All File Changes
v260_preview2 to v260_base (2011-11-22 to 2011-12-06) v260
- python/lib/ucscgenomics/mkChangeNotes.py
- lines changed 5, context: html, text, full: html, text
changes the str output of printsize to be just the megabytes with no unit
- lines changed 1, context: html, text, full: html, text
made it so that tablesize also reprots an int
- python/lib/ucscgenomics/ra.py
- lines changed 0, context: html, text, full: html, text
rebalanced whitespace to use 4 spaces instead of tab
- lines changed 190, context: html, text, full: html, text
added in willy's changed to the ra.py library, only went over changeSummary and updateDiffFilter with him so far, the rest still need to be looked over
- python/lib/ucscgenomics/track.py
- lines changed 2, context: html, text, full: html, text
added line to ignore comments in trackDb.wgEncde.ra
- lines changed 2, context: html, text, full: html, text
patched in support to ignore folders in the release directory not named supplemental
- lines changed 1, context: html, text, full: html, text
corrected an incorrect exception, should be KeyError, FileError is not defined
- lines changed 1, context: html, text, full: html, text
fixed a bad regex for supplemental
- lines changed 13, context: html, text, full: html, text
track files will now generate their md5sum on the fly when it is retrieved when it was originally None. This should be a rare occurance since most files already have an md5sum which is attached through the md5sums.txt file
- 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
- lines changed 2, context: html, text, full: html, text
added -k1,1 to sort options in help message, sort alone doesn't work
- 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/DAFs/3.0/mm9/wgEncodeCaltechRnaSeq.daf
- lines changed 2, context: html, text, full: html, text
Updated bam validation and removed fastq validation, to validate the entire file. Redmine #4156.
- 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/encodeLoad/doEncodeLoad.pl
- src/hg/encode/encodeLoad/doEncodeUnload.pl
- lines changed 12, context: html, text, full: html, text
took out the last remnant of tableSuffix in encodeUnload, missed it in the first pass
- src/hg/encode/encodeMergeReplicates/encodeMergeReplicates.c
- src/hg/encode/encodeMergeReplicatesBatch/encodeMergeReplicatesBatch.c
- src/hg/encode/encodeMkChangeNotes/test/CurrentMkChangeNotes.py
- lines changed 34, context: html, text, full: html, text
moving over mkChangeNotes to current one, passed all internal tests, failed expected end to ends (output changed due to bug fixes)
- src/hg/encode/encodeQaPrepareRelease/encodeQaPrepareRelease
- lines changed 37, context: html, text, full: html, text
changed it so that the lines aren't reordered in trackDb.wgEncode.ra by making the arrays be modified in place instead of a copy
- lines changed 2, context: html, text, full: html, text
added in line to remove trailing whitespace
- src/hg/encode/encodeQaSqlRelease/encodeQaSqlRelease
- lines changed 1, context: html, text, full: html, text
added in close statement for file handle
- src/hg/encode/encodeQaSqlRelease/makefile
- lines changed 1, context: html, text, full: html, text
added compilation check to makefile
- src/hg/encode/encodeRenameObj/encodeRenameObj.c
- src/hg/encode/encodeValidate/doEncodeValidate.pl
- 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/qaRaDiff/qaRaDiff
- lines changed 25, context: html, text, full: html, text
changed RaDiff to use the new ra.py library methods
- lines changed 1, context: html, text, full: html, text
had the comparison backwards
- src/hg/encode/qaUpdateMetadata/qaUpdateMetadata
- lines changed 25, context: html, text, full: html, text
changed to case insensitive sort of vars and added in magic number generation via a temp table in a database
- lines changed 64, context: html, text, full: html, text
rewrite to use library methods
- lines changed 43, context: html, text, full: html, text
fixed qaUpdateMetaData to use libraries and print back out a beta.ra with the magic number, and rebalanced whitespace
- 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/hgFileSearch/hgFileSearch.c
- lines changed 3, context: html, text, full: html, text
More timing in hgFileUi and hgFileSearch led to important efficiency changes. Most notable, I am relying upon cached rsync results now to improve speed.
- src/hg/hgFileUi/hgFileUi.c
- lines changed 1, context: html, text, full: html, text
More timing in hgFileUi and hgFileSearch led to important efficiency changes. Most notable, I am relying upon cached rsync results now to improve speed.
- 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
- lines changed 48, context: html, text, full: html, text
Feature #3707 (VCF in hgTables): Brooke pointed out the annoyance ofVCF custom track's hyperlinks output setting vis to full when it was
already pack. Turns out that the canPack info for all custom tracks
was being discarded due to use of hTrackOpenVis which looks for
trackDb in database. We usually already have the tdb anyway, so when
it's available, look at tdb->canPack and set vis only if the track is
currently hidden.
Also, while looking into a timeout case that Brooke identified, I noticed
that hgTables wasn't calling knetUdc so it was using samtools & tabix's
knetfile library instead of our own -- fixed.
- 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/vcf.c
- lines changed 3, context: html, text, full: html, text
Feature #3707 (VCF+tabix support in hgTables): Brooke reported out-of-memconditions in notes 11 & 12. Fix: add an optional threshold on the number
of records to retrieve in vcfTabixFileMayOpen.
- lines changed 14, context: html, text, full: html, text
Feature #3707 (VCF in hgTables): when calling vcf.c's addFilteredBedsOnRegion ina loop, apply maxOut cumulatively, instead of separately for each region.
Unfortunately, some higher-level code calls vcfGetFilteredBedsOnRegions with
one region at a time, so it doesn't know it's running in a loop. The check for
maxOut needs to move up to top-level (e.g. doSummaryStats), or VCF needs its own
top-level routines, or a true genome-wide query needs to be possible in hgTables.
- 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
- lines changed 10, context: html, text, full: html, text
Imported BUTTON_BY_CSS from branch because it goes with MATRIX_SQUEEZE
- 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/config.c
- lines changed 6, context: html, text, full: html, text
Imported BUTTON_BY_CSS from branch because it goes with MATRIX_SQUEEZE
- src/hg/hgTracks/encode.c
- src/hg/hgTracks/gbrowseTest.c
- src/hg/hgTracks/hapmapTrack.c
- src/hg/hgTracks/hgTracks.c
- lines changed 9, context: html, text, full: html, text
add tdbSetCartVisibility and use in hgTracks to fix #1666
- lines changed 6, context: html, text, full: html, text
Imported BUTTON_BY_CSS from branch because it goes with MATRIX_SQUEEZE
- 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/searchTracks.c
- lines changed 8, context: html, text, full: html, text
Imported BUTTON_BY_CSS from branch because it goes with MATRIX_SQUEEZE
- src/hg/hgTracks/simpleTracks.c
- src/hg/hgTracks/transcriptome.c
- src/hg/hgTracks/variation.c
- src/hg/hgTracks/vcfTrack.c
- lines changed 7, context: html, text, full: html, text
Feature #3711 (VCF haplotype-sorting display): Fixed a silly boundary& rounding error in pixel loop. Also, use lower case for alternate
allele in cluster mouseovers so the relationship to blue and red pixels
is more clear.
- lines changed 1, context: html, text, full: html, text
Fix for buffer overflow case found by Brooke, in vcfToPgSnp allele-abbreviating code.
- lines changed 1, context: html, text, full: html, text
Feature #3707 (VCF+tabix support in hgTables): Brooke reported out-of-memconditions in notes 11 & 12. Fix: add an optional threshold on the number
of records to retrieve in vcfTabixFileMayOpen.
- lines changed 164, context: html, text, full: html, text
Feature #3711 (VCF haplo-sorting display): Implemented Richard Durbin'ssuggestions as new defaults:
1. Instead of ref=blue, alt=red, simply ignore ref and draw only alt, in black.
Draw top & bottom bounds of variants in extra pixel rows.
2. Draw the tree using open triangles instead of open rectangles.
- 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/gencodeClick.c
- lines changed 22, context: html, text, full: html, text
display gencode annotation remarks
- src/hg/hgc/hgc.c
- lines changed 5, context: html, text, full: html, text
Jacob Pedersen noticed evofold was failing hgc because low type said double but actually the column contained a blob.
- 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/t2g.c
- lines changed 4, context: html, text, full: html, text
added copyright notice for elsevier t2g data
- lines changed 5, context: html, text, full: html, text
variable scope changes after hiram code review
- lines changed 11, context: html, text, full: html, text
variable name changes after hiram code review
- src/hg/hgc/txCdsInfo.c
- src/hg/hgc/vcfClick.c
- lines changed 1, context: html, text, full: html, text
oops, forgot cartSaveSession() in VCF details page's little form to anchor haplotype sorting to this variant.
- lines changed 1, context: html, text, full: html, text
Feature #3707 (VCF+tabix support in hgTables): Brooke reported out-of-memconditions in notes 11 & 12. Fix: add an optional threshold on the number
of records to retrieve in vcfTabixFileMayOpen.
- 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/htdocs/ENCODE/downloads.html
- lines changed 5, context: html, text, full: html, text
removing HAIB TFBS hg18 because it has been revoked, redmine #4558
- lines changed 5, context: html, text, full: html, text
Added Haib Methlyl450, redmine #4234
- src/hg/htdocs/ENCODE/downloadsMouse.html
- lines changed 4, context: html, text, full: html, text
adding Caltech TFBS mm9, redmine# 4154
- lines changed 4, context: html, text, full: html, text
adding Caltech Histone mm9, redmine# 4155
- lines changed 1, context: html, text, full: html, text
Noticed that the long lable had a duplicate: Caltech Histone mm9, redmine# 4155
- src/hg/htdocs/ENCODE/pubs.html
- src/hg/htdocs/FAQ/FAQdownloads.html
- lines changed 1, context: html, text, full: html, text
Changed mailto:genome@soe.ucsc.edu link in the 'Converting genome coordinates between assemblies' section to point to the Contacts page
- src/hg/htdocs/FAQ/FAQreleases.html
- lines changed 2, context: html, text, full: html, text
Added gorilla and gibbon to release list.
- src/hg/htdocs/goldenPath/credits.html
- lines changed 7, context: html, text, full: html, text
Updated gorilla + gibbon credits, per Steve.
- src/hg/htdocs/goldenPath/help/customTrackText.html
- lines changed 5, context: html, text, full: html, text
clarified text explaining how to remove custom tracks
- src/hg/htdocs/goldenPath/help/vcf.html
- lines changed 2, context: html, text, full: html, text
Feature #2822 (VCF customFactory): Fixing typo caught by Brooke.
- lines changed 2, context: html, text, full: html, text
adding the VCF file versions that we support per http://redmine.soe.ucsc.edu/issues/5529#note-19
- src/hg/htdocs/goldenPath/newsarch.html
- lines changed 3, context: html, text, full: html, text
Made a few more edits; fixed a typo found by Steve.
