All File Changes

v300_base to v301_preview (2014-05-19 to 2014-05-26) v301

• src/fuse/udcFuse/udcFuse.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/affyGnf/affyPslAndAtlasToBed.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/affyGnf/affyUclaMergePslData.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/affyGnf/pslAffySelect.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/affyTransciptome/affyPairsToSample.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/affyTransciptome/affyTransLiftedToSample.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/affyTransciptome/averageZoomLevels.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/affyTransciptome/avgTranscriptomeExps.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/affyTransciptome/bulkChr2XRegression.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/affyTransciptome/groupSamples.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/affyTransciptome/htmlFromBeds.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/affyTransciptome/maxTranscriptomeExps.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/affyTransciptome/mergeAffyFiles.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/affyTransciptome/nmerAlign.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/affyTransciptome/nmerParasolGenome.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/affyTransciptome/normalizeSampleFile.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/affyTransciptome/pickCassettePcrPrimers.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/affyTransciptome/samplesForCoordinates.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/affyTransciptome/scaleSampleFiles.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/affyTransciptome/trackFromLifts.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/agpAllToFaFile/agpAllToFaFile.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/agpCloneCheck/agpCloneCheck.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/agpCloneList/agpCloneList.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/agpMergeChromScaf/agpMergeChromScaf.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/agpSangerUnfinished/agpSangerUnfinished.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/agpToFa/agpToFa.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/agpToGl/agpToGl.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/agpTweak/agpTweak.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/baseMask/baseMask.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/baseMask/baseMaskToBed.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/baseMask/bedToBaseMask.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/baseMask/cachedMask.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/baseMask/trackToBaseMask.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/bedIntersect/bedIntersect.c
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    fixed problem in command line argument check, updated usage output
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/bedItemOverlapCount/bedItemOverlapCount.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/bedOrBlocks/bedOrBlocks.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/bedOverlap/bedOverlap.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/bedSort/bedSort.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/bedSplitOnChrom/bedSplitOnChrom.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/bedThickOnly/bedThickOnly.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/bedToGenePred/bedToGenePred.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/bioImage/bioImageLoad/bioImageLoad.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/bioImage/hgBioImage/hgBioImage.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/bioImage/hgBioImage/hgBioImage.h
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/bioImage/knownToBioImage/knownToBioImage.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/bioImage/loadMahoney/loadMahoney.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/bioImage/loadMahoney/mahoney.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/bioImage/loadMahoney/mahoney.h
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/blastToPsl/blastToPsl.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/blastToPsl/blastXmlToPsl.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/blastToPsl/ncbiBlast.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/blastToPsl/ncbiBlast.h
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/blastToPsl/pslBuild.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/blastToPsl/pslBuild.h
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/borfBig/borfBig.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/cartDump/cartDump.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/cartReset/cartReset.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/ccTrack/bedToBinDex/bedToBinDex.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/cgiExample/cgiExample.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/checkCoverageGaps/checkCoverageGaps.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/checkHgFindSpec/checkHgFindSpec.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/checkTableCoords/checkTableCoords.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/chimpStuff/chimpChromContigAgp/chimpChromContigAgp.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/chimpStuff/chimpHiQualDiffs/chimpHiQualDiffs.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/chimpStuff/chimpSuperQuals/chimpSuperQuals.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/ctgFaToFa/ctgFaToFa.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/ctgToChromFa/ctgToChromFa.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/das/das.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/dbTrash/dbTrash.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/dnaGene/dnaGene.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode/converters/pairedTagToBed12/pairedTagToBed12.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode/converters/tagToBed12/tagToBed12.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode/docId/docIdReport/docIdReport.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode/docId/docIdSubmitDir/docIdSubmitDir.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode/docId/docIdTidy/docIdTidy.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode/docId/docIdView/docIdView.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode/docId/inc/docId.h
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode/docId/lib/docIdSub.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode/encodeCvTerm/encodeCvTerm.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode/encodeExp/encodeExp.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode/encodeMergeReplicates/encodeMergeReplicates.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode/encodeMergeReplicatesBatch/encodeMergeReplicatesBatch.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode/encodePatchTdb/encodePatchTdb.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode/encodeRenameObj/encodeRenameObj.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode/hgEncodeApi/hgEncodeApi.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode/hgEncodeDataVersions/hgEncodeDataVersions.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode/hgEncodeScheduler/hgEncodeScheduler.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode/hgEncodeVocab/hgEncodeVocab.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode/inc/bedLogR.h
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode/inc/encodePatchTdb.h
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode/ldGencodeIntron/ldGencodeIntron.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode/lib/bedLogR.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode/lib/encodePatchTdb.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode/metaCheck/metaCheck.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode/metaCollect/metaCollect.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode/metaRename/metaRename.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode/regionAgp/regionAgp.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode/regionOrtho/regionOrtho.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode/regionOrtho/regionOrtho.h
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode/validateCv/validateCv.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode3/eap/eapAddSoftware/eapAddSoftware.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode3/eap/eapAddStep/eapAddStep.c
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    Adding eapBamFilter to steps where it is used.
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode3/eap/eapDaemon/eapDaemon.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode3/eap/eapFinish/eapFinish.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode3/eap/eapFreen/eapFreen.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode3/eap/eapMetaSync/eapMetaSync.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode3/eap/eapMonitor/eapMonitor.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode3/eap/eapSchedule/eapSchedule.c
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    Rearranging code to put usage at top as usual. Making an explicit targetsCompatible function, and a target command line option.
  • lines changed 3, context: html, text, full: html, text
    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode3/eap/eapUpdateSoftware/eapUpdateSoftware.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode3/eap/fix/eapDepricateUntracked/eapDepricateUntracked.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode3/eap/inc/eapDb.h
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode3/eap/inc/eapGraph.h
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode3/eap/inc/eapLib.h
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode3/eap/lib/addSoftware
  • lines changed 86, context: html, text, full: html, text
    Separating out kill all the tables part from initialize tables part.
• src/hg/encode3/eap/lib/eapDb.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode3/eap/lib/eapGraph.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode3/eap/lib/eapLib.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode3/eap/lib/resetDb
  • lines changed 4, context: html, text, full: html, text
    Added some software to track on the pipeline.
  • lines changed 83, context: html, text, full: html, text
    Separating out kill all the tables part from initialize tables part.
• src/hg/encode3/eap/oneShot/eapRunAddJson/eapRunAddJson.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode3/eap/oneShot/eapToHub/eapToHub.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode3/encodeDataWarehouse/edwAddAssembly/edwAddAssembly.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode3/encodeDataWarehouse/edwAddQaContamTarget/edwAddQaContamTarget.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode3/encodeDataWarehouse/edwAddQaEnrichTarget/edwAddQaEnrichTarget.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode3/encodeDataWarehouse/edwAddSubscriber/edwAddSubscriber.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode3/encodeDataWarehouse/edwChangeFormat/edwChangeFormat.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode3/encodeDataWarehouse/edwCorrectFileTags/edwCorrectFileTags.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode3/encodeDataWarehouse/edwCreateUser/edwCreateUser.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode3/encodeDataWarehouse/edwFakeManifestFromSubmit/edwFakeManifestFromSubmit.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode3/encodeDataWarehouse/edwJob/edwJob.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode3/encodeDataWarehouse/edwMakeContaminationQa/edwMakeContaminationQa.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode3/encodeDataWarehouse/edwMakeEnrichments/edwMakeEnrichments.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode3/encodeDataWarehouse/edwMakePairedEndQa/edwMakePairedEndQa.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode3/encodeDataWarehouse/edwMakeRepeatQa/edwMakeRepeatQa.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode3/encodeDataWarehouse/edwMakeReplicateQa/edwMakeReplicateQa.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode3/encodeDataWarehouse/edwMakeValidFile/edwMakeValidFile.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode3/encodeDataWarehouse/edwMetaManiToTdb/edwMetaManiToTdb.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode3/encodeDataWarehouse/edwQaEvaluate/edwQaEvaluate.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode3/encodeDataWarehouse/edwReallyRemoveFiles/edwReallyRemoveFiles.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode3/encodeDataWarehouse/edwRetryJob/edwRetryJob.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode3/encodeDataWarehouse/edwRsyncEdwUser/edwRsyncEdwUser.c
  • lines changed 3, context: html, text, full: html, text
    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode3/encodeDataWarehouse/edwRunDaemon/edwRunDaemon.c
  • lines changed 3, context: html, text, full: html, text
    Added an error message for when system call to launch a program fails (generally because it can't find the command on your path.)
  • lines changed 3, context: html, text, full: html, text
    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode3/encodeDataWarehouse/edwRunOnIds/edwRunOnIds.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode3/encodeDataWarehouse/edwScriptSubmit/edwScriptSubmit.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode3/encodeDataWarehouse/edwScriptSubmitStatus/edwScriptSubmitStatus.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode3/encodeDataWarehouse/edwSubmit/edwSubmit.c
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    Adding a verbose message for tracking the validation wait.
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode3/encodeDataWarehouse/edwWebAuthLogin/edwWebAuthLogin.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode3/encodeDataWarehouse/edwWebAuthLogout/edwWebAuthLogout.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode3/encodeDataWarehouse/edwWebBrowse/edwWebBrowse.c
  • lines changed 2, context: html, text, full: html, text
    Remove autorefresh from EDW browse page as it made copy/paste and maintaining scroll position difficult. refs Stanford #1372
  • lines changed 3, context: html, text, full: html, text
    Hide menu buttons when user not logged in.
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode3/encodeDataWarehouse/edwWebCreateUser/edwWebCreateUser.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode3/encodeDataWarehouse/edwWebDeprecate/edwWebDeprecate.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode3/encodeDataWarehouse/edwWebRegisterScript/edwWebRegisterScript.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode3/encodeDataWarehouse/edwWebSubmit/edwWebSubmit.c
  • lines changed 6, context: html, text, full: html, text
    Hide menu buttons when user not logged in.
