/pslHitPercent.c
- src/hg/pslIntronsOnly/pslIntronsOnly.c
- src/hg/pslPartition/pslPartition.c
- src/hg/pslPretty/pslPretty.c
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- src/hg/pslRecalcMatch/pslRecalcMatch.c
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- src/hg/pslSplit/pslSplit.c
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- src/hg/pslStats/pslStats.c
- src/hg/pslToPileup/pslToPileup.c
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- src/hg/snp/snpLoad/snpCheckCluster.c
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- src/hg/snp/snpMask/snpMaskGenes.c
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- src/hg/splitFaIntoContigs/splitFaIntoContigs.c
- src/hg/sqlToXml/sqlToXml.c
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- src/hg/txGene/txGeneFromBed/txGeneFromBed.c
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- src/hg/var/fixConrad.c
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- src/hg/visiGene/gensat/gensatRandomXml/gensatRandomXml.c
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- src/hg/visiGene/visiGeneTest/visiGeneTest.c
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- src/hg/xmlCat/xmlCat.c
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- src/index/bptMakeStringToBits64/bptMakeStringToBits64.c
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- src/lib/net.c
- src/lib/nib.c
- src/lib/nibTwo.c
- src/lib/nt4.c
- src/lib/obscure.c
- src/lib/oldGff.c
- src/lib/oligoTm.c
- src/lib/options.c
- src/lib/osunix.c
- src/lib/oswin9x.c
- src/lib/pairHmm.c
- src/lib/phyloTree.c
- src/lib/pngwrite.c
- src/lib/portimpl.c
- src/lib/psGfx.c
- src/lib/psPoly.c
- src/lib/pscmGfx.c
- src/lib/psl.c
- src/lib/pslGenoShow.c
- src/lib/pslShow.c
- src/lib/pthreadWrap.c
- src/lib/qa.c
- src/lib/quickHeap.c
- src/lib/quotedP.c
- src/lib/ra.c
- src/lib/rangeTree.c
- src/lib/rbTree.c
- src/lib/repMask.c
- src/lib/rle.c
- src/lib/rqlEval.c
- src/lib/rqlParse.c
- src/lib/rudp.c
- src/lib/scoreWindow.c
- src/lib/seg.c
- src/lib/seqOut.c
- src/lib/servBrcMcw.c
- src/lib/servCrunx.c
- src/lib/servcis.c
- src/lib/servcl.c
- src/lib/servmsII.c
- src/lib/servpws.c
- src/lib/shaRes.c
- src/lib/slog.c
- src/lib/snof.c
- src/lib/snofmake.c
- src/lib/snofsig.c
- src/lib/spaceSaver.c
- src/lib/spacedColumn.c
- src/lib/spacedSeed.c
- src/lib/splatAli.c
- src/lib/sqlList.c
- src/lib/sqlNum.c
- src/lib/subText.c
- src/lib/synQueue.c
- src/lib/tabRow.c
- src/lib/tests/mimeDecodeTest.c
- src/lib/tests/mimeTester.c
- src/lib/tests/pipelineTester.c
- src/lib/tests/udcTest.c
- src/lib/tests/vcfParseTest.c
- src/lib/textOut.c
- src/lib/tokenizer.c
- src/lib/trix.c
- src/lib/twoBit.c
- src/lib/udc.c
- src/lib/vGfx.c
- src/lib/vGif.c
- src/lib/vPng.c
- src/lib/verbose.c
- src/lib/wildcmp.c
- src/lib/wormdna.c
- src/lib/xAli.c
- src/lib/xa.c
- src/lib/xap.c
- src/lib/xenshow.c
- src/lib/xmlEscape.c
- src/lib/xp.c
- src/oneShot/clusterClone/clusterClone.c
- src/oneShot/dateXmlCgi/dateXmlCgi.c
- src/oneShot/jccTest/jccTest.c
- src/oneShot/mungeAuthors/mungeAuthors.c
- src/oneShot/onePassBedToBigBed/onePassBedToBigBed.c
- src/oneShot/preProcGgfAndy/preProcGgfAndy.c
- src/oneShot/rbIntTest/rbIntTest.c
- src/oneShot/rgbaGfxTest/rgbaGfxTest.c
- src/oneShot/rt1dTest/rt1dTest.c
- src/oneShot/scrapeCruzBiotech/scrapeCruzBiotech.c
- src/oneShot/testCache/testCache.c
- src/oneShot/testGitRename/justAnotherTest.c