- src/hg/htdocs/goldenPath/pubs.html
- lines changed 7, context: html, text, full: html, text
Added Heiser pub at David's request.
- src/hg/htdocs/indexNews.html
- lines changed 10, context: html, text, full: html, text
Made a few more edits to cow announcement, fixed a few format glitches and typos, including some noted by Steve.
- src/hg/htdocs/style/HGStyle.css
- lines changed 11, context: html, text, full: html, text
Imported BUTTON_BY_CSS from branch because it goes with MATRIX_SQUEEZE
- lines changed 14, context: html, text, full: html, text
More style for matrix sqeeze that was developed in a branch
- lines changed 1, context: html, text, full: html, text
Hopefully these are the last missing pieces of MATRIX_SQUEEZE
- lines changed 2, context: html, text, full: html, text
Moved calculating of squeezed matrix label heights to js, since it is so browser dependent.
- src/hg/inc/cart.h
- lines changed 2, context: html, text, full: html, text
add tdbSetCartVisibility and use in hgTracks to fix #1666
- src/hg/inc/fileUi.h
- lines changed 1, context: html, text, full: html, text
More timing in hgFileUi and hgFileSearch led to important efficiency changes. Most notable, I am relying upon cached rsync results now to improve speed.
- 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/inc/jsHelper.h
- lines changed 3, context: html, text, full: html, text
Imported BUTTON_BY_CSS from branch because it goes with MATRIX_SQUEEZE
- lines changed 2, context: html, text, full: html, text
Katrina is not ready for BUTTONS_BY_CSS in this release.
- src/hg/inc/mdb.h
- lines changed 3, context: html, text, full: html, text
More timing in hgFileUi and hgFileSearch led to important efficiency changes. Most notable, I am relying upon cached rsync results now to improve speed.
- src/hg/inc/trackDb.h
- lines changed 9, context: html, text, full: html, text
add tdbSetCartVisibility and use in hgTracks to fix #1666
- src/hg/inc/vcfUi.h
- lines changed 7, context: html, text, full: html, text
Feature #3711 (VCF haplo-sorting display): Implemented Richard Durbin'ssuggestions as new defaults:
1. Instead of ref=blue, alt=red, simply ignore ref and draw only alt, in black.
Draw top & bottom bounds of variants in extra pixel rows.
2. Draw the tree using open triangles instead of open rectangles.
- src/hg/inc/versionInfo.h
- src/hg/intronEnds/intronEnds.c
- src/hg/intronSizes/intronSizes.c
- src/hg/js/hgTracks.js
- lines changed 2, context: html, text, full: html, text
Imported BUTTON_BY_CSS from branch because it goes with MATRIX_SQUEEZE
- src/hg/js/hui.js
- lines changed 44, context: html, text, full: html, text
Hopefully these are the last missing pieces of MATRIX_SQUEEZE
- lines changed 1, context: html, text, full: html, text
Katrina is very particular about colors
- lines changed 1, context: html, text, full: html, text
At this point, IE can't handle the matrix hover highlite.
- lines changed 29, context: html, text, full: html, text
Moved calculating of squeezed matrix label heights to js, since it is so browser dependent.
- src/hg/js/utils.js
- lines changed 30, context: html, text, full: html, text
Imported BUTTON_BY_CSS from branch because it goes with MATRIX_SQUEEZE
- 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
- lines changed 1, context: html, text, full: html, text
Feature #3707 (VCF+tabix support in hgTables): Brooke reported out-of-memconditions in notes 11 & 12. Fix: add an optional threshold on the number
of records to retrieve in vcfTabixFileMayOpen.
- src/hg/lib/customPp.c
- src/hg/lib/customTrack.c
- src/hg/lib/cutter.c
- src/hg/lib/cv.c
- lines changed 7, context: html, text, full: html, text
cache NULLs in cvTermHash to avoid repeated lookups (part of attempt to speedup hgFileUi)
- lines changed 28, context: html, text, full: html, text
Improved cv efficiency by only reading the cv.ra file once.
- 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.as
- lines changed 1, context: html, text, full: html, text
used blob for annotation remarks
- src/hg/lib/encode/wgEncodeGencodeAnnotationRemark.c
- src/hg/lib/encode/wgEncodeGencodeAnnotationRemark.sql
- lines changed 2, context: html, text, full: html, text
used blob for annotation remarks
- 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/fileUi.c
- lines changed 46, context: html, text, full: html, text
Minor efficiency improvements to hgFileUi. Mostly added measureTiming support.
- lines changed 7, context: html, text, full: html, text
If field were NULL, then a bad pointer error could occur
- lines changed 85, context: html, text, full: html, text
More timing in hgFileUi and hgFileSearch led to important efficiency changes. Most notable, I am relying upon cached rsync results now to improve speed.
- 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/hui.c
- lines changed 44, context: html, text, full: html, text
Imported BUTTON_BY_CSS from branch because it goes with MATRIX_SQUEEZE
- lines changed 22, context: html, text, full: html, text
Merging in update to MATRIX_SQUEEZE that was left on branch.
- lines changed 12, context: html, text, full: html, text
New calculation for squeezed label height
- lines changed 3, context: html, text, full: html, text
Basing calc on font size has improved things, but height needs to be declared as em not pix. Now this looks perfect in my Linux/FF but not on Katrina's. No doubt there are still tweeks to be done.
- lines changed 36, context: html, text, full: html, text
Moved calculating of squeezed matrix label heights to js, since it is so browser dependent.
- 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
- lines changed 6, context: html, text, full: html, text
Imported BUTTON_BY_CSS from branch because it goes with MATRIX_SQUEEZE
- lines changed 33, context: html, text, full: html, text
Allow minimizing json output with -1 indent level. While having the apache server DEFLATE will make this change of little value, I thought I would check it in, rather than loose it.
- 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
- lines changed 47, context: html, text, full: html, text
More timing in hgFileUi and hgFileSearch led to important efficiency changes. Most notable, I am relying upon cached rsync results now to improve speed.
- 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/search.c
- lines changed 5, context: html, text, full: html, text
Imported BUTTON_BY_CSS from branch because it goes with MATRIX_SQUEEZE
- 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
- lines changed 23, context: html, text, full: html, text
add tdbSetCartVisibility and use in hgTracks to fix #1666
- 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/vcfUi.c
- lines changed 1, context: html, text, full: html, text
Feature #3711 (VCF haplotype-sorting display): reduce min height to 4, because there can be as few as 4 haplotypes to sort.
- lines changed 16, context: html, text, full: html, text
Feature #3710 (vcfTabix UI options): added section headers forhaplo-sorting display and filters; added some explanatory text at
the beginning of the haplo-sorting section.
- lines changed 1, context: html, text, full: html, text
Feature #3707 (VCF+tabix support in hgTables): Brooke reported out-of-memconditions in notes 11 & 12. Fix: add an optional threshold on the number
of records to retrieve in vcfTabixFileMayOpen.
- lines changed 26, context: html, text, full: html, text
Feature #3711 (VCF haplo-sorting display): Implemented Richard Durbin'ssuggestions as new defaults:
1. Instead of ref=blue, alt=red, simply ignore ref and draw only alt, in black.
Draw top & bottom bounds of variants in extra pixel rows.
2. Draw the tree using open triangles instead of open rectangles.
- 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/doc/dipOrd1.txt
- src/hg/makeDb/doc/encodeDccHg19/wgEncodeHaibMethyl450.release1.notes
- lines changed 164, context: html, text, full: html, text
Adding notes file for HaibMethyl450
- lines changed 3, context: html, text, full: html, text
updating size of supplemental
- src/hg/makeDb/doc/encodeDccHg19/wgEncodeRikenCage.release2.notes
- lines changed 117, context: html, text, full: html, text
Fixed the release notes to take out clusters
- src/hg/makeDb/doc/encodeDccHg19/wgEncodeUwRepliSeq.release1.notes
- lines changed 777, context: html, text, full: html, text
Added notes file for first release. Redmine #4577.
- src/hg/makeDb/doc/encodeDccHg19/wgEncodeUwTfbs.release2.notes
- lines changed 80, context: html, text, full: html, text
put the cell lines without inputs as attic files
- src/hg/makeDb/doc/encodeDccMm9/wgEncodeCaltechHist.release1.notes
- lines changed 18, context: html, text, full: html, text
Re-ran changeNotes since gbdb paths were using /usr/local/apache instead of /gbdb.
- src/hg/makeDb/doc/fr3.txt
- lines changed 366, context: html, text, full: html, text
done with genbank and starting lastz runs with other fish
- lines changed 96, context: html, text, full: html, text
first set of lastz runs done, experiment underway with gasAcu1
- lines changed 45, context: html, text, full: html, text
done with gasAcu1 lastz experiments and all fish lastz runs
- src/hg/makeDb/doc/gasAcu1.txt
- lines changed 59, context: html, text, full: html, text
add WGS link information, and document the WindowMasker run
- src/hg/makeDb/doc/gorGor3.txt
- lines changed 22, context: html, text, full: html, text
first pass of 11-way multiz has been loaded
- src/hg/makeDb/doc/hetGla1.txt
- lines changed 817, context: html, text, full: html, text
Initial work for naked mole-rat Heterocephalus glaber
- src/hg/makeDb/doc/hg19.txt
- lines changed 3, context: html, text, full: html, text
Tweak to make less editing work in the future: derive dated directoryname from output of date command instead of search & replace.
- lines changed 15, context: html, text, full: html, text
Updating the commands for setting up the Rfam data used by UCSC Genes. Now that we're getting Rfam coordinates from the Rfam team, this process is a whole lot simpler
- lines changed 53, context: html, text, full: html, text
Track #5630 SIB Alt-Splicing using true hg19 data.
- lines changed 5, context: html, text, full: html, text
Changed the Rfam parsing to generate BED 12 data rather than BED 6
- src/hg/makeDb/doc/oreNil1.txt
- lines changed 234, context: html, text, full: html, text
done with masking, prepare for kluster runs
- lines changed 1, context: html, text, full: html, text
make a comment actually a comment
- lines changed 19, context: html, text, full: html, text
add blat server for tilapia and default position, minor notes in oryLat2, tetNig2 and xenTro3
- src/hg/makeDb/doc/ornAna1.txt
- lines changed 96, context: html, text, full: html, text
Finished CpG Islands for Platypus.