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode3/encodeDataWarehouse/edwWebXSendFile/edwWebXSendFile.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode3/encodeDataWarehouse/edwWebXSendFile/edwWebXSendFile.h
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode3/encodeDataWarehouse/fix/eapFixSortedBams/eapFixSortedBams.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode3/encodeDataWarehouse/fix/edwFixAddFastq/edwFixAddFastq.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode3/encodeDataWarehouse/fix/edwFixBasesInSample/edwFixBasesInSample.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode3/encodeDataWarehouse/fix/edwFixBzip/edwFixBzip.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode3/encodeDataWarehouse/fix/edwFixCshlSpikeins/edwFixCshlSpikeins.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode3/encodeDataWarehouse/fix/edwFixGbb2/edwFixGbb2.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode3/encodeDataWarehouse/fix/edwFixGtfBigBed/edwFixGtfBigBed.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode3/encodeDataWarehouse/fix/edwFixQualsAtPos/edwFixQualsAtPos.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode3/encodeDataWarehouse/fix/edwFixRenamed/edwFixRenamed.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode3/encodeDataWarehouse/fix/edwFixReplaced/edwFixReplaced.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode3/encodeDataWarehouse/fix/edwFixRevoked/edwFixRevoked.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode3/encodeDataWarehouse/fix/edwFixTarget2/edwFixTarget2.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode3/encodeDataWarehouse/fix/edwFixTargetSeq/edwFixTargetSeq.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode3/encodeDataWarehouse/fix/edwFixTechRep1/edwFixTechRep1.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode3/encodeDataWarehouse/fix/edwFixTechRepsFromTarballs/edwFixTechRepsFromTarballs.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode3/encodeDataWarehouse/fix/edwFixTstToTstff/edwFixTstToTstff.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode3/encodeDataWarehouse/fix/edwFixUniqueMapRatio/edwFixUniqueMapRatio.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode3/encodeDataWarehouse/inc/edwBamFileFromRa.h
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode3/encodeDataWarehouse/inc/edwFastqFileFromRa.h
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode3/encodeDataWarehouse/inc/edwLib.h
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode3/encodeDataWarehouse/inc/edwQaWigSpotFromRa.h
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode3/encodeDataWarehouse/inc/encodeDataWarehouse.h
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode3/encodeDataWarehouse/lib/edwBamFileFromRa.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode3/encodeDataWarehouse/lib/edwFastqFileFromRa.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode3/encodeDataWarehouse/lib/edwLib.c
  • lines changed 6, context: html, text, full: html, text
    Changes for HTML standards compliance (add type to script tag)
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode3/encodeDataWarehouse/lib/edwQaWigSpotFromRa.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode3/encodeDataWarehouse/lib/resetEdw
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    Adding some more assemblies, especially involving hg38 and sexed assemblies. Fixed DEV vs DEVFF prefix.
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    Polishing up handling of eap tables, and launching of daemons.
• src/hg/encode3/encodeDataWarehouse/makefile
  • lines changed 2, context: html, text, full: html, text
    Adding encodeDataWarehouse/utils to build.
• src/hg/encode3/encodeDataWarehouse/oneShot/edwFakeBiosample/edwFakeBiosample.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode3/encodeDataWarehouse/oneShot/edwFakeEncode2Submit/edwFakeEncode2Submit.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode3/encodeDataWarehouse/oneShot/edwToEap1/edwAnalysis.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode3/encodeDataWarehouse/oneShot/edwToEap1/edwAnalysis.h
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode3/encodeDataWarehouse/oneShot/edwToEap1/edwToEap1.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode3/encodeDataWarehouse/oneShot/rsyncEdwExpDataType/rsyncEdwExpDataType.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode3/encodeDataWarehouse/oneShot/sampleBam/sampleBam.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode3/encodeDataWarehouse/utils/edwBamFilter/edwBamFilter.c
  • lines changed 102, context: html, text, full: html, text
    Adding a somewhat more general purpose bam filtering routine. The command line interface should let us expand filtering options as needed compatibly.
  • lines changed 6, context: html, text, full: html, text
    Adding version info.
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    Addes sponge option.
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode3/encodeDataWarehouse/utils/edwBamFilter/makefile
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    Adding a somewhat more general purpose bam filtering routine. The command line interface should let us expand filtering options as needed compatibly.
• src/hg/encode3/encodeDataWarehouse/utils/edwBamRemoveChrom/edwBamRemoveChrom.c
  • lines changed 13, context: html, text, full: html, text
    Renaming samMustOpen to bamMustOpenLocal and putting in library.
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode3/encodeDataWarehouse/utils/edwBamStats/edwBamStats.c
  • lines changed 12, context: html, text, full: html, text
    Renaming samMustOpen to bamMustOpenLocal and putting in library.
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/encode3/encodeDataWarehouse/utils/edwBamToWig/edwBamToWig.c
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• src/hg/encode3/encodeDataWarehouse/utils/edwComparePeaks/edwComparePeaks.c
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• src/hg/encode3/encodeDataWarehouse/utils/edwReplicatedPeaks/edwReplicatedPeaks.c
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• src/hg/encode3/encodeDataWarehouse/utils/edwReplicatedPeaks/makefile
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    CHecking in this utility, that might never be used, that merges peaks from two replicates.
• src/hg/encode3/encodeDataWarehouse/utils/edwSamPairedEndStats/edwSamPairedEndStats.c
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• src/hg/encode3/encodeDataWarehouse/utils/edwSamRepeatAnalysis/edwSamRepeatAnalysis.c
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• src/hg/encode3/encodeDataWarehouse/utils/edwSamRepeatAnalysis/makefile
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    Adjusting to new position in subdirectory.
• src/hg/encode3/encodeDataWarehouse/utils/edwSolexaToSangerFastq/edwSolexaToSangerFastq.c
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• src/hg/encode3/encodeDataWarehouse/utils/makefile
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    Adding encodeDataWarehouse/utils to build.
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    Adding edwBamFilter to the made utilities.
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    Removing edwBamToWig from build. It doesn't work and is not committed
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    Removing edwValidKey from build, it is not for public consumption.
• src/hg/encode3/importEncode2/encode2BedDoctor/encode2BedDoctor.c
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• src/hg/encode3/importEncode2/encode2BedPlusDoctor/encode2BedPlusDoctor.c
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• src/hg/encode3/importEncode2/encode2CmpMd5/encode2CmpMd5.c
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• src/hg/encode3/importEncode2/encode2ExpDumpFlat/encode2ExpDumpFlat.c
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• src/hg/encode3/importEncode2/encode2FlattenFastqSubdirs/encode2FlattenFastqSubdirs.c
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• src/hg/encode3/importEncode2/encode2GffDoctor/encode2GffDoctor.c
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• src/hg/encode3/importEncode2/encode2MakeEncode3/encode2MakeEncode3.c
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• src/hg/encode3/importEncode2/encode2Manifest/encode2Manifest.c
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• src/hg/encode3/importEncode2/encode2Md5UpdateManifest/encode2Md5UpdateManifest.c
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• src/hg/encode3/importEncode2/encode2Meta/encode2Meta.c
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• src/hg/encode3/importEncode2/encode2MetaPatchRenamed/encode2MetaPatchRenamed.c
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• src/hg/encode3/importEncode2/encodeCvToDb/encodeCvToDb.c
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• src/hg/encode3/importEncode2/encodeExpToCvDb/encodeExpToCvDb.c
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• src/hg/encode3/validateFiles/validateFiles.c
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• src/hg/encode3/validateManifest/VERSION.TXT
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    v1.9 - adding some new bed-related formats, plus ability to use any bed-related format in a non-bigBed way by simply prefixing the format with "bed_" as indicated in RM1042 encodedcc.
• src/hg/encode3/validateManifest/validateManifest.c
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    v1.9 - adding some new bed-related formats, plus ability to use any bed-related format in a non-bigBed way by simply prefixing the format with "bed_" as indicated in RM1042 encodedcc.
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/hg/extractPslForLfs/extractPslForLfs.c
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• src/hg/fakeFinContigs/fakeFinContigs.c
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• src/hg/featureBits/featureBits.c
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• src/hg/ffaToFa/ffaToFa.c
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• src/hg/fishClones/fishClones.c
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• src/hg/formatZfishSts/formatZfishSts.c
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• src/hg/fqToQa/fqToQa.c
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• src/hg/fqToQac/fqToQac.c
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• src/hg/fragPart/fragPart.c
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• src/hg/gbGetEntries/gbGetEntries.c
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• src/hg/geneOverlap/geneOverlap.c
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• src/hg/genePredCheck/genePredCheck.c
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• src/hg/genePredHisto/genePredHisto.c
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• src/hg/genePredSingleCover/genePredSingleCover.c
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• src/hg/genePredSingleCover/geneScore.c
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• src/hg/genePredSingleCover/geneScore.h
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• src/hg/genePredToBed/genePredToBed.c
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• src/hg/genePredToFakePsl/genePredToFakePsl.c
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• src/hg/genePredToGtf/genePredToGtf.c
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• src/hg/genePredToMafFrames/finishMafFrames.c
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• src/hg/genePredToMafFrames/finishMafFrames.h
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• src/hg/genePredToMafFrames/frameIncr.h
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• src/hg/genePredToMafFrames/genePredToMafFrames.c
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• src/hg/genePredToMafFrames/mkMafFrames.c
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• src/hg/genePredToMafFrames/mkMafFrames.h
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• src/hg/genePredToMafFrames/orgGenes.c
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• src/hg/genePredToMafFrames/orgGenes.h
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• src/hg/genePredToMafFrames/splitMultiMappings.c
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• src/hg/genePredToMafFrames/splitMultiMappings.h
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• src/hg/genePredToMrna/genePredToMrna.c
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• src/hg/genoPheno/gpFakeData/gpFakeData.c
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• src/hg/genoPheno/gpShuffleData/gpShuffleData.c
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• src/hg/getFeatDna/getFeatDna.c
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• src/hg/getRna/getRna.c
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• src/hg/getRnaPred/getRnaPred.c
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• src/hg/getallpep/getallpep.c
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• src/hg/gisaid/gisaidSample/demog.c
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• src/hg/gisaid/gisaidSample/gisaidSample.c
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• src/hg/gisaid/gisaidSample/gisaidSample.h
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• src/hg/gisaid/gisaidSample/sequence.c
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• src/hg/gisaid/gisaidSubj/demog.c
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• src/hg/gisaid/gisaidSubj/gisaidSubj.c
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• src/hg/gisaid/gisaidSubj/gisaidSubj.h
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• src/hg/gisaid/gisaidSubj/sequence.c
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• src/hg/gisaid/gisaidTable/advFilter.c
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• src/hg/gisaid/gisaidTable/configure.c
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• src/hg/gisaid/gisaidTable/getSeq.c
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• src/hg/gisaid/gisaidTable/gisaidSubjInfo.c
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• src/hg/gisaid/gisaidTable/gisaidTable.c
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• src/hg/gisaid/gisaidTable/gisaidTable.h
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• src/hg/gpStats/gpStats.c
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• src/hg/gpToGtf/gpToGtf.c
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• src/hg/gpcrParser/gpcrParser.c
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• src/hg/gsBig/gsBig.c
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• src/hg/gsid/gsIdXref/gsIdXref.c
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• src/hg/gsid/gsidAaMsa/gsidAaMsa.c
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• src/hg/gsid/gsidGetConsensus/gsidGetConsensus.c
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• src/hg/gsid/gsidMember/bio.c
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• src/hg/gsid/gsidMember/bio.h
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• src/hg/gsid/gsidMember/gsidMember.c
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• src/hg/gsid/gsidMember/gsidMember.h
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• src/hg/gsid/gsidMember/paypalSignEncrypt.c
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• src/hg/gsid/gsidMember/paypalSignEncrypt.h
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• src/hg/gsid/gsidMsa/gsidMsa.c
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• src/hg/gsid/gsidMsaToTab/gsidMsaToTab.c
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• src/hg/gsid/gsidPbGateway/gsidPbGateway.c
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• src/hg/gsid/gsidPosSelect/gsidPosSelect.c
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• src/hg/gsid/gsidSubj/clinical.c
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• src/hg/gsid/gsidSubj/demog.c
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• src/hg/gsid/gsidSubj/gsidSubj.c
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• src/hg/gsid/gsidSubj/gsidSubj.h
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• src/hg/gsid/gsidSubj/sequence.c
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• src/hg/gsid/gsidSubj/vaccine.c
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• src/hg/gsid/gsidSubj3/clinical.c
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• src/hg/gsid/gsidSubj3/demog.c
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• src/hg/gsid/gsidSubj3/gsidSubj3.c
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• src/hg/gsid/gsidSubj3/gsidSubj3.h
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• src/hg/gsid/gsidSubj3/sequence.c
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• src/hg/gsid/gsidTable/gsidSubjInfo.c
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• src/hg/gsid/inc/gsid.h
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• src/hg/gsid/pwdtest/bio.h
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• src/hg/gsid/pwdtest/members.h
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• src/hg/gsid/pwdtest/paypalSignEncrypt.h
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• src/hg/gsid/pwdtest/pwdtest.c
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• src/hg/gsid/pwdtest/pwdtest.h
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• src/hg/hgApi/hgApi.c
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• src/hg/hgBatch/hgBatch.c
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• src/hg/hgBlat/hgBlat.c
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• src/hg/hgBlatTest/hgBlatTest.c
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• src/hg/hgChroms/hgChroms.c
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• src/hg/hgGene/alleles.c
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• src/hg/hgGene/dnaBindMotif.c
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• src/hg/hgGene/links.c
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• src/hg/hgGene/localization.c
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• src/hg/hgGene/makefile
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    Altered makefiles to gracefully make the demo machines without tripping on permissions. This change was approved by Hiram.