- src/oneShot/testScripters/wordUse/wordUse.c
- src/parasol/para/jobDb.c
- src/parasol/para/para.c
- src/parasol/paraHub/paraHub.c
- src/parasol/paraNode/paraNode.c
- src/parasol/parasol/parasol.c
- src/product/ex.hg.conf
- lines changed 4, context: html, text, full: html, text
fiddle a bit with the hg.conf variables to change hubPublc and hubStatus (#6162)
- src/shortReads/bfastMafFix/bfastMafFix.c
- src/shortReads/bwtFind/bwtFind.c
- src/shortReads/bwtMake/bwtMake.c
- src/shortReads/bwtReverse/bwtReverse.c
- src/shortReads/elandToSplat/elandToSplat.c
- src/shortReads/i16Find/i16Dump.c
- src/shortReads/i16Find/i16Find.c
- src/shortReads/i16Make/i16Make.c
- src/shortReads/itsaDump/itsaDump.c
- src/shortReads/itsaFind/itsaFind.c
- src/shortReads/itsaMake/itsaMake.c
- src/shortReads/shortRepeatFind/shortRepeatFind.c
- src/shortReads/shortRepeatMerge/shortRepeatMerge.c
- src/shortReads/splat/splat.c
- src/shortReads/splatCheck1/splatCheck1.c
- src/shortReads/splatCheck2/splatCheck2.c
- src/shortReads/splatMerge/splatMerge.c
- src/shortReads/splatTestSet/splatTestSet.c
- src/shortReads/splatToEland/splatToEland.c
- src/shortReads/splixMake/splixMake.c
- src/shortReads/streamer/streamer.c
- src/shortReads/sufaFind/sufaFind.c
- src/shortReads/sufaMake/sufaMake.c
- src/shortReads/sufaRepeatFind/sufaRepeatFind.c
- src/shortReads/sufxDump/sufxDump.c
- src/shortReads/sufxFind/sufxFind.c
- src/shortReads/sufxMake/sufxMake.c
- src/utils/aNotB/aNotB.c
- src/utils/addCols/addCols.c
- src/utils/ave/ave.c
- src/utils/aveCols/aveCols.c
- src/utils/bbTest/bbTest.c
- src/utils/bdfToGem/bdfToGem.c
- src/utils/bedClip/bedClip.c
- src/utils/bedCommonRegions/bedCommonRegions.c
- src/utils/bedGeneParts/bedGeneParts.c
- src/utils/bedGraphToBigWig/bedGraphToBigWig.c
- src/utils/bedRemoveOverlap/bedRemoveOverlap.c
- src/utils/bedRestrictToPositions/bedRestrictToPositions.c
- src/utils/bedToBigBed/bedToBigBed.c
- src/utils/bedToClosestPoint/bedToClosestPoint.c
- src/utils/bestThreshold/bestThreshold.c
- src/utils/bigBedInfo/bigBedInfo.c
- src/utils/bigBedSummary/bigBedSummary.c
- src/utils/bigBedToBed/bigBedToBed.c
- src/utils/bigWigAverageOverBed/bigWigAverageOverBed.c
- src/utils/bigWigInfo/bigWigInfo.c
- src/utils/bigWigMerge/bigWigMerge.c
- src/utils/bigWigSummary/bigWigSummary.c
- src/utils/bigWigToBedGraph/bigWigToBedGraph.c
- src/utils/bigWigToWig/bigWigToWig.c
- src/utils/cCp/cCp.c
- src/utils/calc/calc.c
- src/utils/catDir/catDir.c
- src/utils/catUncomment/catUncomment.c
- src/utils/ccCp/ccCp.c
- src/utils/ccCpLock/ccCp.3.c
- src/utils/ccCpLock/ccCp.c
- src/utils/ccCpLock/ccCp_rsh.c
- src/utils/chainDist/chainDist.c
- src/utils/chopFaLines/chopFaLines.c
- src/utils/colCount/colCount.c
- src/utils/colTransform/colTransform.c
- src/utils/colorConv/colorConv.c
- src/utils/convolve/convolve.c
- src/utils/correlate/correlate.c
- src/utils/countChars/countChars.c
- src/utils/detab/detab.c
- src/utils/dnsInfo/dnsInfo.c
- src/utils/endsInLf/endsInLf.c
- src/utils/est2genomeToPsl/est2genomeToPsl.c
- src/utils/faAlign/faAlign.c
- src/utils/faCat/faCat.c
- src/utils/faCmp/faCmp.c
- src/utils/faCount/faCount.c
- src/utils/faFilter/faFilter.c
- src/utils/faFilterN/faFilterN.c
- src/utils/faFlyBaseToUcsc/faFlyBaseToUcsc.c
- src/utils/faFrag/faFrag.c
- src/utils/faGapLocs/faGapLocs.c
- src/utils/faGapSizes/faGapSizes.c
- src/utils/faLowerToN/faLowerToN.c
- src/utils/faNcbiToUcsc/faNcbiToUcsc.c