- src/hg/makeDb/doc/oryLat2.txt
- lines changed 2, context: html, text, full: html, text
add blat server for tilapia and default position, minor notes in oryLat2, tetNig2 and xenTro3
- src/hg/makeDb/doc/tetNig2.txt
- lines changed 3, context: html, text, full: html, text
add blat server for tilapia and default position, minor notes in oryLat2, tetNig2 and xenTro3
- src/hg/makeDb/doc/ucscGenes/hg19.ucscGenes13.csh
- lines changed 10, context: html, text, full: html, text
Fixing the bug described in Redmine # 411, Question #10, on size discrepancies between the sequence in knownGeneTxMrna and the alignment in kgTargetAli. Lo and behold, the executable txCdsToGene makes occasional changes to the gene structure and outputs a new bed file, but txGeneProtAndRna (which creates ucscGenesTx.fa) wasn't working with this new bed file but was working with the outdated file
- lines changed 16, context: html, text, full: html, text
Setting up UCSC Genes for Round 3. Two differences from last time: (1) we now getting Rfam coordinates from the Rfam group, so the Rfam processing is greatly simplified, and (2) the related genomes include now sacCer3 instead of sacCer2, and ce6 instead of ce9 (that last one had been an error)
- lines changed 17, context: html, text, full: html, text
Updated the Rfam repository. We are now getting hg19 genomic alignments from the Rfam group, so we no longer have to re-derive the Rfam regions. This not only simplifies our own processing (greatly), it puts the ball in the Rfam court if any user takes exception with any of the Rfam hits
- src/hg/makeDb/doc/xenTro3.txt
- lines changed 2, context: html, text, full: html, text
add blat server for tilapia and default position, minor notes in oryLat2, tetNig2 and xenTro3
- src/hg/makeDb/genbank/etc/align.dbs
- src/hg/makeDb/genbank/etc/genbank.conf
- lines changed 1, context: html, text, full: html, text
no per-chrom tables on fr3
- src/hg/makeDb/genbank/etc/hgwdev.dbs
- src/hg/makeDb/genbank/etc/rr.dbs
- lines changed 2, context: html, text, full: html, text
Added gorGor3 and nomLeu1
- 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/all.joiner
- lines changed 5, context: html, text, full: html, text
removed one line and added rgdPathwayId definitiion
- lines changed 9, context: html, text, full: html, text
Added rgdGenePathway.pathwayId minCheck=.90 to rgdPathwayId.
- 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/trackDb/all_est.html
- lines changed 2, context: html, text, full: html, text
Full text of BLAT article is now free. Changed the URL from abstract to full. Also updated 'Genbank: update' URL
- src/hg/makeDb/trackDb/all_mrna.html
- lines changed 2, context: html, text, full: html, text
Full text of BLAT article is now free. Changed the URL from abstract to full. Also updated 'Genbank: update' URL
- src/hg/makeDb/trackDb/cow/bosTau6/description.html
- lines changed 10, context: html, text, full: html, text
Fixed up some typos and made a few edits.
- lines changed 1, context: html, text, full: html, text
Made some more edits, fixed some format glitches and typos.
- src/hg/makeDb/trackDb/cpgIslandExt.html
- lines changed 5, context: html, text, full: html, text
Got rid of useless <tt> tag. Simplified final sentence before equation to make more sense and get rid of unneeded text.
- lines changed 36, context: html, text, full: html, text
html cleanup: lowercased tags, added missing end tags, made formatting more readable, change <em> to <i> for semantic reasons.
- src/hg/makeDb/trackDb/cv/alpha/cv.ra
- lines changed 1, context: html, text, full: html, text
Adding 2 donors to PanIslets description
- lines changed 8, context: html, text, full: html, text
Updating diffProtA, Adding day2,fixing day 0 and 14
- lines changed 10, context: html, text, full: html, text
Changing treatment to 9 day
- lines changed 7, context: html, text, full: html, text
Beta fixes being done on alpha
- lines changed 1, context: html, text, full: html, text
Using full vendor ID in label
- lines changed 10, context: html, text, full: html, text
Fixing eGFP cousins labels
- lines changed 5, context: html, text, full: html, text
Added 2x100 paried-end read for Caltech RNA-Seq track. Redmine #4156.
- lines changed 36, context: html, text, full: html, text
Trying to add the RNA Treatments
- lines changed 1, context: html, text, full: html, text
Fixed broken link on alpha, that had incorrect syntax. Redmine #1012.
- lines changed 3, context: html, text, full: html, text
Removed links to files that didn't exist and update with missing, which is the standard. Redmine #1012.
- src/hg/makeDb/trackDb/cv/beta/cv.ra
- lines changed 10, context: html, text, full: html, text
Fixing eGFP cousins targets
- lines changed 377, context: html, text, full: html, text
Copying alpha cv to beta
- src/hg/makeDb/trackDb/cv/public/cv.ra
- lines changed 7, context: html, text, full: html, text
Fixed some labels that missed when moving labels from beta/cv.ra to public/cv.ra
1. FOS -> eGFP-FOS
2. GATA1 (GATA-1) -> GATA-1
3. GATA1 ( sc-265) -> GATA1 (sc-265) "removed extra space"
4. IKZF1 (IKZF1_(IkN)) ->IKZF1 (IkN)
5. PLU1 (PLU1) -> PLU1
6. TR4 (TR4) -> TR4
7. ELAVL1 (SC-5261) -> ELAVL1 (sc-5261) "lower case sc"
8. SLBP (06-1376; 26522; MA156353) -> SLBP "Need to talk to Jeff about multiple antibodies."
- lines changed 1, context: html, text, full: html, text
forogt 8. SLBP (06-1376; 26522; MA156353) -> SLBP 'Need to talk to Jeff about multiple antibodies.' in last commit.
- lines changed 93, context: html, text, full: html, text
These changes have been approved and moved from beta/cv.ra to public. Redmine #6100. Note: This doesn't need to be code reviewed.
- src/hg/makeDb/trackDb/est.html
- lines changed 1, context: html, text, full: html, text
Full text of BLAT article is now free. Changed the URL from abstract to full.
- src/hg/makeDb/trackDb/gibbon/nomLeu1/description.html
- lines changed 1, context: html, text, full: html, text
Moved a period from inside to outside a link
- lines changed 5, context: html, text, full: html, text
Add version numbers are ignored in mRNA serach example.
- lines changed 2, context: html, text, full: html, text
Removed '.2' and the note about version numbers from the sample query since the query including version numbers causes an error on beta and the RR
- src/hg/makeDb/trackDb/gorilla/gorGor3/description.html
- lines changed 4, context: html, text, full: html, text
Removed the trailing '.2' from the sample queries because they caused an error when searching with the. Removed unnecessary period from a URL.
- lines changed 1, context: html, text, full: html, text
Removed a period from inside a link
- src/hg/makeDb/trackDb/human/encodeEgaspFull.html
- lines changed 14, context: html, text, full: html, text
Fixed a broken link and updated various outdated links
- lines changed 1, context: html, text, full: html, text
Changed genome.imim.es to genome.crg.es
- lines changed 1, context: html, text, full: html, text
Changed Aceview to AceView
- lines changed 5, context: html, text, full: html, text
Changed 'Jigsaw' to 'JIGSAW'
- src/hg/makeDb/trackDb/human/encodeEgaspSuper.html
- lines changed 46, context: html, text, full: html, text
Fixed broken link and updated several outdated linkes
- src/hg/makeDb/trackDb/human/hapmapSnps.html
- lines changed 15, context: html, text, full: html, text
Fixed a broken link. Updated some outdated links.
- src/hg/makeDb/trackDb/human/hg16/encodeMlaganAlign.html
- lines changed 17, context: html, text, full: html, text
Removed a link that was no longer valid. Updated some outdated links.
- lines changed 2, context: html, text, full: html, text
Corrected journal citation format
- lines changed 7, context: html, text, full: html, text
Corrected journal citation format
- src/hg/makeDb/trackDb/human/hg16/hg17Kg.html
- lines changed 18, context: html, text, full: html, text
Fixed a broken link. Updated some outdated links.
- lines changed 1, context: html, text, full: html, text
Changed link to point directly to UniProt
- src/hg/makeDb/trackDb/human/hg17/encodeGisChipPetAll.html
- lines changed 3, context: html, text, full: html, text
Fixed broken link and updated some outdated links
- lines changed 1, context: html, text, full: html, text
Removed comma before et. al.
- src/hg/makeDb/trackDb/human/hg17/encodeMlaganAlign.html
- lines changed 16, context: html, text, full: html, text
Removed a link that was no longer valid. Updated some outdated links.
- lines changed 7, context: html, text, full: html, text
Corrected journal citation format
- src/hg/makeDb/trackDb/human/hg17/encodeTbaAlign.html
- lines changed 18, context: html, text, full: html, text
Corrected journal citation format
- src/hg/makeDb/trackDb/human/hg17/encodeUppsalaChip.html
- lines changed 6, context: html, text, full: html, text
Fixed a broken link. Updated some outdated links. Corrected citation format.
- lines changed 1, context: html, text, full: html, text
Updated an outdated link.
- src/hg/makeDb/trackDb/human/hg17/encodeUppsalaChipBut.html
- lines changed 56, context: html, text, full: html, text
Fixed a broken link. Updated some outdated links. Corrected citation format.
- src/hg/makeDb/trackDb/human/hg17/encodeYaleChipRfbr.html
- lines changed 6, context: html, text, full: html, text
Fixed a broken link. Updated an outdated link.
- src/hg/makeDb/trackDb/human/hg17/knownGene.html
- lines changed 17, context: html, text, full: html, text
Fixed a broken link and updated some outdated links
- src/hg/makeDb/trackDb/human/hg17/retroposons.html
- lines changed 8, context: html, text, full: html, text
Removed broken link. Created link to Roswell Park Cancer Institute. Updated outdated links.
- src/hg/makeDb/trackDb/human/hg17/sangamoDnaseHs.html
- lines changed 13, context: html, text, full: html, text
Fixed a broken link and updated some outdated links
- src/hg/makeDb/trackDb/human/hg17/snpArray.html
- src/hg/makeDb/trackDb/human/hg18/knownGene.html
- lines changed 14, context: html, text, full: html, text
Fixed a broken link and updated some outdated links
- src/hg/makeDb/trackDb/human/hg18/stsMap.html
- lines changed 7, context: html, text, full: html, text
Fixed a broken link and updated some outdated links
- src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
- lines changed 3, context: html, text, full: html, text
Removing hg18 HAIB TFBS track
- src/hg/makeDb/trackDb/human/hg18/wgEncodeGisChipPetAll.html
- lines changed 8, context: html, text, full: html, text
Fixed a broken link and updated some outdated links
- src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaMethyl27.html
- src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaMethylSeq.html
- lines changed 4, context: html, text, full: html, text
Fixed a broken link and updated an outdated link
- src/hg/makeDb/trackDb/human/hg19/knownGeneNew.html
- lines changed 5, context: html, text, full: html, text
In response to Redmine # 5002, Question # 9: added a brief description of the knownToRefSeq table and how its content differs from the RefSeq portion of kgXref
- src/hg/makeDb/trackDb/human/hg19/lincRNAs.html
- lines changed 16, context: html, text, full: html, text
Added a key to show what the track's colors mean. Brian and I are looking into this a bit more and might put up a more accurate key later.