• src/hg/hgGene/method.c
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• src/hg/hgGene/microarray.c
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• src/hg/hgGene/mrnaDescriptions.c
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• src/hg/hgGene/otherOrgs.c
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• src/hg/hgGene/pseudoGene.c
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• src/hg/hgGene/rgdInfo.c
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• src/hg/hgGene/rnaStructure.c
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• src/hg/hgGene/sequence.c
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• src/hg/hgGene/swissProtComments.c
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• src/hg/hgGene/synonym.c
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• src/hg/hgGeneRing/hgGeneRing.c
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• src/hg/hgGeneRing/interaction.c
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• src/hg/hgGeneRing/interaction.h
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• src/hg/hgGenome/bedList.c
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• src/hg/hgGenome/browseRegions.c
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• src/hg/hgGenome/clickOnImage.c
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• src/hg/hgGenome/configure.c
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• src/hg/hgGenome/correlate.c
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• src/hg/hgGenome/custom.c
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• src/hg/hgGenome/hgGenome.c
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• src/hg/hgGenome/hgGenome.h
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• src/hg/hgGenome/import.c
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• src/hg/hgGenome/maf.c
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• src/hg/hgGenome/mainPage.c
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• src/hg/hgGenome/sortGenes.c
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• src/hg/hgGenome/upload.c
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• src/hg/hgGenome/wiggle.c
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• src/hg/hgGetAnn/hgGetAnn.c
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• src/hg/hgHubConnect/hgHubConnect.c
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    fix a couple problems found in code review, add some comments, andrearrange the code a little
    
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    updates to hgHubConnect to interface to make it less confusing. Nowconnection and disconnection put you on the gateway page.
    
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• src/hg/hgKnownGeneList/hgKnownGeneList.c
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• src/hg/hgLiftOver/hgLiftOver.c
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• src/hg/hgLogin/gbMembers.c
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• src/hg/hgLogin/hgLogin.c
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• src/hg/hgLogin/hgLogin.h
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• src/hg/hgNotAvail/hgNotAvail.c
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• src/hg/hgNotYet/hgNotYet.c
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• src/hg/hgPal/hgPal.c
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• src/hg/hgPcr/hgPcr.c
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• src/hg/hgSelect/hgSelect.c
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• src/hg/hgSession/hgSession.c
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• src/hg/hgSession/hgSession.h
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• src/hg/hgSpeciesRna/hgSpeciesRna.c
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• src/hg/hgTables/asFilter.c
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• src/hg/hgTables/asFilter.h
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• src/hg/hgTables/bam.c
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• src/hg/hgTables/bedList.c
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• src/hg/hgTables/bigBed.c
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• src/hg/hgTables/bigWig.c
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• src/hg/hgTables/chromGraph.c
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• src/hg/hgTables/correlate.c
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• src/hg/hgTables/correlate.h
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• src/hg/hgTables/correlatePlot.c
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• src/hg/hgTables/custom.c
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• src/hg/hgTables/galaxy.c
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• src/hg/hgTables/great.c
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• src/hg/hgTables/hgTables.c
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• src/hg/hgTables/hgTables.h
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• src/hg/hgTables/identifiers.c
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• src/hg/hgTables/intersect.c
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• src/hg/hgTables/schema.c
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• src/hg/hgTables/wiggle.c
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• src/hg/hgTables/wikiTrack.c
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• src/hg/hgTablesTest/hgTablesTest.c
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• src/hg/hgTrackUi/hgTrackUi.c
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• src/hg/hgTracks/altGraphXTrack.c
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• src/hg/hgTracks/bamTrack.c
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• src/hg/hgTracks/bigBedTrack.c
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• src/hg/hgTracks/bigWigTrack.c
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• src/hg/hgTracks/cutterTrack.h
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• src/hg/hgTracks/cytoBandTrack.c
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• src/hg/hgTracks/encode.c
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• src/hg/hgTracks/hapmapTrack.h
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• src/hg/hgTracks/hgTracks.c
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• src/hg/hgTracks/hgTracks.h
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• src/hg/hgTracks/imageV2.c
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• src/hg/hgTracks/imageV2.h
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• src/hg/hgTracks/loweLabTracks.c
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• src/hg/hgTracks/loweLabTracks.h
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• src/hg/hgTracks/mafTrack.c
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• src/hg/hgTracks/mafTrack.h
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• src/hg/hgTracks/mainMain.c
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• src/hg/hgTracks/makeItemsTrack.c
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• src/hg/hgTracks/multiWig.c
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• src/hg/hgTracks/oneTrack.h
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• src/hg/hgTracks/pslTrack.c
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• src/hg/hgTracks/pubsTracks.c
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• src/hg/hgTracks/pubsTracks.h
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• src/hg/hgTracks/renderMain.c
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• src/hg/hgTracks/retroGene.c
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• src/hg/hgTracks/retroTracks.h
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• src/hg/hgTracks/rmskTrack.c
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• src/hg/hgTracks/rnaFoldTrack.c
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• src/hg/hgTracks/rnaPLFoldTrack.c
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• src/hg/hgTracks/rnaPLFoldTrack.h
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• src/hg/hgTracks/sampleTracks.c
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• src/hg/hgTracks/searchTracks.c
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• src/hg/hgTracks/simpleTracks.c
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• src/hg/hgTracks/snakeTrack.c
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• src/hg/hgTracks/switchGear.c
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• src/hg/hgTracks/switchGear.h
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• src/hg/hgTracks/transMapTracks.c
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• src/hg/hgTracks/transMapTracks.h
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• src/hg/hgTracks/transcriptome.c
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• src/hg/hgTracks/variation.c
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• src/hg/hgTracks/vcfTrack.c
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• src/hg/hgTracks/wabaTrack.c
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• src/hg/hgTracks/wigCommon.h
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• src/hg/hgTracks/wigMafTrack.c
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• src/hg/hgTracks/wigTrack.c
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• src/hg/hgTracks/wiki.c
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• src/hg/hgVai/hgVai.c
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• src/hg/hgVai/libifyMe.c
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• src/hg/hgVai/libifyMe.h
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• src/hg/hgVarAnnogrator/hgVarAnnogrator.c
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• src/hg/hgc/bamClick.c
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• src/hg/hgc/bigBedClick.c
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• src/hg/hgc/ccdsClick.c
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• src/hg/hgc/ccdsClick.h
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• src/hg/hgc/cgapSageClick.c
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• src/hg/hgc/dbRIP.c
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• src/hg/hgc/encodeClick.c
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• src/hg/hgc/expClick.c
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• src/hg/hgc/gencodeClick.c
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• src/hg/hgc/gencodeClick.h
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• src/hg/hgc/geneReviewsClick.c
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• src/hg/hgc/geneReviewsClick.h
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• src/hg/hgc/gvfClick.c
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• src/hg/hgc/hgc.c
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• src/hg/hgc/hgc.h
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• src/hg/hgc/hgdpClick.c
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• src/hg/hgc/lowelab.c
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• src/hg/hgc/lrgClick.c
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• src/hg/hgc/mafClick.c
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• src/hg/hgc/makeItemsClick.c
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• src/hg/hgc/mgcClick.c
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• src/hg/hgc/mgcClick.h
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• src/hg/hgc/numtsClick.c
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• src/hg/hgc/numtsClick.h
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• src/hg/hgc/parClick.c
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• src/hg/hgc/parClick.h
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• src/hg/hgc/peakClusters.c
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• src/hg/hgc/pubs.c
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• src/hg/hgc/regMotif.c
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• src/hg/hgc/retroClick.c
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• src/hg/hgc/retroClick.h
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• src/hg/hgc/rnaFoldClick.c
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• src/hg/hgc/transMapClick.c
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• src/hg/hgc/transMapClick.h
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• src/hg/hgc/txCdsInfo.c
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• src/hg/hgc/variomeClick.c
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• src/hg/hgc/vcfClick.c
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• src/hg/hgc/virusClick.c
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• src/hg/hgc/virusClick.h
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• src/hg/hgc/wiggleClick.c
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• src/hg/hgc/wikiTrack.c
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• src/hg/hgcentralTidy/hgcentralTidy.c
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• src/hg/hgsql/hgsql.c
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• src/hg/hgsqlLocal/hgsqlLocal.c
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• src/hg/hgsqlSwapTables/hgsqlSwapTables.c
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• src/hg/hgsqlTableDate/hgsqlTableDate.c
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• src/hg/hgsqladmin/hgsqladmin.c
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• src/hg/hgsqldump/hgsqldump.c
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• src/hg/hgsqldumpLocal/hgsqldumpLocal.c
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• src/hg/hgsqlimport/hgsqlimport.c
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• src/hg/htdocs/goldenPath/credits.html
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    Changing DHGP to point to BDGP page, refs #13272
• src/hg/htdocs/goldenPath/help/hgQuickStartHub.html
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    Adding code review changes for new QuickStart Hub guide refs #13251
• src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
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    add some text to describe descriptionUrl
• src/hg/htdocs/goldenPath/newsarch.html
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    Changing DHGP to point to BDGP page, refs #13272
• src/hg/htdocs/images/donateNow.jpg
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    adding Donate Now button
• src/hg/htdocs/indexIntro.html
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    adding Donte Now button to home page
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• src/hg/inc/HInv.h
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• src/hg/inc/acemblyClass.h
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• src/hg/inc/affy10K.h
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• src/hg/inc/affy10KDetails.h
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• src/hg/inc/affy120KDetails.h
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• src/hg/inc/affyAllExonProbe.h