- src/utils/faNoise/faNoise.c
- src/utils/faOneRecord/faOneRecord.c
- src/utils/faPolyASizes/faPolyASizes.c
- src/utils/faRc/faRc.c
- src/utils/faRenameRecords/faRenameRecords.c
- src/utils/faSimplify/faSimplify.c
- src/utils/faSize/faSize.c
- src/utils/faSomeRecords/faSomeRecords.c
- src/utils/faSplit/faSplit.c
- src/utils/faSplit/t.c
- src/utils/faToFastq/faToFastq.c
- src/utils/faToNib/faToNib.c
- src/utils/faToTwoBit/faToTwoBit.c
- src/utils/faTrans/faTrans.c
- src/utils/faTrimPolyA/faTrimPolyA.c
- src/utils/fastqToFa/fastqToFa.c
- src/utils/fileExists/fileExists.c
- src/utils/findMotif/findMotif.c
- src/utils/fixCr/fixCr.c
- src/utils/fixCr/test/fa.c
- src/utils/fixCr/test/gotCr.c
- src/utils/geneStarts/geneStarts.c
- src/utils/git-reports/git-reports.c
- src/utils/greedyPack/greedyPack.c
- src/utils/headRest/headRest.c
- src/utils/htmlCheck/htmlCheck.c
- src/utils/htmlPics/htmlPics.c
- src/utils/jimgrep/jimgrep.c
- src/utils/jkShell/jkShell.c
- src/utils/jkUniq/jkUniq.c
- src/utils/lineCount/lineCount.c
- src/utils/lineFileSplit/lineFileSplit.c
- src/utils/lineRange/lineRange.c
- src/utils/linesInAllFiles/linesInAllFiles.c
- src/utils/makeRgbRainbow/makeRgbRainbow.c
- src/utils/maxEachRow/maxEachRow.c
- src/utils/minEachRow/minEachRow.c
- src/utils/newProg/newProg.c
- src/utils/nibFrag/nibFrag.c
- src/utils/nibSize/nibSize.c
- src/utils/nt4Frag/nt4Frag.c
- src/utils/plotDataMatrix/plotDataMatrix.c
- src/utils/pslLiftSubrangeBlat/pslLiftSubrangeBlat.c
- src/utils/pslToPslx/pslToPslx.c
- src/utils/pslToXa/pslToXa.c
- src/utils/raFromTab/raFromTab.c
- src/utils/raMerge/raMerge.c
- src/utils/raSqlQuery/raRecord.c
- src/utils/raSqlQuery/raSqlQuery.c
- src/utils/raToLines/linesToRa.c
- src/utils/raToLines/raToLines.c
- src/utils/raToSvmLight/raToSvmLight.c
- src/utils/raToTab/raToTab.c
- src/utils/randomLines/randomLines.c
- src/utils/rmFaDups/rmFaDups.c
- src/utils/scaffoldFaToAgp/scaffoldFaToAgp.c
- src/utils/scrambleFa/scrambleFa.c
- src/utils/shuffleLines/shuffleLines.c
- src/utils/sortFa/sortFa.c
- src/utils/spacedToTab/spacedToTab.c
- src/utils/splitFile/splitFile.c
- src/utils/stringify/stringify.c
- src/utils/subChar/subChar.c
- src/utils/subColumn/subColumn.c
- src/utils/subs/subs.c
- src/utils/tableSum/tableSum.c
- src/utils/tailLines/tailLines.c
- src/utils/textHist2/textHist2.c
- src/utils/textHistogram/textHistogram.c
- src/utils/tickToDate/tickToDate.c
- src/utils/timing/gmtime.c
- src/utils/timing/localtime.c
- src/utils/timing/mktime.c
- src/utils/toLower/toLower.c
- src/utils/toUpper/toUpper.c
- src/utils/twoBitInfo/twoBitInfo.c
- src/utils/twoBitToFa/twoBitToFa.c
- src/utils/udcCleanup/udcCleanup.c
- src/utils/undupFa/undupFa.c
- src/utils/upper/upper.c
- src/utils/venn/venn.c
- src/utils/vennIds/vennIds.c
- src/utils/weedLines/weedLines.c
- src/utils/wgetMd5/wgetMd5.c
- src/utils/wigAsciiCrunch/wigAsciiCrunch.c
- src/utils/wigAsciiToBinary/wigAsciiToBinary.c
- src/utils/wigAsciiToBinary/wigBedToBinary.c
- src/utils/wigAsciiToBinary/wigZoom.c
- src/utils/wigCorrelate/wigCorrelate.c
- src/utils/wigSetSpanOrStep/wigSetSpanOrStep.c
- src/utils/wigSort/wigSort.c
- src/utils/wigTestMaker/wigTestMaker.c
- src/utils/wigToBed/wigToBed.c
- src/utils/wigToBedGraph/wigToBedGraph.c
- src/utils/wigToBigWig/wigToBigWig.c
- src/utils/wordLine/wordLine.c
- src/weblet/bottleneck/bottleneck.c
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