- src/hg/makeDb/trackDb/human/hg19/merkPolyA.html
- lines changed 449, context: html, text, full: html, text
Created merkPolyA.html.
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/makefile
- lines changed 1, context: html, text, full: html, text
Adding Gencode V9 to the makefile
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGencodeV9.ra
- lines changed 276, context: html, text, full: html, text
Adding the metaData for GencodeV9
- lines changed 46, context: html, text, full: html, text
Added an object, removed md5sums and subIds, added dccAccession
- lines changed 17, context: html, text, full: html, text
added subIds and fixed a link to downloadable file
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethyl450.ra
- lines changed 170, context: html, text, full: html, text
Ticket 4234, added dccAccessions, added an expVar, changed the labels for 116 from Stanford to HAIB, fixed some spacing issues in the html
- lines changed 4, context: html, text, full: html, text
Adding replicate number back to the Stanford sample
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra
- lines changed 2, context: html, text, full: html, text
Removing the -m for Caltech, these are only human, the lab must have used the wrong DAF
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromChip.ra
- lines changed 20, context: html, text, full: html, text
first step of rename, renamed to have donor id
- lines changed 73, context: html, text, full: html, text
restored old trackDb and metaDb entries
- lines changed 6, context: html, text, full: html, text
fixed metadata to reflect renamed status for old objects
- lines changed 4, context: html, text, full: html, text
changed cell line to proper term
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeRikenCage.ra
- lines changed 63, context: html, text, full: html, text
Changes according to Katrina in ticket 2020
- lines changed 42, context: html, text, full: html, text
Adding the metaData link and changing the TssHmm files to say bed
- lines changed 1323, context: html, text, full: html, text
Adding back the clusters as .bed files and attic
- lines changed 155, context: html, text, full: html, text
Added back the TssHmm bedRnaElements
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDgf.ra
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDnase.ra
- lines changed 5, context: html, text, full: html, text
changed CD20+ > CD20+_RO01778
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwRepliSeq.ra
- lines changed 857, context: html, text, full: html, text
Added experiments with 2 new cell lines GM12812 and GM12813. Redmine #4577.
- lines changed 430, context: html, text, full: html, text
Updated md5sum and expVars. Redmine #4577.
- lines changed 705, context: html, text, full: html, text
Added dccAccession and experimentIds for track. 15 unique experiments. Redmine #4577.
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwTfbs.ra
- lines changed 62, context: html, text, full: html, text
made the cell lines missing inputs attic files
- src/hg/makeDb/trackDb/human/hg19/metaDb/beta/makefile
- lines changed 1, context: html, text, full: html, text
staging Haib Methyl450, Redmine# 4234
- lines changed 1, context: html, text, full: html, text
added the missing seprarater to the make file
- src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeBroadHistone.ra
- lines changed 920, context: html, text, full: html, text
updated betaMdb with dccAccessions.
- lines changed 920, context: html, text, full: html, text
Revert "updated betaMdb with dccAccessions."
This reverts commit b3f4b90175570e64e2464c758d3b3dbf780769fb.
- lines changed 920, context: html, text, full: html, text
added dccAccessions to tracks that are missing them
- src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeCshlShortRnaSeq.ra
- lines changed 54, context: html, text, full: html, text
updated betaMdb with dccAccessions.
- lines changed 54, context: html, text, full: html, text
Revert "updated betaMdb with dccAccessions."
This reverts commit b3f4b90175570e64e2464c758d3b3dbf780769fb.
- lines changed 54, context: html, text, full: html, text
added dccAccessions to tracks that are missing them
- src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeHaibMethyl450.ra
- lines changed 1455, context: html, text, full: html, text
staging Haib Methyl450, Redmine# 4234
- src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeHaibTfbs.ra
- lines changed 25, context: html, text, full: html, text
revoking HEY1 and K562/BCL3 experiments in beta only
- src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeOpenChromChip.ra
- lines changed 271, context: html, text, full: html, text
updated betaMdb with dccAccessions.
- lines changed 271, context: html, text, full: html, text
Revert "updated betaMdb with dccAccessions."
This reverts commit b3f4b90175570e64e2464c758d3b3dbf780769fb.
- lines changed 270, context: html, text, full: html, text
added dccAccessions to tracks that are missing them
- src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeOpenChromDnase.ra
- lines changed 328, context: html, text, full: html, text
updated betaMdb with dccAccessions.
- lines changed 328, context: html, text, full: html, text
Revert "updated betaMdb with dccAccessions."
This reverts commit b3f4b90175570e64e2464c758d3b3dbf780769fb.
- lines changed 328, context: html, text, full: html, text
added dccAccessions to tracks that are missing them
- src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeOpenChromFaire.ra
- lines changed 179, context: html, text, full: html, text
updated betaMdb with dccAccessions.
- lines changed 179, context: html, text, full: html, text
Revert "updated betaMdb with dccAccessions."
This reverts commit b3f4b90175570e64e2464c758d3b3dbf780769fb.
- lines changed 179, context: html, text, full: html, text
added dccAccessions to tracks that are missing them
- src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeRikenCage.ra
- lines changed 101, context: html, text, full: html, text
updated betaMdb with dccAccessions.
- lines changed 101, context: html, text, full: html, text
Revert "updated betaMdb with dccAccessions."
This reverts commit b3f4b90175570e64e2464c758d3b3dbf780769fb.
- lines changed 102, context: html, text, full: html, text
added dccAccessions to tracks that are missing them
- lines changed 2, context: html, text, full: html, text
restored order of var val pair
- lines changed 1, context: html, text, full: html, text
fixing typo: fileiIndex -> fileIndex
- lines changed 100, context: html, text, full: html, text
changed to case insensitive sort of vars and added in magic number generation via a temp table in a database
- lines changed 5676, context: html, text, full: html, text
staging RIKEN CAGE Loc Release2 on beta, #2020
- src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeSunyAlbanyTiling.ra
- lines changed 8, context: html, text, full: html, text
updated betaMdb with dccAccessions.
- lines changed 8, context: html, text, full: html, text
Revert "updated betaMdb with dccAccessions."
This reverts commit b3f4b90175570e64e2464c758d3b3dbf780769fb.
- lines changed 8, context: html, text, full: html, text
added dccAccessions to tracks that are missing them
- src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeUwAffyExonArray.ra
- lines changed 135, context: html, text, full: html, text
updated betaMdb with dccAccessions.
- lines changed 135, context: html, text, full: html, text
Revert "updated betaMdb with dccAccessions."
This reverts commit b3f4b90175570e64e2464c758d3b3dbf780769fb.
- lines changed 135, context: html, text, full: html, text
added dccAccessions to tracks that are missing them
- src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeUwDgf.ra
- lines changed 114, context: html, text, full: html, text
updated betaMdb with dccAccessions.
- lines changed 114, context: html, text, full: html, text
Revert "updated betaMdb with dccAccessions."
This reverts commit b3f4b90175570e64e2464c758d3b3dbf780769fb.
- lines changed 114, context: html, text, full: html, text
added dccAccessions to tracks that are missing them
- src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeUwTfbs.ra
- lines changed 483, context: html, text, full: html, text
updated betaMdb with dccAccessions.
- lines changed 483, context: html, text, full: html, text
Revert "updated betaMdb with dccAccessions."
This reverts commit b3f4b90175570e64e2464c758d3b3dbf780769fb.
- lines changed 483, context: html, text, full: html, text
added dccAccessions to tracks that are missing them
- src/hg/makeDb/trackDb/human/hg19/metaDb/public/makefile
- lines changed 1, context: html, text, full: html, text
Added Haib Methlyl450, redmine #4234
- src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeCaltechRnaSeq.ra
- lines changed 98, context: html, text, full: html, text
adding dccAccessions to Caltech RNA-seq track, redmine #6067
- src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeHaibMethyl450.ra
- lines changed 1455, context: html, text, full: html, text
Added Haib Methlyl450, redmine #4234
- src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeRikenCage.ra
- lines changed 101, context: html, text, full: html, text
releasing dccAccesssions and a typo fix to RR for wgEncodeRikenCage, redmine #6067
- src/hg/makeDb/trackDb/human/hg19/trackDb.merckPolyA.all.ra
- lines changed 306, context: html, text, full: html, text
Created trackDb.merckPolyA.all.ra.
- src/hg/makeDb/trackDb/human/hg19/trackDb.ra
- lines changed 7, context: html, text, full: html, text
Added a search stanza for Old UCSC Genes, so that you can search for name for old UCSC Genes transcripts in the Position/Search box
- lines changed 62, context: html, text, full: html, text
Changed ordering of organisms in placental and vertebrate section
- lines changed 37, context: html, text, full: html, text
Changed gorGor1 to gorGor3 and added nomLeu1 to primate section
- lines changed 2, context: html, text, full: html, text
Track #5630 SIB Alt-Splicing using true hg19 data.
- lines changed 1, context: html, text, full: html, text
Added include of trackDb.merckPolyA.all.ra.