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• src/hg/inc/affyAtlas.h
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• src/hg/inc/affyGenoDetails.h
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• src/hg/inc/affyOffset.h
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• src/hg/inc/affyPairs.h
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• src/hg/inc/affyTransLifted.h
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• src/hg/inc/affyTranscriptome.h
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• src/hg/inc/agp.h
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• src/hg/inc/agpFrag.h
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• src/hg/inc/alignInfo.h
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• src/hg/inc/alignSeqSizes.h
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• src/hg/inc/alleleFreqs.h
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• src/hg/inc/allpredictions.h
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• src/hg/inc/altGraph.h
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• src/hg/inc/altGraphX.h
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• src/hg/inc/ancientRref.h
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• src/hg/inc/annoFormatVep.h
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• src/hg/inc/annoGrateWigDb.h
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• src/hg/inc/annoGratorGpVar.h
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• src/hg/inc/annoStreamDb.h
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• src/hg/inc/annoStreamWig.h
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• src/hg/inc/api.h
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• src/hg/inc/arCOGs.h
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• src/hg/inc/arcogdesc.h
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• src/hg/inc/atomDb.h
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• src/hg/inc/axtInfo.h
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• src/hg/inc/axtLib.h
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• src/hg/inc/bacCloneAlias.h
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• src/hg/inc/bacCloneXRef.h
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• src/hg/inc/bacEndAlias.h
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• src/hg/inc/bactigPos.h
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• src/hg/inc/baseMaskCommon.h
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• src/hg/inc/bdgpExprLink.h
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• src/hg/inc/bdgpGeneInfo.h
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• src/hg/inc/bdgpSwissProt.h
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• src/hg/inc/bed.h
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• src/hg/inc/bed12Source.h
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• src/hg/inc/bed12wSeq.h
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• src/hg/inc/bed5FloatScore.h
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• src/hg/inc/bed5Pval.h
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• src/hg/inc/bed6FloatScore.h
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• src/hg/inc/bed8Attrs.h
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• src/hg/inc/bedCart.h
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• src/hg/inc/bedDetail.h
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• src/hg/inc/bedGraph.h
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• src/hg/inc/bgiGeneInfo.h
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• src/hg/inc/bgiGeneSnp.h
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• src/hg/inc/bgiSnp.h
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• src/hg/inc/bioImage.h
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• src/hg/inc/blastTab.h
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• src/hg/inc/blastzNet.h
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• src/hg/inc/blatServers.h
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• src/hg/inc/borf.h
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• src/hg/inc/borkPseudoHom.h
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• src/hg/inc/botDelay.h
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• src/hg/inc/gpFx.h
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    For intergenic variants, I was assuming that each variant would havea firstAltAllele -- but for reference-only "variants", that's not the
    case so we need to check first. If there's no actual variation,
    drop the "variant".
    fixes #13310 - thanks Jonathan for finding.
    
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• src/hg/inc/hapmapPhaseIIISummary.h
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• src/hg/inc/hapmapPrimateAlleles.h
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• src/hg/inc/hapmapSnps.h
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• src/hg/inc/hapmapSnpsCombined.h
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• src/hg/inc/hubConnect.h
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    updates to hgHubConnect to interface to make it less confusing. Nowconnection and disconnection put you on the gateway page.
    
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• src/hg/inc/hui.h
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• src/hg/inc/stsInfoRat.h
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• src/hg/inc/stsMap.h
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• src/hg/inc/stsMapMouse.h
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• src/hg/inc/stsMapRat.h
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• src/hg/inc/suggest.h
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• src/hg/inc/synteny100000.h
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• src/hg/inc/syntenyBerk.h
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• src/hg/inc/syntenySanger.h
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• src/hg/inc/tRNAs.h
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• src/hg/inc/tableDescriptions.h
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• src/hg/inc/tableStatus.h
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• src/hg/inc/tagAlign.h
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• src/hg/inc/targetDb.h
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• src/hg/inc/taxonDivision.h
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• src/hg/inc/taxonGeneticCode.h
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• src/hg/inc/taxonXref.h
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• src/hg/inc/tfbsCons.h
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• src/hg/inc/tfbsConsMap.h
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• src/hg/inc/tfbsConsSites.h
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• src/hg/inc/tigrCmrGene.h
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• src/hg/inc/tigrOperon.h
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• src/hg/inc/tilingPath.h
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• src/hg/inc/trackDb.h
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• src/hg/inc/trackHub.h
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    updates to hgHubConnect to interface to make it less confusing. Nowconnection and disconnection put you on the gateway page.
    
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• src/hg/inc/trackLayout.h
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• src/hg/inc/trackTable.h
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• src/hg/inc/trackVersion.h
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• src/hg/inc/transMapGene.h
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• src/hg/inc/transMapInfo.h
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• src/hg/inc/transMapSrc.h
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• src/hg/inc/transMapStuff.h
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• src/hg/inc/transRegCode.h
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• src/hg/inc/transRegCodeCondition.h
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• src/hg/inc/transRegCodeProbe.h
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• src/hg/inc/trashDir.h
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• src/hg/inc/txCluster.h
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• src/hg/inc/txCommon.h
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• src/hg/inc/txEdgeBed.h
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• src/hg/inc/txEdgeOrtho.h
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• src/hg/inc/txGraph.h
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• src/hg/inc/txInfo.h
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• src/hg/inc/txRnaAccs.h
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• src/hg/inc/ucscRetroInfo.h
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• src/hg/inc/ucscRetroOrtho.h
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• src/hg/inc/variant.h
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• src/hg/inc/variome.h
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• src/hg/inc/vcfUi.h
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• src/hg/inc/vegaInfo.h
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• src/hg/inc/vegaInfoZfish.h
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• src/hg/inc/versionInfo.h
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• src/hg/inc/visiGene.h
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• src/hg/inc/vntr.h
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• src/hg/inc/web.h
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• src/hg/inc/wgRna.h
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• src/hg/inc/wiggle.h
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• src/hg/inc/wikiLink.h
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• src/hg/inc/wikiTrack.h
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• src/hg/inc/yaleGencodeAssoc.h
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• src/hg/inc/zdobnovSynt.h
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• src/hg/intronEnds/intronEnds.c
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• src/hg/intronSizes/intronSizes.c
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• src/hg/js/edwPersona.js
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    Code improvement from Tim's review
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    No good deed goes unpunished
• src/hg/lfsOverlap/lfsOverlap.c
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• src/hg/lib/HInv.c
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• src/hg/lib/acemblyClass.c
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• src/hg/lib/affy10K.c
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• src/hg/lib/affy10KDetails.c
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• src/hg/lib/affy120KDetails.c
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• src/hg/lib/affyAllExonProbe.c
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• src/hg/lib/affyAtlas.c
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• src/hg/lib/affyGenoDetails.c
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• src/hg/lib/affyOffset.c
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• src/hg/lib/affyPairs.c
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• src/hg/lib/affyTransLifted.c
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• src/hg/lib/affyTranscriptome.c
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• src/hg/lib/agp.c
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• src/hg/lib/agpFrag.c
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• src/hg/lib/agpGap.c
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• src/hg/lib/alignInfo.c
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• src/hg/lib/alignSeqSizes.c
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• src/hg/lib/alleleFreqs.c
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• src/hg/lib/allpredictions.c
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• src/hg/lib/altGraph.c
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• src/hg/lib/altGraphX.c
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• src/hg/lib/ancientRref.c
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• src/hg/lib/annoFormatVep.c
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• src/hg/lib/annoGrateWigDb.c
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• src/hg/lib/annoGratorGpVar.c
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    For intergenic variants, I was assuming that each variant would havea firstAltAllele -- but for reference-only "variants", that's not the
    case so we need to check first. If there's no actual variation,
    drop the "variant".
    fixes #13310 - thanks Jonathan for finding.
    
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• src/hg/lib/annoStreamDb.c
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• src/hg/lib/annoStreamWig.c
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• src/hg/lib/api.c
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• src/hg/lib/arCOGs.c
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• src/hg/lib/arcogdesc.c
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• src/hg/lib/atomDb.c
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• src/hg/lib/axtInfo.c
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• src/hg/lib/axtLib.c
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• src/hg/lib/bacCloneAlias.c
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• src/hg/lib/bacCloneXRef.c
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• src/hg/lib/bacEndAlias.c
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• src/hg/lib/bactigPos.c
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• src/hg/lib/baseMaskCommon.c
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• src/hg/lib/bdgpExprLink.c
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• src/hg/lib/bed.c
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• src/hg/lib/bed5Pval.c
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• src/hg/lib/bed6FloatScore.c
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• src/hg/lib/bed8Attrs.c
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• src/hg/lib/bedCart.c
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• src/hg/lib/bedDetail.c
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• src/hg/lib/bgiGeneInfo.c
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• src/hg/lib/bgiGeneSnp.c
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• src/hg/lib/bioImage.c
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• src/hg/lib/borf.c
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• src/hg/lib/borkPseudoHom.c
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• src/hg/lib/cart.c
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    updates to hgHubConnect to interface to make it less confusing. Nowconnection and disconnection put you on the gateway page.
    
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• src/hg/lib/ccdsGeneMap.c
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• src/hg/lib/chainDb.c
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• src/hg/lib/chicken13kInfo.c
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• src/hg/lib/chr18deletions.c
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• src/hg/lib/clusterInputAwgDnase.c
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• src/hg/lib/clusterInputAwgDnase.h
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• src/hg/lib/cnpIafrate.c
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• src/hg/lib/cnpSebat.c
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• src/hg/lib/cnpSebat2.c
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• src/hg/lib/cnpSharp2.c
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• src/hg/lib/cnpSharpCutoff.c
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• src/hg/lib/cnpSharpSample.c
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• src/hg/lib/cogs.c
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• src/hg/lib/columnInfo.c
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• src/hg/lib/contigAcc.c
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• src/hg/lib/coordConv.c
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• src/hg/lib/cpgIsland.c
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• src/hg/lib/cpgIslandExt.c
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• src/hg/lib/ctgPos.c
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• src/hg/lib/ctgPos2.c
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• src/hg/lib/customFactory.c
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• src/hg/lib/customTrack.c
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• src/hg/lib/cutter.c
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• src/hg/lib/cv.c
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• src/hg/lib/cytoBand.c
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• src/hg/lib/dbDb.c
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• src/hg/lib/dbRIP.c
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• src/hg/lib/dbSnpRs.c
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• src/hg/lib/defaultDb.c
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• src/hg/lib/delConrad2.c
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• src/hg/lib/delHinds2.c
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• src/hg/lib/dgv.c
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• src/hg/lib/dgvPlus.c
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• src/hg/lib/dless.c
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• src/hg/lib/dnaMarkovSql.c
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• src/hg/lib/dnaMotifSql.c
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• src/hg/lib/dnaProbe.c
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• src/hg/lib/dv.c
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• src/hg/lib/dvBed.c
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• src/hg/lib/dvXref2.c
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• src/hg/lib/easyGene.c
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• src/hg/lib/ec.c
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• src/hg/lib/encode/bedMethyl.as
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• src/hg/lib/encode/encodeErge.c
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• src/hg/lib/encode/encodeErgeHssCellLines.c
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• src/hg/lib/encode/encodeExp.c
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• src/hg/lib/encode/encodeHapMapAlleleFreq.c
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• src/hg/lib/encode/encodeIndels.c
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• src/hg/lib/encode/encodePeak.c
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• src/hg/lib/encode/encodeRegionInfo.c
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• src/hg/lib/encode/encodeRegionInfoCustom.c
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• src/hg/lib/encode/encodeRna.c
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• src/hg/lib/encode/encodeStanfordPromoters.c
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• src/hg/lib/expRecord.c
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• src/hg/lib/exprBed.c
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• src/hg/lib/factorSource.c
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• src/hg/lib/flyBase2004Xref.c
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• src/hg/lib/flyBaseSwissProt.c
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• src/hg/lib/flyreg2.c
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• src/hg/lib/fosEndPairs.c
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• src/hg/lib/gbExtFile.c
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• src/hg/lib/gbProtAnn.c
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• src/hg/lib/gbWarn.c
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• src/hg/lib/gcPercent.c
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• src/hg/lib/genMapDb.c
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• src/hg/lib/gencodeGeneClass.c
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• src/hg/lib/geneTree.c
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• src/hg/lib/genoLay.c
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• src/hg/lib/genomeRangeTreeFile.c
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• src/hg/lib/genomicDups.c
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• src/hg/lib/genomicSuperDups.c
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• src/hg/lib/genotype.c
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• src/hg/lib/geoMirror.c
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• src/hg/lib/ggMrnaAli.c
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• src/hg/lib/ggTypes.c
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• src/hg/lib/glDbRep.c
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• src/hg/lib/goa.c
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• src/hg/lib/goaPart.c
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• src/hg/lib/googleAnalytics.c
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• src/hg/lib/gpFx.c
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    For intergenic variants, I was assuming that each variant would havea firstAltAllele -- but for reference-only "variants", that's not the
    case so we need to check first. If there's no actual variation,
    drop the "variant".
    fixes #13310 - thanks Jonathan for finding.
    
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• src/hg/lib/growthCondition.c
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• src/hg/lib/gwasCatalog.c
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• src/hg/lib/hCommon.c
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• src/hg/lib/hCytoBand.c
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• src/hg/lib/hPrint.c
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• src/hg/lib/hVarSubst.c
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• src/hg/lib/haplotypes.c
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• src/hg/lib/hapmapAlleleFreq.c
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• src/hg/lib/hapmapAlleles.c
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• src/hg/lib/hapmapAllelesCombined.c
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• src/hg/lib/hapmapAllelesOrtho.c
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• src/hg/lib/hapmapAllelesSummary.c
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• src/hg/lib/hapmapLd.c
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• src/hg/lib/hapmapPhaseIIISummary.c
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• src/hg/lib/hapmapPrimateAlleles.c
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• src/hg/lib/hapmapSnps.c
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• src/hg/lib/hapmapSnpsCombined.c
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• src/hg/lib/hdb.c
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• src/hg/lib/hgColors.c
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• src/hg/lib/hgConfig.c
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• src/hg/lib/hgExp.c
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• src/hg/lib/hgMaf.c
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• src/hg/lib/hgSeq.c
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• src/hg/lib/hubConnect.c
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• src/hg/lib/hui.c
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• src/hg/lib/hvGfx.c
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• src/hg/lib/jgiGene.c
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• src/hg/lib/kg1ToKg2.c
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• src/hg/lib/kgColor.c
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• src/hg/lib/kgMapName.c
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• src/hg/lib/lav.c
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• src/hg/lib/ld.c
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• src/hg/lib/liftUp.c
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• src/hg/lib/lowelabPfamHit.h
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• src/hg/lib/lsSnpPdbChimera.c
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• src/hg/lib/mammalPsg.c
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• src/hg/lib/mdb.c
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• src/hg/lib/microarray.c
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• src/hg/lib/minGeneInfo.c
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• src/hg/lib/mrnaMisMatch.c
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• src/hg/lib/newfoo/cytoBand.c
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• src/hg/lib/nonCodingUi.c
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• src/hg/lib/omicia.c
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• src/hg/lib/oregannoUi.c
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• src/hg/lib/orthoAlleles.c
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• src/hg/lib/pal.c
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• src/hg/lib/pbStamp.c
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• src/hg/lib/pcrResult.c
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• src/hg/lib/pepPred.c
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• src/hg/lib/pgPhenoAssoc.c
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• src/hg/lib/pgPolyphenPred.c
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• src/hg/lib/pgSiftPred.c
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• src/hg/lib/pgSnp.c
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• src/hg/lib/plasEndPairs.c
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• src/hg/lib/polyGenotype.c
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• src/hg/lib/protFeat.c
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• src/hg/lib/protVar.c
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• src/hg/lib/pseudoGeneLink.c
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• src/hg/lib/pslWQueryID.c
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• src/hg/lib/pslWScore.c
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• src/hg/lib/putaInfo.c
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• src/hg/lib/qaSeq.c
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• src/hg/lib/rangeTreeFile.c
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• src/hg/lib/rankProp.c
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• src/hg/lib/recombRate.c
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• src/hg/lib/recombRateMouse.c
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• src/hg/lib/recombRateRat.c
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• src/hg/lib/refLink.c
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• src/hg/lib/refSeqStatus.c
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• src/hg/lib/retroMrnaInfo.c
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• src/hg/lib/rgdQtl.c
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• src/hg/lib/rhMapInfo.c
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• src/hg/lib/tests/genePredTester.c
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• src/hg/lib/tfbsConsSites.c
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    updates to hgHubConnect to interface to make it less confusing. Nowconnection and disconnection put you on the gateway page.