- src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
- lines changed 2, context: html, text, full: html, text
staging RIKEN CAGE Loc Release2 on beta, #2020
- lines changed 1, context: html, text, full: html, text
staging Haib Methyl450, Redmine# 4234
- lines changed 1, context: html, text, full: html, text
Added Haib Methlyl450, redmine #4234
- src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHistone.html
- lines changed 1, context: html, text, full: html, text
added in line about metadata location to html descriptions
- src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHmm.html
- lines changed 1, context: html, text, full: html, text
added in line about metadata location to html descriptions
- src/hg/makeDb/trackDb/human/hg19/wgEncodeCaltechRnaSeq.new.html
- src/hg/makeDb/trackDb/human/hg19/wgEncodeChromSuper.html
- lines changed 2, context: html, text, full: html, text
Making release notes match supertrack schema
- src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.new.html
- lines changed 2, context: html, text, full: html, text
Added a line about metaData arrow in display
- src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.new.html
- lines changed 1, context: html, text, full: html, text
Added a line about metaData arrow in display
- src/hg/makeDb/trackDb/human/hg19/wgEncodeDukeAffyExon.html
- lines changed 1, context: html, text, full: html, text
added in line about metadata location to html descriptions
- src/hg/makeDb/trackDb/human/hg19/wgEncodeDukeAffyExon.new.html
- lines changed 1, context: html, text, full: html, text
added in line about metadata location to html descriptions
- src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV9.html
- lines changed 1, context: html, text, full: html, text
Fixing Version 7 to Version 9
- lines changed 1, context: html, text, full: html, text
Added a line about metaData arrow in display
- src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV9.ra
- lines changed 1, context: html, text, full: html, text
Added an object, removed md5sums and subIds, added dccAccession
- src/hg/makeDb/trackDb/human/hg19/wgEncodeGisChiaPet.html
- lines changed 1, context: html, text, full: html, text
Added a line about metaData arrow in display
- src/hg/makeDb/trackDb/human/hg19/wgEncodeGisRnaPet.release2.html
- lines changed 1, context: html, text, full: html, text
Added a line about metaData arrow in display
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibGenotype.new.html
- lines changed 2, context: html, text, full: html, text
Added a line about metaData arrow in display
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethyl27.html
- lines changed 1, context: html, text, full: html, text
The link to the cell culture protocols was incorrect
- lines changed 2, context: html, text, full: html, text
Added a line about metaData arrow in display
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethyl450.html
- lines changed 3, context: html, text, full: html, text
Ticket 4234, added dccAccessions, added an expVar, changed the labels for 116 from Stanford to HAIB, fixed some spacing issues in the html
- lines changed 1, context: html, text, full: html, text
Adding replicate number back to the Stanford sample
- lines changed 3, context: html, text, full: html, text
Changed the links to the supplemental directory and changed the order of the treatments to be alphabetical
- lines changed 7, context: html, text, full: html, text
Ticket 4324 addressing Jacobs requests
- lines changed 1, context: html, text, full: html, text
Changed to past tense at jacobs request
- lines changed 1, context: html, text, full: html, text
Adding the line about the metaData
- lines changed 1, context: html, text, full: html, text
The link to the cell culture protocols was incorrect
- lines changed 1, context: html, text, full: html, text
Changing the release year for HAIB Methyl450, redmine #4234
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethyl450.ra
- lines changed 4, context: html, text, full: html, text
Ticket 4234, added dccAccessions, added an expVar, changed the labels for 116 from Stanford to HAIB, fixed some spacing issues in the html
- lines changed 4, context: html, text, full: html, text
Adding replicate number back to the Stanford sample
- lines changed 1, context: html, text, full: html, text
Changed the links to the supplemental directory and changed the order of the treatments to be alphabetical
- lines changed 61, context: html, text, full: html, text
Changed the sort order for Vanessa 4234
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylRrbs.new.html
- lines changed 6, context: html, text, full: html, text
Added a line about metaData arrow in display
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibRnaSeq.html
- lines changed 1, context: html, text, full: html, text
Added a line about metaData arrow in display
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibRnaSeq.new.html
- lines changed 2, context: html, text, full: html, text
Added a line about metaData arrow in display
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.html
- lines changed 2, context: html, text, full: html, text
added in line about metadata location to html descriptions
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.ra
- lines changed 64, context: html, text, full: html, text
revokeing HEY1 tracks in trackDb, this will leak out at the the of the week.
- lines changed 28, context: html, text, full: html, text
the K562/BCL3 objects need to be revoke also
- src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromChip.html
- lines changed 2, context: html, text, full: html, text
added in line about metadata location to html descriptions
- src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromChip.new.ra
- lines changed 2, context: html, text, full: html, text
checking trackDb changes for rename
- lines changed 9, context: html, text, full: html, text
restored old trackDb and metaDb entries
- src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromDnase.html
- lines changed 2, context: html, text, full: html, text
added in line about metadata location to html descriptions
- src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromFaire.html
- lines changed 2, context: html, text, full: html, text
added in line about metadata location to html descriptions
- src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromSynth.html
- lines changed 2, context: html, text, full: html, text
added in line about metadata location to html descriptions
- src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.new.html
- lines changed 24, context: html, text, full: html, text
Changes for Katrina ticket 2020, note 48
- lines changed 7, context: html, text, full: html, text
Adding changes acording to Katrina's requests ticket 2020
- lines changed 2, context: html, text, full: html, text
Ticket 2020 Addressing Katrina Requests
- lines changed 2, context: html, text, full: html, text
Changes according to Katrina in ticket 2020
- lines changed 2, context: html, text, full: html, text
Adding the metaData link and changing the TssHmm files to say bed
- lines changed 6, context: html, text, full: html, text
Adding back the clusters as .bed files and attic
- src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.new.ra
- lines changed 66, context: html, text, full: html, text
Changes according to Katrina in ticket 2020
- lines changed 1, context: html, text, full: html, text
Ticket 2020 Changes for katrina
- src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhHistone.html
- lines changed 1, context: html, text, full: html, text
added in line about metadata location to html descriptions
- src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhHistone.new.html
- lines changed 1, context: html, text, full: html, text
added in line about metadata location to html descriptions
- src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhNsome.html
- lines changed 1, context: html, text, full: html, text
added in line about metadata location to html descriptions
- src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.html
- lines changed 1, context: html, text, full: html, text
added in line about metadata location to html descriptions
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProtFasp.html
- lines changed 1, context: html, text, full: html, text
Added a line about metaData arrow in display
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwAffyExonArray.new.html
- lines changed 1, context: html, text, full: html, text
Added a line about metaData arrow in display
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDgf.html
- lines changed 2, context: html, text, full: html, text
added in line about metadata location to html descriptions
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDgf.new.html
- lines changed 2, context: html, text, full: html, text
added in line about metadata location to html descriptions
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.html
- lines changed 1, context: html, text, full: html, text
added in line about metadata location to html descriptions
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.new.html
- lines changed 2, context: html, text, full: html, text
added in line about metadata location to html descriptions
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.html
- lines changed 2, context: html, text, full: html, text
added in line about metadata location to html descriptions
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.new.html
- lines changed 2, context: html, text, full: html, text
added in line about metadata location to html descriptions
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.new.ra
- lines changed 1, context: html, text, full: html, text
reordered cell lines to be alphabetical
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.ra
- lines changed 1, context: html, text, full: html, text
reordered cell lines to be alphabetical
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwRepliSeq.html
- lines changed 128, context: html, text, full: html, text
Added track description. Redmine #4577.
- lines changed 1, context: html, text, full: html, text
Fixed spelling error of methdology. Redmine #4577.
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwRepliSeq.ra
- lines changed 181, context: html, text, full: html, text
Added experiments with 2 new cell lines GM12812 and GM12813. Redmine #4577.
- lines changed 5, context: html, text, full: html, text
Updated default's on track. Redmine #4577.
- lines changed 222, context: html, text, full: html, text
First pass at long and short labels for track. Redmine #4577.
- lines changed 81, context: html, text, full: html, text
Updated defaults to be tier 1 and 2 cells. Also updated tags, to force sorting of cells in tier order and alphabetical order. Redmine #4577.
- lines changed 1, context: html, text, full: html, text
Added fileSortOrder for track. Redmine #4577.
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwTfbs.html
- lines changed 2, context: html, text, full: html, text
added in line about metadata location to html descriptions
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwTfbs.new.html
- lines changed 2, context: html, text, full: html, text
added in line about metadata location to html descriptions
- src/hg/makeDb/trackDb/human/perlegen.html
- lines changed 9, context: html, text, full: html, text
Perlegen Sciences is no longer in business, so removed links. Also updated the journal link.
- src/hg/makeDb/trackDb/human/stsMap.html
- lines changed 6, context: html, text, full: html, text
Updated some outdated links
- src/hg/makeDb/trackDb/human/trackDb.ra
- lines changed 10, context: html, text, full: html, text
Made changes to ISCA shortLabels/longLabels, redmine #34
- lines changed 1, context: html, text, full: html, text
changed mim2gene to omim2gene for tableBrowser off of omimGene2.
- lines changed 2, context: html, text, full: html, text
Made changes to ISCA shortlabels, redmine#34
- src/hg/makeDb/trackDb/human/vistaEnhancers.html
- lines changed 2, context: html, text, full: html, text
Fixed a broken link and updated some outdated links
- src/hg/makeDb/trackDb/intronEst.html
- lines changed 1, context: html, text, full: html, text
Full text of BLAT article is now free. Changed the URL from abstract to full.
- src/hg/makeDb/trackDb/knownGene.html
- lines changed 19, context: html, text, full: html, text
Fixed a broken link and updated some outdated links
- lines changed 1, context: html, text, full: html, text
Made a correction regarding UniProt
- lines changed 2, context: html, text, full: html, text
Made corrections regarding UniProt
- src/hg/makeDb/trackDb/makefile
- lines changed 1, context: html, text, full: html, text
adding oreNil1 to the build
- src/hg/makeDb/trackDb/merckPolyA.html
- lines changed 429, context: html, text, full: html, text
Created merckPolyA.html.
- src/hg/makeDb/trackDb/mouse/mm7/knownGene.html
- lines changed 23, context: html, text, full: html, text
Fixed a broken link and updated some outdated links
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/makefile
- lines changed 1, context: html, text, full: html, text
staging Caltech Histone mm9, redmine# 4234
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/wgEncodeCaltechHist.ra
- lines changed 1925, context: html, text, full: html, text
staging Caltech Histone mm9, redmine# 4234
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/public/makefile
- lines changed 1, context: html, text, full: html, text
Releasing Caltech TFBS mm9, redmine# 4154
- lines changed 2, context: html, text, full: html, text
Releasing Caltech Histone mm9, redmine# 4155
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/public/wgEncodeCaltechHist.ra
- lines changed 1925, context: html, text, full: html, text
Releasing Caltech Histone mm9, redmine# 4155
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/public/wgEncodeCaltechTfbs.ra
- lines changed 3758, context: html, text, full: html, text
Releasing Caltech TFBS mm9, redmine# 4154
- src/hg/makeDb/trackDb/mouse/mm9/trackDb.wgEncode.ra
- lines changed 1, context: html, text, full: html, text
Releasing Caltech TFBS mm9, redmine# 4154
- lines changed 1, context: html, text, full: html, text
staging Caltech Histone mm9, redmine# 4234
- lines changed 1, context: html, text, full: html, text
Releasing Caltech Histone mm9, redmine# 4155
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCaltechHist.html
- lines changed 3, context: html, text, full: html, text
Added new wording for how to access metadata under "Display Conventions and Configuration" sectionfor Redmine #4154 and #4155 based on Redmine # 6083
- lines changed 3, context: html, text, full: html, text
Fixes affect Redmine #4154 and #4155
1. Fixed spelling of constructed in "Libraries were contsructed using the Illumina ChIP-seq Sample.."
2. Fixed spelling of chromosomes in "...excluding the _random chromomosomes in the assembly..."
3. Removed reference on how to access meta-data since this is now in View information "(click the down arrow in the subtrack list)"
- lines changed 1, context: html, text, full: html, text
Corrected this typo for Caltech Histone which I realized I forgot to correct on Caltech TFBS also, redmine#4155
- lines changed 1, context: html, text, full: html, text
Fixes affect Redmine #4155
1. Removed Replicate from filtering and sortOrder, since there is only 1 replicate
2. Made intensity lower case in "... all mapped read Intensity of the signal ... "
Above change affects CaltechTfbs track Redmine #4144
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCaltechHist.ra
- lines changed 4, context: html, text, full: html, text
Fixes affect Redmine #4155
1. Removed Replicate from filtering and sortOrder, since there is only 1 replicate
2. Made intensity lower case in "... all mapped read Intensity of the signal ... "
Above change affects CaltechTfbs track Redmine #4144
- lines changed 1, context: html, text, full: html, text
Fixed redudant information in long label. Redmine #4155.