    
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• src/hg/lib/trackTable.c
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• src/hg/lib/trashDir.c
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• src/hg/lib/txCluster.c
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• src/hg/lib/txRnaAccs.c
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• src/hg/lib/ucscRetroInfo.c
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• src/hg/lib/ucscRetroOrtho.c
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• src/hg/lib/validateGisaid.c
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• src/hg/lib/variant.c
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• src/hg/lib/variome.c
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• src/hg/lib/vcfUi.c
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• src/hg/lib/vegaInfo.c
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• src/hg/lib/vegaInfoZfish.c
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• src/hg/lib/visiGene.c
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• src/hg/lib/vntr.c
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• src/hg/lib/wabAli.c
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• src/hg/lib/web.c
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• src/hg/lib/wgRna.c
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• src/hg/lib/wigAsciiToBinary.c
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• src/hg/lib/wigDataStream.c
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• src/hg/lib/wiggle.c
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• src/hg/lib/wiggleCart.c
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• src/hg/lib/wiggleUtils.c
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• src/hg/lib/yaleGencodeAssoc.c
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• src/hg/lib/zdobnovSynt.c
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• src/hg/liftAcross/liftAcross.c
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• src/hg/liftAgp/liftAgp.c
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• src/hg/liftFrags/liftFrags.c
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• src/hg/liftOver/liftOver.c
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• src/hg/liftOver/liftOverMerge.c
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• src/hg/liftUp/liftUp.c
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• src/hg/logCrawl/accessLogFilter/accessLogFilter.c
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• src/hg/logCrawl/accessLogMerge/accessLogMerge.c
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• src/hg/logCrawl/accessLogSort/accessLogSort.c
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• src/hg/logCrawl/accessLogWigs/accessLogWigs.c
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• src/hg/logCrawl/crawlForHogs/crawlForHogs.c
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• src/hg/logCrawl/crawlForPosAndTime/crawlForPosAndTime.c
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• src/hg/logCrawl/encodeUserDbCrawl/encodeUserDbCrawl.c
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• src/hg/logCrawl/hgAccessCrawl/hgAccessCrawl.c
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• src/hg/logCrawl/sessionDbCrawl/sessionDbCrawl.c
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• src/hg/logCrawl/ticksToWig/ticksToWig.c
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• src/hg/makeDb/doc/encodeRegHg19.txt
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    Fixes for TFBS Clusters table join problems reported by Angie
• src/hg/makeDb/doc/hg38.txt
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    makeDoc and all.joiner change to supportTrack #13281: GeneReviews for hg38
    
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• src/hg/makeDb/doc/mm10.txt
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    running up rheMac2 to mm10 liftOver refs #13319
• src/hg/makeDb/doc/rn5.txt
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    Adding entries for rn5 multiz. refs #8212
• src/hg/makeDb/genbank/etc/genbank.conf
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• src/hg/makeDb/genbank/src/align/gbAlignCommon.c
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• src/hg/makeDb/genbank/src/align/gbAlignInstall.c
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• src/hg/makeDb/genbank/src/ccds/ccdsImport.c
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• src/hg/makeDb/genbank/src/ccds/ccdsLocationsJoin.c
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• src/hg/makeDb/genbank/src/ccds/ccdsLocationsJoin.h
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• src/hg/makeDb/genbank/src/ccds/mkCcdsGeneMap.c
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• src/hg/makeDb/genbank/src/dbload/dbLoadPartitions.h
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• src/hg/makeDb/genbank/src/dbload/gbAlignData.c
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• src/hg/makeDb/genbank/src/dbload/gbAlignData.h
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• src/hg/makeDb/genbank/src/dbload/gbAlignTbl.c
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• src/hg/makeDb/genbank/src/dbload/gbAlignTbl.h
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• src/hg/makeDb/genbank/src/dbload/gbBuildState.c
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• src/hg/makeDb/genbank/src/dbload/gbBuildState.h
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• src/hg/makeDb/genbank/src/dbload/gbGeneTbl.c
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• src/hg/makeDb/genbank/src/dbload/gbIgnoreDelete.c
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• src/hg/makeDb/genbank/src/dbload/gbLoadRna.c
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• src/hg/makeDb/genbank/src/dbload/gbMDParse.c
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• src/hg/makeDb/genbank/src/dbload/gbMDParse.h
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• src/hg/makeDb/genbank/src/dbload/gbMetaData.c
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• src/hg/makeDb/genbank/src/dbload/gbMetaData.h
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• src/hg/makeDb/genbank/src/extFileUpdate/raInfoTbl.h
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• src/hg/makeDb/genbank/src/gbConf/gbConf.c
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• src/hg/makeDb/genbank/src/gbGetSeqs/gbGetSeqs.c
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• src/hg/makeDb/genbank/src/gbGetSeqs/raData.c
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• src/hg/makeDb/genbank/src/gbGetSeqs/raData.h
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• src/hg/makeDb/genbank/src/gbGetSeqs/seqData.c
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• src/hg/makeDb/genbank/src/gbGetSeqs/seqData.h
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• src/hg/makeDb/genbank/src/gbSanity/chkAlignTbls.c
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• src/hg/makeDb/genbank/src/gbSanity/chkAlignTbls.h
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• src/hg/makeDb/genbank/src/gbSanity/chkCommon.c
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• src/hg/makeDb/genbank/src/gbSanity/chkCommon.h
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• src/hg/makeDb/genbank/src/gbSanity/chkGbIndex.c
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• src/hg/makeDb/genbank/src/gbSanity/chkMetaDataTbls.c
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• src/hg/makeDb/genbank/src/gbSanity/chkMetaDataTbls.h
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• src/hg/makeDb/genbank/src/gbSanity/chkSeqTbl.c
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• src/hg/makeDb/genbank/src/gbSanity/chkSeqTbl.h
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• src/hg/makeDb/genbank/src/gbSanity/gbSanity.c
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• src/hg/makeDb/genbank/src/gbSanity/metaData.c
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• src/hg/makeDb/genbank/src/gbSanity/metaData.h
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• src/hg/makeDb/genbank/src/inc/extFileTbl.h
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• src/hg/makeDb/genbank/src/inc/gbAligned.h
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• src/hg/makeDb/genbank/src/inc/gbConf.h
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• src/hg/makeDb/genbank/src/inc/gbDefs.h
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• src/hg/makeDb/genbank/src/inc/gbEntry.h
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• src/hg/makeDb/genbank/src/inc/gbFa.h
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• src/hg/makeDb/genbank/src/inc/gbFileOps.h
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• src/hg/makeDb/genbank/src/inc/gbGenome.h
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• src/hg/makeDb/genbank/src/inc/gbLoadedTbl.h
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• src/hg/makeDb/genbank/src/inc/gbPipeline.h
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• src/hg/makeDb/genbank/src/inc/seqTbl.h
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• src/hg/makeDb/genbank/src/lib/extFileTbl.c
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• src/hg/makeDb/genbank/src/lib/gbConf.c
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• src/hg/makeDb/genbank/src/lib/gbDefs.c
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• src/hg/makeDb/genbank/src/lib/gbEntry.c
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• src/hg/makeDb/genbank/src/lib/gbFileOps.c
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• src/hg/makeDb/genbank/src/lib/gbVerb.c
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• src/hg/makeDb/genbank/src/lib/imageCloneTbl.c
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• src/hg/makeDb/genbank/src/lib/uniqueStrTbl.c
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• src/hg/makeDb/genbank/src/process/gbParse.c
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• src/hg/makeDb/genbank/src/process/gbParse.h
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• src/hg/makeDb/genbank/src/process/gbProcess.c
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• src/hg/makeDb/genbank/src/selectWithPsl/selectWithPsl.c
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• src/hg/makeDb/hgAddLiftOverChain/hgAddLiftOverChain.c
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• src/hg/makeDb/hgBedsToBedExps/bToBeCfg.c
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• src/hg/makeDb/hgBedsToBedExps/bToBeCfg.h
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• src/hg/makeDb/hgBedsToBedExps/hgBedsToBedExps.c
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• src/hg/makeDb/hgCgiData/Mouse/microarrayGroups.ra
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• src/hg/makeDb/hgCountAlign/align.c
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• src/hg/makeDb/hgCountAlign/align.h
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• src/hg/makeDb/hgCountAlign/hgCountAlign.c
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• src/hg/makeDb/hgCountAlign/slidingWin.h
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• src/hg/makeDb/hgCountAlign/winCounts.h
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• src/hg/makeDb/hgCtgPos/liftSpec.c
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• src/hg/makeDb/hgCutters/hgCutters.c
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• src/hg/makeDb/hgDeleteChrom/hgDeleteChrom.c
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• src/hg/makeDb/hgFakeAgp/hgFakeAgp.c
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• src/hg/makeDb/hgFindSpec/hgFindSpec.c
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• src/hg/makeDb/hgGetKgUrls/hgGetKgUrls.c
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• src/hg/makeDb/hgGetNrOmimGene/hgGetNrOmimGene.c
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• src/hg/makeDb/hgKgMrna/hgKgMrna.c
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• src/hg/makeDb/hgKnownMore/hugoMulti.c
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• src/hg/makeDb/hgLoadAxt/hgLoadAxt.c
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• src/hg/makeDb/hgLoadBed/hgLoadBed.c
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• src/hg/makeDb/hgLoadBlastTab/hgLoadBlastTab.c
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• src/hg/makeDb/hgLoadCdsEvidence/hgLoadCdsEvidence.c
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• src/hg/makeDb/hgLoadChain/hgLoadChain.c
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• src/hg/makeDb/hgLoadChromGraph/hgLoadChromGraph.c
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• src/hg/makeDb/hgLoadMaf/hgLoadMaf.c
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• src/hg/makeDb/hgLoadMaf/hgLoadMafSummary.c
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• src/hg/makeDb/hgLoadMafFrames/hgLoadMafFrames.c
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• src/hg/makeDb/hgLoadNet/hgLoadNet.c
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• src/hg/makeDb/hgLoadOut/hgLoadOut.c
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• src/hg/makeDb/hgLoadSample/hgLoadSample.c
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• src/hg/makeDb/hgLoadSeq/hgLoadSeq.c
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• src/hg/makeDb/hgLoadWiggle/hgDumpWiggle.c
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• src/hg/makeDb/hgMedianMicroarray/hgMedianMicroarray.c
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• src/hg/makeDb/hgMrnaRefseq/hgMrnaRefseq.c
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• src/hg/makeDb/hgRenameSplitTable/hgRenameSplitTable.c
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• src/hg/makeDb/hgRgdParsePathwayObo/hgRgdParsePathwayObo.c
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• src/hg/makeDb/hgStanfordMicroarray/hgStanfordMicroarray.c
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• src/hg/makeDb/hgStsAlias/hgStsAlias.c
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• src/hg/makeDb/outside/allenBrain/allenCleanup/allenCleanup.c
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• src/hg/makeDb/outside/allenBrain/allenCollectSeq/allenCollectSeq.c
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• src/hg/makeDb/outside/cgapSage/cgapSageBedAddFreqs/cgapSageBedAddFreqs.c
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• src/hg/makeDb/outside/cgapSage/cgapSageFind/cgapSageFind.c
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• src/hg/makeDb/outside/cgapSage/cgapSageFind/cgapSageFind.h
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• src/hg/makeDb/outside/exonerateGffDoctor/exonerateGffDoctor.c
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• src/hg/makeDb/outside/hgFlyBase/hgFlyBase.c
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• src/hg/makeDb/outside/hgGnfMicroarray/hgGnfMicroarray.c
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• src/hg/makeDb/outside/hgJaxQtl/hgJaxQtl.c
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• src/hg/makeDb/outside/hgLoadEranModules/esMotif.c
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• src/hg/makeDb/outside/hgLoadEranModules/esMotif.h
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• src/hg/makeDb/outside/hgLoadEranModules/hgLoadEranModules.c
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• src/hg/makeDb/outside/hgLsSnpPdbLoad/hgLsSnpPdbLoad.c
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• src/hg/makeDb/outside/hgRnaGenes/hgRnaGenes.c
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• src/hg/makeDb/outside/hgSoftPromoter/hgSoftPromoter.c
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• src/hg/makeDb/outside/hgSoftberryHom/hgSoftberryHom.c
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• src/hg/makeDb/outside/hgSuperfam/hgSuperfam.c
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• src/hg/makeDb/outside/nibb/nibbImageProbes/nibbImageProbes.c
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• src/hg/makeDb/outside/nibb/nibbNameFix/nibbNameFix.c
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• src/hg/makeDb/outside/nibb/nibbParseImageDir/nibbParseImageDir.c
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• src/hg/makeDb/outside/nibb/nibbPrepImages/nibbPrepImages.c
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• src/hg/makeDb/outside/samHit/samHit.c
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• src/hg/makeDb/outside/sanger22gtf/sanger22gtf.c
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• src/hg/makeDb/outside/vegaBuildInfo/vegaBuildInfo.c
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• src/hg/makeDb/outside/yeast/checkSgdSync/checkSgdSync.c
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• src/hg/makeDb/outside/yeast/fixHarbisonMotifs/fixHarbisonMotifs.c
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• src/hg/makeDb/outside/yeast/hgSgdGff3/hgSgdGff3.c
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• src/hg/makeDb/outside/yeast/hgSgdGfp/hgSgdGfp.c
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• src/hg/makeDb/outside/yeast/hgSgdPep/hgSgdPep.c
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• src/hg/makeDb/outside/yeast/hgYeastRegCode/hgYeastRegCode.c
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• src/hg/makeDb/tfbsConsLoc/seq.c
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• src/hg/makeDb/tfbsConsLoc/seq.h
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• src/hg/makeDb/tfbsConsLoc/tfbsConsLoc.c
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• src/hg/makeDb/tfbsConsLoc/tfbsConsLoc.h
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• src/hg/makeDb/tfbsConsLoc/tfbsConsLocUtil.c
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• src/hg/makeDb/tfbsConsLoc/tfbsConsLocUtil.h
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• src/hg/makeDb/tfbsConsLoc/util.c
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• src/hg/makeDb/tfbsConsLoc/util.h
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• src/hg/makeDb/tfbsConsSort/tfbsConsSort.c
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• src/hg/makeDb/trackDb/drosophila/dm2/description.html
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    Changing DHGP to point to BDGP page, refs #13272
• src/hg/makeDb/trackDb/drosophila/dm3/description.html
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    Changing DHGP to point to BDGP page, refs #13272
• src/hg/makeDb/trackDb/drosophila/dm3/flyBaseGene.html
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    Changing DHGP to point to BDGP page, refs #13272
• src/hg/makeDb/trackDb/drosophila/dm3/flyBaseNoncoding.html
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    Changing DHGP to point to BDGP page, refs #13272
• src/hg/makeDb/trackDb/mouse/trackDb.ra
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    Adding entries to display facebase microarray track. refs #12606
• src/hg/makeDb/trackDbPatch/trackDbPatch.c
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• src/hg/makeDb/trackDbRaFormat/trackDbRaFormat.c
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• src/hg/makeSeqs/makeSeqs.c
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• src/hg/makefile
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    Removing encode3 from targets to avoid making everyone install bamtools or us having to ifdef around everything that uses BAM.
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    Making it so that the ENCODE data warehouse doesn't even try to compile under Mac OS. It doesn't need to, and Mac OS lacks some of the libraries it uses.
• src/hg/maskOutFa/maskOutFa.c
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• src/hg/mdToNcbiLift/mdToNcbiLift.c
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• src/hg/monitor/cacti/cactiSine/cactiSine.c
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• src/hg/mouseStuff/afsCombine/afsCombine.c
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• src/hg/mouseStuff/aliFragScore/aliFragScore.c
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• src/hg/mouseStuff/axtChain/axtChain.c
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• src/hg/mouseStuff/axtDropOverlap/axtDropOverlap.c
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• src/hg/mouseStuff/axtDropSelf/axtDropSelf.c
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• src/hg/mouseStuff/axtFilter/axtFilter.c
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• src/hg/mouseStuff/axtIndex/axtIndex.c
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• src/hg/mouseStuff/axtRecipBest/axtRecipBest.c
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• src/hg/mouseStuff/axtRescore/axtRescore.c
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• src/hg/mouseStuff/axtSomeRecords/axtSomeRecords.c
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• src/hg/mouseStuff/axtSplitByTarget/axtSplitByTarget.c
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• src/hg/mouseStuff/axtSwap/axtSwap.c
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• src/hg/mouseStuff/axtToMaf/axtToMaf.c
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• src/hg/mouseStuff/bedCoverage/bedCoverage.c
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• src/hg/mouseStuff/blastzPaper/blastzPaper.c
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• src/hg/mouseStuff/calcGap/calcGap.c
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• src/hg/mouseStuff/chainAntiRepeat/chainAntiRepeat.c
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• src/hg/mouseStuff/chainDbToFile/chainDbToFile.c
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• src/hg/mouseStuff/chainFilter/chainFilter.c
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• src/hg/mouseStuff/chainIndex/chainIndex.c
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• src/hg/mouseStuff/chainInfo/chainInfo.c
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• src/hg/mouseStuff/chainInfo/chainInfo.h
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• src/hg/mouseStuff/chainMergeSort/chainMergeSort.c
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• src/hg/mouseStuff/chainNet/chainNet.c
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• src/hg/mouseStuff/chainOverlap/chainOverlap.c
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• src/hg/mouseStuff/chainPreNet/chainPreNet.c
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• src/hg/mouseStuff/chainScore/chainScore.c
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• src/hg/mouseStuff/chainSort/chainSort.c
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• src/hg/mouseStuff/chainSplit/chainSplit.c
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• src/hg/mouseStuff/chainStats/chainStats.c
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• src/hg/mouseStuff/chainStitch/chainStitch.c
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• src/hg/mouseStuff/chainStitchId/chainStitchId.c
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• src/hg/mouseStuff/chainSwap/chainSwap.c
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• src/hg/mouseStuff/chainToAxt/chainToAxt.c
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• src/hg/mouseStuff/correctEst/correctEst.c
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• src/hg/mouseStuff/exonMap/exonMap.c
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• src/hg/mouseStuff/gcForBed/gcForBed.c
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• src/hg/mouseStuff/ggcPic/ggcPic.c
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• src/hg/mouseStuff/knownVsBlat/blatStats.c
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• src/hg/mouseStuff/knownVsBlat/blatStats.h
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• src/hg/mouseStuff/knownVsBlat/knownVsBlat.c
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• src/hg/mouseStuff/knownVsBlat/kvsSummary.c
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• src/hg/mouseStuff/lavToAxt/lavToAxt.c
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• src/hg/mouseStuff/lavToPsl/lavToPsl.c
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• src/hg/mouseStuff/libScan/libScan.c
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• src/hg/mouseStuff/mafCoverage/mafCoverage.c
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• src/hg/mouseStuff/mafFetch/mafFetch.c
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• src/hg/mouseStuff/mafRanges/mafRanges.c
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• src/hg/mouseStuff/mafToAxt/mafToAxt.c
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• src/hg/mouseStuff/mafToClustalw/mafToClustalw.c
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• src/hg/mouseStuff/mafToFa/mafToFa.c
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• src/hg/mouseStuff/mafToPsl/mafToPsl.c
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• src/hg/mouseStuff/mafToXmfa/mafToXmfa.c
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• src/hg/mouseStuff/mousePoster/mousePoster.c
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• src/hg/mouseStuff/netChainSubset/netChainSubset.c
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• src/hg/mouseStuff/netClass/netClass.c
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• src/hg/mouseStuff/netContigs/netContigs.c
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• src/hg/mouseStuff/netFilter/netFilter.c
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• src/hg/mouseStuff/netSplit/netSplit.c
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• src/hg/mouseStuff/netStats/netStats.c
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• src/hg/mouseStuff/netSyntenic/netSyntenic.c
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• src/hg/mouseStuff/netToAxt/netToAxt.c
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• src/hg/mouseStuff/netToBed/netToBed.c
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• src/hg/mouseStuff/netToBedWithId/netToBedWithId.c
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• src/hg/mouseStuff/orthologBySynteny/orthologBySynteny.c
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• src/hg/mouseStuff/phToPsl/phToPsl.c
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• src/hg/mouseStuff/pslMrnaCover/pslMrnaCover.c
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• src/hg/mouseStuff/regionPicker/regionPicker.c
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• src/hg/mouseStuff/rikenBestInCluster/rikenBestInCluster.c
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• src/hg/mouseStuff/simpleChain/simpleChain.c
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• src/hg/mouseStuff/splitSim/splitSim.c
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• src/hg/mouseStuff/subsetTraces/subsetTraces.c
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• src/hg/mouseStuff/whyConserved/trackOverlap.c
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• src/hg/mouseStuff/whyConserved/whyConserved.c
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• src/hg/mouseStuff/xmfaToMaf/xmfaToMaf.c
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• src/hg/mrnaToGene/mrnaToGene.c
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• src/hg/nci60/findStanAlignments.c
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• src/hg/nci60/stanToBedAndExpRecs.c
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• src/hg/near/hgCeOrfToGene/hgCeOrfToGene.c
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• src/hg/near/hgClusterGenes/hgClusterGenes.c
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• src/hg/near/hgEmblProtLinks/hgEmblProtLinks.c
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• src/hg/near/hgExpDistance/diffDistTables.c
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• src/hg/near/hgExpDistance/hgExpDistance.c
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• src/hg/near/hgExpDistance/hgExpDistance_fm.c
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• src/hg/near/hgExpDistance/hgExpDistance_fm_tm.c
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• src/hg/near/hgExpDistance/hgExpDistance_fq.c
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• src/hg/near/hgExpDistance/hgExpDistance_fq_tm.c
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• src/hg/near/hgGoAssociation/hgGoAssociation.c
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• src/hg/near/hgKnownToSuper/hgKnownToSuper.c
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• src/hg/near/hgMapToGene/hgMapToGene.c
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• src/hg/near/hgMapViaSwissProt/hgMapViaSwissProt.c
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• src/hg/near/hgNear/advFilter.c
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• src/hg/near/hgNear/afiAli.c
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• src/hg/near/hgNear/association.c
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• src/hg/near/hgNear/colTemplate.c
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• src/hg/near/hgNear/configure.c
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• src/hg/near/hgNear/customColumn.c
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• src/hg/near/hgNear/examples.c
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• src/hg/near/hgNear/expRatio.c
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• src/hg/near/hgNear/flyBase.c
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• src/hg/near/hgNear/getSeq.c
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• src/hg/near/hgNear/go.c
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• src/hg/near/hgNear/hgNear.c
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• src/hg/near/hgNear/hgNear.h
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• src/hg/near/hgNear/intronSize.c
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• src/hg/near/hgNear/knownGene.c
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• src/hg/near/hgNear/makefile
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• src/hg/near/hgNear/order.c
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• src/hg/near/hgNear/pfam.c
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• src/hg/near/hgNear/search.c
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• src/hg/near/hgNear/userSettings.c
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• src/hg/near/hgNearTest/hgNearTest.c
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• src/hg/near/hgNetDist/hgLoadNetDist.c
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• src/hg/near/hgNetDist/hgNetDist.c
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• src/hg/near/hgProtIdToGenePred/hgProtIdToGenePred.c
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• src/hg/near/hgWormLinks/hgWormLinks.c
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• src/hg/near/hgZfishEnsXRef/hgEnsGeneXRef.c
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• src/hg/near/hprdXmlToTab/hprd.c
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• src/hg/near/hprdXmlToTab/hprd.h
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• src/hg/near/hprdXmlToTab/hprdXmlToTab.c
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• src/hg/near/knownToHprd/knownToHprd.c
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• src/hg/near/pepPredToFa/pepPredToFa.c
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• src/hg/oneShot/addChrPsl/addChrPsl.c
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• src/hg/oneShot/addMhcClones/addMhcClones.c
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• src/hg/oneShot/addTopoToPrimers/addTopoToPrimers.c
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    A program to help tag source with copyrights.