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCaltechTfbs.html
- lines changed 3, context: html, text, full: html, text
Added new wording for how to access metadata under "Display Conventions and Configuration" sectionfor Redmine #4154 and #4155 based on Redmine # 6083
- lines changed 3, context: html, text, full: html, text
Fixes affect Redmine #4154 and #4155
1. Fixed spelling of constructed in "Libraries were contsructed using the Illumina ChIP-seq Sample.."
2. Fixed spelling of chromosomes in "...excluding the _random chromomosomes in the assembly..."
3. Removed reference on how to access meta-data since this is now in View information "(click the down arrow in the subtrack list)"
- lines changed 1, context: html, text, full: html, text
Corrected this typo for Caltech Histone which I realized I forgot to correct on Caltech TFBS also, redmine#4155
- lines changed 1, context: html, text, full: html, text
Fixes affect Redmine #4155
1. Removed Replicate from filtering and sortOrder, since there is only 1 replicate
2. Made intensity lower case in "... all mapped read Intensity of the signal ... "
Above change affects CaltechTfbs track Redmine #4144
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuHistone.html
- lines changed 1, context: html, text, full: html, text
Added new Meta description in html files. Redmine #6083.
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuTfbs.html
- lines changed 2, context: html, text, full: html, text
Added new Meta description in html files. Redmine #6083.
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhTfbs.new.html
- lines changed 1, context: html, text, full: html, text
Added new Meta description in html files. Redmine #6083.
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwDnase.new.html
- lines changed 112, context: html, text, full: html, text
Added new Meta description in html files. Redmine #6083.
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwDnase.new.ra
- lines changed 1, context: html, text, full: html, text
Added new Meta description in html files. Redmine #6083.
- src/hg/makeDb/trackDb/mrna.html
- lines changed 1, context: html, text, full: html, text
Full text of BLAT article is now free. Changed the URL from abstract to full.
- src/hg/makeDb/trackDb/oreNil/oreNil1/description.html
- lines changed 129, context: html, text, full: html, text
initial files from makeGenomeDb.pl
- src/hg/makeDb/trackDb/oreNil/oreNil1/gap.html
- lines changed 64, context: html, text, full: html, text
initial files from makeGenomeDb.pl
- src/hg/makeDb/trackDb/oreNil/oreNil1/gold.html
- lines changed 23, context: html, text, full: html, text
initial files from makeGenomeDb.pl
- src/hg/makeDb/trackDb/oreNil/oreNil1/trackDb.ra
- lines changed 8, context: html, text, full: html, text
initial files from makeGenomeDb.pl
- src/hg/makeDb/trackDb/refGene.html
- lines changed 1, context: html, text, full: html, text
Full text of BLAT article is now free. Changed the URL from abstract to full.
- src/hg/makeDb/trackDb/trackDb.ra
- lines changed 2, context: html, text, full: html, text
wording changes for publications track
- src/hg/makeDb/trackDb/xenTro/xenTro3/trackDb.ra
- lines changed 1, context: html, text, full: html, text
do not allow the reference species to exist on the sGroup_vertebrate line
- src/hg/makeDb/trackDb/xenoMrna.html
- lines changed 1, context: html, text, full: html, text
Full text of BLAT article is now free. Changed the URL from abstract to full.
- src/hg/makeDb/trackDb/xenoRefGene.html
- lines changed 1, context: html, text, full: html, text
Full text of journal article is now free. Changed the URL from abstract to full.
- 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
- lines changed 14, context: html, text, full: html, text
added monospace font option to phyloGif
- 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
- lines changed 15, context: html, text, full: html, text
Removed some commented out lines.
- 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
- src/hg/pslCoverage/pslCoverage.c
- 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
- src/hg/pslPseudo/checkExp/checkExp.c
- src/hg/pslPseudo/pslPseudo.c
- src/hg/pslRecalcMatch/pslRecalcMatch.c
- src/hg/pslReps/pslReps.c
- src/hg/pslSelect/pslSelect.c
- src/hg/pslSimp/pslSimp.c
- src/hg/pslSort/pslSort.c
- src/hg/pslSortAcc/pslSortAcc.c
- src/hg/pslSplit/pslSplit.c
- src/hg/pslSplitOnTarget/pslSplitOnTarget.c
- src/hg/pslStats/pslStats.c
- src/hg/pslToPileup/pslToPileup.c
- src/hg/pslUnpile/pslUnpile.c
- src/hg/qa/apacheMonitor.c
- src/hg/qa/checkChain.c
- src/hg/qa/countNib.c
- src/hg/qa/dumpNib.c
- src/hg/qa/getChroms.c
- src/hg/qa/testSearch.c
- src/hg/qa/timePosTable.c
- src/hg/qaPushQ/qaPushQ.c
- src/hg/qaToQac/qaToQac.c
- src/hg/qacAgpLift/qacAgpLift.c
- src/hg/qacToQa/qacToQa.c
- src/hg/qacToWig/qacToWig.c
- src/hg/ratStuff/faToMaf/faToMaf.c
- src/hg/ratStuff/mafAddIRows/mafAddIRows.c
- src/hg/ratStuff/mafBedSubset/mafBedSubset.c
- src/hg/ratStuff/mafBreak/mafBreak.c
- src/hg/ratStuff/mafFastFrags/mafFastFrags.c
- src/hg/ratStuff/mafFilter/mafFilter.c
- src/hg/ratStuff/mafFrag/mafFrag.c
- src/hg/ratStuff/mafFrags/mafFrags.c
- src/hg/ratStuff/mafIndex/mafIndex.c
- src/hg/ratStuff/mafMeFirst/mafMeFirst.c
- src/hg/ratStuff/mafOrder/mafOrder.c
- src/hg/ratStuff/mafOrtholog/mafOrtholog.c
- src/hg/ratStuff/mafSpeciesList/mafSpeciesList.c
- src/hg/ratStuff/mafSpeciesSubset/mafSpeciesSubset.c
- src/hg/ratStuff/mafSplit/mafSplit.c
- src/hg/ratStuff/mafSplitPos/mafSplitPos.c
- src/hg/ratStuff/mafStats/mafStats.c
- src/hg/ratStuff/mafToAnc/mafToAnc.c
- src/hg/ratStuff/mafsInRegion/mafsInRegion.c
- src/hg/ratStuff/multizzy/multizzy.c
- src/hg/ratStuff/segExpandToAnchors/segExpandToAnchors.c
- src/hg/ratStuff/segInfo/segInfo.c
- src/hg/ratStuff/segSplitPairwise/segSplitPairwise.c
- src/hg/ratStuff/stageMultiz/stageMultiz.c
- src/hg/recycleDb/bedDown/bedDown.c
- src/hg/recycleDb/bedUp/bedUp.c
- src/hg/regulate/companion/regCompanion5C/regCompanion5C.c
- src/hg/regulate/companion/regCompanionCalcBedGraphNorm/regCompanionCalcBedGraphNorm.c
- src/hg/regulate/companion/regCompanionChia/regCompanionChia.c
- src/hg/regulate/companion/regCompanionCorrelateEnhancerAndExpression/regCompanionCorrelateEnhancerAndExpression.c
- src/hg/regulate/companion/regCompanionEnhProCellSpecificPairs/regCompanionEnhProCellSpecificPairs.c
- src/hg/regulate/companion/regCompanionEntropy/regCompanionEntropy.c
- src/hg/regulate/companion/regCompanionGraphVsFixedPoints/regCompanionGraphVsFixedPoints.c
- src/hg/regulate/companion/regCompanionHistoneBox/regCompanionHistoneBox.c
- src/hg/regulate/companion/regCompanionPickEnhancers/regCompanionPickEnhancers.c
- src/hg/regulate/regBeadPos/regBeadPos.c
- src/hg/regulate/regBedStats/regBedStats.c
- src/hg/regulate/regChromiaMergeWindows/regChromiaMergeWindows.c
- src/hg/regulate/regCluster/regCluster.c
- src/hg/regulate/regClusterAttachMetadataToTableOfTables/regClusterAttachMetadataToTableOfTables.c
- src/hg/regulate/regClusterBedExpCfg/regClusterBedExpCfg.c
- src/hg/regulate/regClusterMakeTableOfTables/regClusterMakeTableOfTables.c
- src/hg/regulate/regClusterTreeCells/regClusterTreeCells.c
- src/hg/regulate/regStartSampleEmbl/regStartSampleEmbl.c
- src/hg/relPairs/relPairs.c
- src/hg/reviewSanity/reviewSanity.c
- src/hg/rnaStructure/hgLoadRnaFold/hgLoadRnaFold.c
- src/hg/rnaStructure/rnaFoldBig/rnaFoldBig.c
- src/hg/rnaStructure/rnaPhylo/rnaPhylo.c
- src/hg/rnaStructure/utrFa/utrFa.c
- src/hg/sage/addAveMedScoreToPsls.c
- src/hg/sage/createSageSummary.c
- src/hg/scanRa/scanRa.c
- src/hg/secure/secure.c
- src/hg/semiNorm/semiNorm.c
- src/hg/sim4big/sim4big.c
- src/hg/snp/details/dbSnp.c
- src/hg/snp/fixedDiffs/fixedDiffs.c
- src/hg/snp/pbToAlleleCounts/pbToAlleleCounts.c
- src/hg/snp/snpLoad/affyCheck.c
- src/hg/snp/snpLoad/affyLookup.c
- src/hg/snp/snpLoad/cnpLookup.c
- src/hg/snp/snpLoad/fetchSeq.c
- src/hg/snp/snpLoad/hapmap1.c
- src/hg/snp/snpLoad/hapmap2.c
- src/hg/snp/snpLoad/hapmapLookup.c
- src/hg/snp/snpLoad/hapmapMixed.c
- src/hg/snp/snpLoad/hapmapOrtho.c
- src/hg/snp/snpLoad/hapmapPhaseIIISummary.c
- src/hg/snp/snpLoad/hapmapSummary.c
- src/hg/snp/snpLoad/hapmapValidate.c
- src/hg/snp/snpLoad/illuminaLookup.c
- src/hg/snp/snpLoad/illuminaLookup1M.c
- src/hg/snp/snpLoad/illuminaLookup2.c
- src/hg/snp/snpLoad/snpCheckAlleles.c
- src/hg/snp/snpLoad/snpCheckClassAndObserved.c
- src/hg/snp/snpLoad/snpCheckCluster.c
- src/hg/snp/snpLoad/snpCheckCluster2.c
- src/hg/snp/snpLoad/snpCheckLocTypeSize.c
- src/hg/snp/snpLoad/snpClassAndObserved.c
- src/hg/snp/snpLoad/snpCleanSeq.c
- src/hg/snp/snpLoad/snpCompare.c
- src/hg/snp/snpLoad/snpCompareLoctype.c
- src/hg/snp/snpLoad/snpCompareWeight.c
- src/hg/snp/snpLoad/snpContigLocFilter.c
- src/hg/snp/snpLoad/snpContigLocFilter125.c
- src/hg/snp/snpLoad/snpContigLocusIdCondense.c
- src/hg/snp/snpLoad/snpContigLocusIdFilter.c
- src/hg/snp/snpLoad/snpContigLocusIdFilter125.c
- src/hg/snp/snpLoad/snpExceptionCheck.c
- src/hg/snp/snpLoad/snpExceptions.c
- src/hg/snp/snpLoad/snpExpandAllele.c
- src/hg/snp/snpLoad/snpFinalTable.c
- src/hg/snp/snpLoad/snpFreq.c
- src/hg/snp/snpLoad/snpFunction.c
- src/hg/snp/snpLoad/snpFunctionCheck.c
- src/hg/snp/snpLoad/snpGetDeletions.c
- src/hg/snp/snpLoad/snpGetInsertions.c
- src/hg/snp/snpLoad/snpGetSeqDup.c
- src/hg/snp/snpLoad/snpGetSimple.c
- src/hg/snp/snpLoad/snpLoad.c
- src/hg/snp/snpLoad/snpLoadFasta.c
- src/hg/snp/snpLoad/snpLoadFromTmp.c
- src/hg/snp/snpLoad/snpLocType.c
- src/hg/snp/snpLoad/snpLocType125.c
- src/hg/snp/snpLoad/snpMissing.c
- src/hg/snp/snpLoad/snpMoltype.c
- src/hg/snp/snpLoad/snpMultiple.c
- src/hg/snp/snpLoad/snpNcbiToUcsc.c
- src/hg/snp/snpLoad/snpOrtho.c
- src/hg/snp/snpLoad/snpOrthoJoin.c
- src/hg/snp/snpLoad/snpOrthoLookup.c
- src/hg/snp/snpLoad/snpOrthoStats.c
- src/hg/snp/snpLoad/snpPAR.c
- src/hg/snp/snpLoad/snpReadFasta.c
- src/hg/snp/snpLoad/snpReadSeq.c
- src/hg/snp/snpLoad/snpReadSeq2.c
- src/hg/snp/snpLoad/snpRefUCSC.c
- src/hg/snp/snpLoad/snpSNP.c
- src/hg/snp/snpLoad/snpSort.c
- src/hg/snp/snpLoad/snpSplit.c
- src/hg/snp/snpLoad/snpSplitByChrom.c
- src/hg/snp/snpLoad/snpSplitByChrom2.c
- src/hg/snp/snpLoad/snpSplitSimple.c
- src/hg/snp/snpLoad/subSnpCondense.c
- src/hg/snp/snpLoad/trimHeader.c
- src/hg/snp/snpMask/seqWithInsertions.c
- src/hg/snp/snpMask/seqWithoutDeletions.c
- src/hg/snp/snpMask/snpMapToExon.c
- src/hg/snp/snpMask/snpMask.c
- src/hg/snp/snpMask/snpMaskAddInsertions.c
- src/hg/snp/snpMask/snpMaskChrom.c
- src/hg/snp/snpMask/snpMaskCutDeletions.c
- src/hg/snp/snpMask/snpMaskFlank.c
- src/hg/snp/snpMask/snpMaskFlankSubset.c
- src/hg/snp/snpMask/snpMaskGenes.c
- src/hg/snp/snpMask/snpMaskSingle.c
- src/hg/snp/snpValid/snpValid.c
- src/hg/snp/snpValid/snpValidOld.c
- src/hg/snp/tajD/tajD.c
- src/hg/snpException/snpException.c
- src/hg/spideyToPsl/spideyToPsl.c
- src/hg/splignToPsl/splignToPsl.c
- src/hg/splitFa/splitFa.c
- src/hg/splitFaIntoContigs/splitFaIntoContigs.c
- src/hg/sqlToXml/sqlToXml.c
- src/hg/synMap/createBinMap.c
- src/hg/synMap/createSlamParaSpec.c
- src/hg/synMap/prep_lc_rm_for_slam.c
- src/hg/synMap/runSlam.c
- src/hg/synMap/synMapTest.c
- src/hg/test/foo.c
- src/hg/test/otest/test1.c
- src/hg/test/test.c
- src/hg/trfBig/trfBig.c
- src/hg/tutorial/affyVsIlluminaCommon/affyVsIlluminaCommon.c
- src/hg/tutorial/bigGene/bigGene.c
- src/hg/tutorial/cgiAlign/cgiAlign.c
- src/hg/tutorial/cgiPicture/cgiPicture.c
- src/hg/tutorial/cgiTaxon/cgiTaxon.c
- src/hg/txCds/txCdsBadBed/txCdsBadBed.c
- src/hg/txCds/txCdsEvFromBed/txCdsEvFromBed.c
- src/hg/txCds/txCdsGoodBed/txCdsGoodBed.c
- src/hg/txCds/txCdsOrfInfo/txCdsOrfInfo.c
- src/hg/txCds/txCdsOrtho/txCdsOrtho.c
- src/hg/txCds/txCdsPredict/txCdsPredict.c
- src/hg/txCds/txCdsRedoUniprotPicks/txCdsRedoUniprotPicks.c
- src/hg/txCds/txCdsRefBestEvOnly/txCdsRefBestEvOnly.c
- src/hg/txCds/txCdsSuspect/txCdsSuspect.c
- src/hg/txCds/txCdsSvmInput/txCdsSvmInput.c
- src/hg/txCds/txCdsWeed/txCdsWeed.c
- src/hg/txGene/txGeneAccession/txGeneAccession.c
- src/hg/txGene/txGeneAddOldUnmapped/txGeneAddOldUnmapped.c
- src/hg/txGene/txGeneAlias/txGeneAlias.c
- src/hg/txGene/txGeneAltProt/txGeneAltProt.c
- src/hg/txGene/txGeneCanonical/txGeneCanonical.c
- src/hg/txGene/txGeneCdsMap/txGeneCdsMap.c
- src/hg/txGene/txGeneColor/txGeneColor.c
- src/hg/txGene/txGeneExplainUpdate1/txGeneExplainUpdate1.c
- src/hg/txGene/txGeneExplainUpdate2/txGeneExplainUpdate2.c
- src/hg/txGene/txGeneFromBed/txGeneFromBed.c
- src/hg/txGene/txGeneProtAndRna/txGeneProtAndRna.c
- src/hg/txGene/txGeneSeparateNoncoding/txGeneSeparateNoncoding.c
- src/hg/txGene/txGeneXref/txGeneXref.c
- src/hg/txGraph/txReadRa/txReadRa.c
- src/hg/txPaper/txGeneBakeOff/refCluster.c
- src/hg/txPaper/txGeneBakeOff/txGeneBakeOff.c
- src/hg/txPaper/txPaperPfam/txPaperPfam.c
- src/hg/txPaper/txPaperScop/txPaperScop.c
- src/hg/ultras/plateOfPrimers/plateOfPrimers.c
- src/hg/ultras/sqlAddCol/sqlAddCol.c
- src/hg/ultras/ultraDb/as/udHistory.c
- src/hg/ultras/ultraPcrRegions/ultraPcrRegions.c
- src/hg/ultras/ultraPlateau/ultraPlateau.c
- src/hg/uniqSize/uniqSize.c
- src/hg/useCount/useCount.c
- src/hg/utils/automation/Encode.pm
- src/hg/utils/automation/makefile
- src/hg/utils/bedExtendRanges/bedExtendRanges.c
- src/hg/utils/bedMergeOverlappingBlocks/bedMergeOverlappingBlocks.c
- src/hg/utils/bedRandom/bedRandom.c
- src/hg/utils/chromGraphFromBin/chromGraphFromBin.c
- src/hg/utils/chromGraphToBin/chromGraphToBin.c
- src/hg/utils/coloredExonToBed/coloredExon.c
- src/hg/utils/crTreeIndexBed/crTreeIndexBed.c
- src/hg/utils/crTreeSearchBed/crTreeSearchBed.c
- src/hg/utils/fiveCToBed/fiveCToBed.c
- src/hg/utils/gff3ToGenePred/gff3ToGenePred.c
- src/hg/utils/gff3ToPsl/gff3ToPsl.c
- src/hg/utils/hubPublicCheck/hubPublicCheck.c
- lines changed 12, context: html, text, full: html, text
make it so it takes an argument that defines the table to use for hubPublic
- src/hg/utils/makeTrackIndex/makeTrackIndex.c
- src/hg/utils/mdbQuery/mdbQuery.c
- src/hg/utils/overlapSelect/chromAnn.c
- src/hg/utils/overlapSelect/chromAnnMap.c
- src/hg/utils/overlapSelect/coordCols.c
- src/hg/utils/overlapSelect/overlapSelect.c
- src/hg/utils/overlapSelect/rowReader.c
- src/hg/utils/overlapSelect/selectTable.c
- src/hg/utils/phyloTrees/57way.dissect.txt
- lines changed 791, context: html, text, full: html, text
the result of: /cluster/bin/phast/tree_doctor --dissect 57way.nh > 57way.dissect.txt
- src/hg/utils/phyloTrees/57way.nh
- lines changed 26, context: html, text, full: html, text
adding hetGla1,sarHar1,croPor1,aliMis1,latCha1,oreNil1
- src/hg/utils/positionalTblCheck/positionalTblCheck.c
- src/hg/utils/pslMap/pslMap.c
- src/hg/utils/pslUniq/pslUniq.c
- src/hg/utils/reTraceUtils/reTraceFixMaf/reTraceFixMaf.c
- src/hg/utils/refSeqGet/refSeqGet.c
- src/hg/utils/safePush/safePush.c
- src/hg/utils/tdbQuery/tdbQuery.c
- src/hg/utils/tdbQuery/tdbRecord.c
- src/hg/utils/toDev64/toDev64.c
- src/hg/utils/twoBitMask/twoBitMask.c
- src/hg/utils/wigAsciiAverageOverBed/wigAsciiAverageOverBed.c
- src/hg/var/fixConrad.c
- src/hg/visiGene/gensat/gensatFixFull/gensatFixFull.c
- src/hg/visiGene/gensat/gensatFtpImages/gensatFtpImages.c
- src/hg/visiGene/gensat/gensatFtpList/gensatFtpList.c
- src/hg/visiGene/gensat/gensatImageDownload/gensatImageDownload.c
- src/hg/visiGene/gensat/gensatRandomXml/gensatRandomXml.c
- src/hg/visiGene/gensat/vgLoadGensat/vgLoadGensat.c
- src/hg/visiGene/hgVisiGene/hgVisiGene.c
- src/hg/visiGene/hgVisiGene/visiSearch.c
- src/hg/visiGene/vgChangeContributors/vgChangeContributors.c
- src/hg/visiGene/vgGetText/vgGetText.c
- src/hg/visiGene/vgGetText/visiGene.c
- src/hg/visiGene/vgLoadAllen/vgLoadAllen.c
- src/hg/visiGene/vgLoadMahoney/mahoney.c
- src/hg/visiGene/vgLoadNibb/vgLoadNibb.c
- src/hg/visiGene/vgPatchJax/vgPatchJax.c
- src/hg/visiGene/vgPrepImage/vgPrepImage.c
- src/hg/visiGene/vgRemoveSubmission/vgRemoveSubmission.c
- src/hg/visiGene/visiGeneSearch/visiGeneSearch.c
- src/hg/visiGene/visiGeneTest/visiGeneTest.c
- src/hg/wikiPlot/wikiPlot.c
- src/hg/xmlCat/xmlCat.c
- src/hg/xmlToSql/xmlToSql.c
- src/hg/zfishBacClonesandSts/zfishBacClonesandSts.c
- src/hg/zoo/alignToPsl/alignToPsl.c
- src/hg/zoo/analyze4d/analyze.c
- src/hg/zoo/pslToFa/pslToFa.c
- src/hg/zoo/pslUnpackBlocks/pslUnpackBlocks.c
- src/hg/zoo/transitivityCheck/transitivity.c
- src/hg/zoo/zooLib/args.c
- src/hg/zoo/zooLib/misc.c
- src/hg/zoo/zooLib/read_malign.c
- src/hg/zoo/zooLib/util.c
- src/inc/common.h
- lines changed 3, context: html, text, full: html, text
New calculation for squeezed label height
- src/inc/common.mk
- lines changed 7, context: html, text, full: html, text
full -Werror only on hgwdev, too much trouble for mirror sites
- src/inc/memgfx.h
- lines changed 3, context: html, text, full: html, text
added monospace font option to phyloGif
- src/inc/ra.h
- lines changed 6, context: html, text, full: html, text
Improved cv efficiency by only reading the cv.ra file once.
- src/inc/vcf.h
- lines changed 6, context: html, text, full: html, text
Feature #3707 (VCF+tabix support in hgTables): Brooke reported out-of-memconditions in notes 11 & 12. Fix: add an optional threshold on the number
of records to retrieve in vcfTabixFileMayOpen.
- src/index/bptForTwoBit/bptForTwoBit.c
- src/index/bptLookupStringToBits64/bptLookupStringToBits64.c
- src/index/bptMakeStringToBits64/bptMakeStringToBits64.c
- src/index/ixIxx/ixIxx.c
- src/isPcr/gfPcr/gfPcr.c
- src/jkOwnLib/bandExt.c
- src/jkOwnLib/crudeali.c
- src/jkOwnLib/ffAliHelp.c
- src/jkOwnLib/ffSeedExtend.c
- src/jkOwnLib/fuzzyFind.c
- src/jkOwnLib/genoFind.c
- src/jkOwnLib/gfBlatLib.c
- src/jkOwnLib/gfInternal.c
- src/jkOwnLib/gfOut.c
- src/jkOwnLib/gfPcrLib.c
- src/jkOwnLib/ooc.c
- src/jkOwnLib/patSpace.c
- src/jkOwnLib/supStitch.c
- src/jkOwnLib/tests/freen/freen.c
- src/jkOwnLib/trans3.c
- src/jkOwnLib/xenbig.c
- src/jkOwnLib/xensmall.c
- src/lib/aliType.c
- src/lib/apacheLog.c
- src/lib/asParse.c
- src/lib/axt.c
- src/lib/axtAffine.c
- src/lib/base64.c
- src/lib/basicBed.c
- src/lib/binRange.c
- src/lib/bits.c
- src/lib/blastOut.c
- src/lib/blastParse.c
- src/lib/boxClump.c
- src/lib/boxLump.c
- src/lib/bwgCreate.c
- src/lib/bwgQuery.c
- src/lib/cda.c
- src/lib/chain.c
- src/lib/chainBlock.c
- src/lib/chainConnect.c
- src/lib/chainToAxt.c
- src/lib/chainToPsl.c
- src/lib/cheapcgi.c
- src/lib/codebias.c
- src/lib/colHash.c
- src/lib/common.c
- lines changed 12, context: html, text, full: html, text
New calculation for squeezed label height
- src/lib/correlate.c
- src/lib/dgRange.c
- src/lib/diGraph.c
- src/lib/dlist.c
- src/lib/dnaLoad.c
- src/lib/dnaMarkov.c
- src/lib/dnaMotif.c
- src/lib/dnaseq.c
- src/lib/dnautil.c
- src/lib/dtdParse.c
- src/lib/dystring.c
- src/lib/emblParse.c
- src/lib/errCatch.c
- src/lib/errabort.c
- lines changed 15, context: html, text, full: html, text
Had to check in code change that is ifdef'd out. This code is primarily used by me and fails in some compilers. Changes are being checked in because git doesn't let me change branches otherwise.
- src/lib/fa.c
- src/lib/ffAli.c
- src/lib/ffScore.c
- src/lib/filePath.c
- src/lib/fixColor.c
- src/lib/flydna.c
- src/lib/fof.c
- src/lib/font/mgCourier10.c
- src/lib/font/mgCourier12.c
- src/lib/font/mgCourier14.c
- src/lib/font/mgCourier18.c
- src/lib/font/mgCourier24.c
- src/lib/font/mgCourier34.c
- src/lib/font/mgCourier8.c
- src/lib/font/mgHelvetica10.c
- src/lib/font/mgHelvetica12.c
- src/lib/font/mgHelvetica14.c
- src/lib/font/mgHelvetica18.c
- src/lib/font/mgHelvetica24.c
- src/lib/font/mgHelvetica34.c
- src/lib/font/mgHelvetica8.c
- src/lib/font/mgHelveticaBold10.c
- src/lib/font/mgHelveticaBold12.c
- src/lib/font/mgHelveticaBold14.c
- src/lib/font/mgHelveticaBold18.c
- src/lib/font/mgHelveticaBold24.c
- src/lib/font/mgHelveticaBold34.c
- src/lib/font/mgHelveticaBold8.c
- src/lib/font/mgMenlo12.c
- lines changed 903, context: html, text, full: html, text
added monospace font option to phyloGif
- src/lib/font/mgSail8.c
- src/lib/font/mgSixhi6.c
- src/lib/font/mgTimes10.c
- src/lib/font/mgTimes12.c
- src/lib/font/mgTimes14.c
- src/lib/font/mgTimes18.c
- src/lib/font/mgTimes24.c
- src/lib/font/mgTimes34.c
- src/lib/font/mgTimes8.c
- src/lib/fuzzyShow.c
- src/lib/gapCalc.c
- src/lib/gdf.c
- src/lib/gemfont.c
- src/lib/genomeRangeTree.c
- src/lib/gfNet.c
- src/lib/gff.c
- src/lib/gfxPoly.c
- src/lib/gifLabel.c
- src/lib/gifcomp.c
- src/lib/gifdecomp.c
- src/lib/gifread.c
- src/lib/gifwrite.c
- src/lib/hash.c
- src/lib/histogram.c
- src/lib/hmmPfamParse.c
- src/lib/hmmstats.c
- src/lib/htmlPage.c
- src/lib/htmshell.c
- src/lib/intExp.c
- src/lib/internet.c
- src/lib/jointalign.c
- src/lib/jpegSize.c
- src/lib/keys.c
- src/lib/knetUdc.c
- src/lib/kxTok.c
- src/lib/localmem.c
- src/lib/log.c
- src/lib/maf.c
- lines changed 1, context: html, text, full: html, text
treat EOF as a legal end of paragraph. (#586)
- src/lib/mafFromAxt.c
- src/lib/mafScore.c
- src/lib/makefile
- lines changed 1, context: html, text, full: html, text
added monospace font option to phyloGif
- src/lib/md5.c
- src/lib/memalloc.c
- src/lib/memgfx.c
- src/lib/mgCircle.c
- src/lib/mgPolygon.c
- src/lib/mime.c
- 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
- lines changed 36, context: html, text, full: html, text
Improved cv efficiency by only reading the cv.ra file once.
- 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
- lines changed 1, context: html, text, full: html, text
Oops, forgot to run 'make test' before committing, and overlookeda test program...
- 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/vcf.c
- lines changed 25, context: html, text, full: html, text
MLQ #6136: adding support for VCF 3.3 header line formats.
- lines changed 9, context: html, text, full: html, text
Feature #3707 (VCF+tabix support in hgTables): Brooke reported out-of-memconditions in notes 11 & 12. Fix: add an optional threshold on the number
of records to retrieve in vcfTabixFileMayOpen.
- 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)
- lines changed 3, context: html, text, full: html, text
add note about creating namedSessionDb table
- src/product/scripts/README
- lines changed 6, context: html, text, full: html, text
add note about second rsync server option
- src/product/scripts/browserEnvironment.txt
- lines changed 3, context: html, text, full: html, text
indicate secondary rsync server available
- 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/bdfToGem/menlo/MesloLGM-Bold.bdf
- lines changed 53062, context: html, text, full: html, text
added monospace font option to phyloGif
- src/utils/bdfToGem/menlo/README
- lines changed 20, context: html, text, full: html, text
added monospace font option to phyloGif
- 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/qa/weeklybld/buildEnv.csh
- 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
- lines changed: 96212
- files changed: 2463