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    A program to help tag source with copyrights.
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    Taking date from input file rather than command line
• src/hg/oneShot/affyAllExonGSColumn/affyAllExonGSColumn.c
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• src/hg/oneShot/clonePos/clonePos.c
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• src/hg/oneShot/doEvoFold/doEvoFold.c
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• src/hg/oneShot/doEvoFoldV2/doEvoFoldV2.c
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• src/hg/oneShot/doRgdGene2UniProt/doRgdGene2UniProt.c
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• src/hg/oneShot/doRgdGene2Xref/doRgdGene2Xref.c
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• src/hg/oneShot/evalEndOverlaps/ocp.c
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• src/hg/oneShot/evalEnds/evalEnds.c
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• src/hg/oneShot/faFiltMasked/faFiltMasked.c
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• src/hg/oneShot/fakeSeqDiffs/fakeSeqDiffs.c
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• src/hg/oneShot/findContigsWithClones/findContigsWithClones.c
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• src/hg/oneShot/findToFixBedGraphLimits/findToFixBedGraphLimits.c
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• src/hg/oneShot/findToFixBedGraphViewLimits/findToFixBedGraphViewLimits.c
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• src/hg/oneShot/fixBlastTrack/fixBlastTrack.c
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• src/hg/oneShot/fixEnsGtf/fixEnsGtf.c
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• src/hg/oneShot/fixGdup/fixGdup.c
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• src/hg/oneShot/flagMhcClones/flagMhcClones.c
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• src/hg/oneShot/freen/freen.c
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• src/hg/oneShot/getHumanBrainRna/getHumanBrainRna.c
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• src/hg/oneShot/getRgdGeneCds/getRgdGeneCds.c
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• src/hg/oneShot/howBadNt/howBadNt.c
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• src/hg/protein/spToDb/spToDb.c
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• src/hg/protein/spXref2/spXref2.c
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• src/hg/protein/spm7/spm7.c
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• src/hg/pslCDnaFilter/cDnaAligns.c
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• src/hg/pslCDnaFilter/cDnaAligns.h
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• src/hg/pslCDnaFilter/cDnaReader.h
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• src/hg/pslCDnaFilter/cDnaStats.c
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• src/hg/pslCDnaFilter/cDnaStats.h
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• src/hg/pslCDnaFilter/globalNearBestFilter.c
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• src/hg/pslCDnaFilter/globalNearBestFilter.h
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• src/hg/pslCDnaFilter/hapRegions.c
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• src/hg/pslCDnaFilter/hapRegions.h
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• src/hg/pslCDnaFilter/localNearBestFilter.c
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• src/hg/pslCDnaFilter/polyASize.c
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• src/hg/pslCDnaFilter/polyASize.h
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• src/hg/pslCDnaFilter/pslCDnaFilter.c
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• src/hg/pslCDnaGenomeMatch/pslCDnaGenomeMatch.c
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• src/hg/pslMaxMap/pslMaxMap.c
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• src/hg/pslOneTwo/chainOneTwo.c
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• src/hg/pslOneTwo/pslOneTwo.c
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• src/hg/pslPairs/pslPairs.c
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• src/hg/pslPartition/pslPartition.c
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• src/hg/pslPseudo/checkExp/checkExp.c
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• src/hg/pslQuickFilter/pslQuickFilter.c
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• src/hg/pslRecalcMatch/pslRecalcMatch.c
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• src/hg/pslSelect/pslSelect.c
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• src/hg/pslSimp/pslSimp.c
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• src/hg/pslSomeRecords/pslSomeRecords.c
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• src/hg/pslSortAcc/pslSortAcc.c
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• src/hg/pslStats/pslStats.c
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• src/hg/pslToBed/pslToBed.c
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    as long as we don't have bigPsl this is some replacement
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• src/hg/pslToChain/pslToChain.c
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• src/hg/pslToFa/pslToFa.c
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• src/hg/pslToPileup/pslToPileup.c
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• src/hg/pslxToFa/pslxToFa.c
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• src/hg/snp/snpLoad/snpSNP.c
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• src/hg/test/test.c
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• src/hg/txCds/txCdsBadBed/txCdsBadBed.c
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• src/hg/txCds/txCdsEvFromBorf/txCdsEvFromBorf.c
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• src/hg/txCds/txCdsEvFromProtein/txCdsEvFromProtein.c
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• src/hg/txCds/txCdsEvFromRna/txCdsEvFromRna.c
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• src/hg/txCds/txCdsGoodBed/txCdsGoodBed.c
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• src/hg/txCds/txCdsOrfInfo/txCdsOrfInfo.c
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• src/hg/txCds/txCdsOrtho/txCdsOrtho.c
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• src/hg/txCds/txCdsPick/txCdsPick.c
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• src/hg/txCds/txCdsPredict/txCdsPredict.c
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• src/hg/txCds/txCdsRaExceptions/txCdsRaExceptions.c
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• src/hg/txCds/txCdsRedoUniprotPicks/txCdsRedoUniprotPicks.c
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• src/hg/txCds/txCdsRefBestEvOnly/txCdsRefBestEvOnly.c
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• src/hg/txCds/txCdsRepick/txCdsRepick.c
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• src/hg/txCds/txCdsSuspect/txCdsSuspect.c
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• src/hg/txCds/txCdsSvmInput/txCdsSvmInput.c
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• src/hg/txCds/txCdsToGene/txCdsToGene.c
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• src/hg/txCds/txInfoAssemble/txInfoAssemble.c
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• src/hg/txGene/txGeneAccession/txGeneAccession.c
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• src/hg/txGene/txGeneAddOldUnmapped/txGeneAddOldUnmapped.c
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• src/hg/txGene/txGeneCdsMap/txGeneCdsMap.c
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• src/hg/txGene/txGeneXref/txGeneXref.c
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• src/hg/txGraph/txPslToBed/txPslToBed.c
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• src/hg/txGraph/txWalk/txWalk.c
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• src/hg/utils/coloredExonToBed/coloredExonToBed.c
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• src/hg/utils/findCutters/findCutters.c
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• src/hg/utils/gapToLift/gapToLift.c
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• src/hg/utils/geoMirrorNode/geoMirrorNode.c
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• src/hg/utils/gff3ToGenePred/gff3ToGenePred.c
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• src/hg/utils/liftUpBedFromTable/liftUpBedFromTable.c
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• src/hg/utils/lrgToPsl/lrgToPsl.c
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• src/hg/utils/randFrag/randFrag.c
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• src/hg/utils/trashLoad/trashLoad.c
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• src/hg/utils/wigAsciiAverageOverBed/wigAsciiAverageOverBed.c
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• src/hg/utils/wigBedToStep/wigBedToStep.c
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• src/hg/visiGene/gensat/gensatImageDownload/gensatImageDownload.c
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• src/lib/aliType.c
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• src/lib/annoAssembly.c
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• src/lib/annoRow.c
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• src/lib/basicBed.c
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• src/lib/bigBed.c
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• src/lib/boxLump.c
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• src/lib/bwgCreate.c
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• src/lib/bwgQuery.c
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• src/lib/bwgValsOnChrom.c
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• src/lib/chain.c
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• src/lib/chainBlock.c
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• src/lib/chainConnect.c
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• src/lib/chainToAxt.c
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• src/lib/chainToPsl.c
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• src/lib/cirTree.c
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• src/lib/colHash.c
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• src/lib/colHash.h
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• src/lib/correlate.c
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• src/lib/crTree.c
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• src/lib/dgRange.c
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• src/lib/dnaLoad.c
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• src/lib/dnaMarkov.c
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• src/lib/dnaMotif.c
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• src/lib/dtdParse.c
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• src/lib/dyOut.c
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• src/lib/elmTree.c
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• src/lib/emblParse.c
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• src/lib/errCatch.c
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• src/lib/ffScore.c
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• src/lib/fieldedTable.c
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• src/lib/filePath.c
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• src/lib/fixColor.c
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• src/lib/gapCalc.c
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• src/lib/genomeRangeTree.c
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    Adding NULL check to genomeRangeTreeFree.
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• src/lib/gfNet.c
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• src/lib/gff3.c
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• src/lib/hacTree.c
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• src/lib/hex.c
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• src/lib/histogram.c
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• src/lib/hmac.c
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• src/lib/hmmPfamParse.c
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• src/lib/htmlPage.c
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    When validating HTML, don't complain about HIDDEN inputs mixed withother input types e.g. CHECKBOX.
    fixes #13212
    
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• src/lib/https.c
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• src/lib/intValTree.c
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• src/lib/internet.c
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• src/lib/iupac.c
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• src/lib/jpegSize.c
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• src/lib/jsonParse.c
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• src/lib/jsonWrite.c
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• src/lib/knetUdc.c
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• src/lib/log.c
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• src/lib/longToList.c
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• src/lib/maf.c
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• src/lib/mafFromAxt.c
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• src/lib/mafScore.c
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• src/lib/mailViaPipe.c
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• src/lib/md5.c
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• src/lib/meta.c
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• src/lib/metaWig.c
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• src/lib/nibTwo.c
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• src/lib/numObscure.c
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• src/lib/obscure.c
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• src/lib/paraFetch.c
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• src/lib/peakCluster.c
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• src/lib/phyloTree.c
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• src/lib/pipeline.c
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• src/lib/psGfx.c
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• src/lib/psPoly.c
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• src/lib/pslGenoShow.c
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• src/lib/pslTbl.c
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• src/lib/pslTransMap.c
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• src/lib/pthreadWrap.c
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• src/lib/qa.c
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• src/lib/quotedP.c
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• src/lib/raToStruct.c
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• src/lib/rangeTree.c
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• src/lib/regexHelper.c
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• src/lib/repMask.c
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• src/lib/rnautil.c
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• src/lib/rqlEval.c
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• src/lib/rqlParse.c
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• src/lib/rudp.c
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• src/lib/scoreWindow.c
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• src/lib/seg.c
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• src/lib/seqStats.c
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• src/lib/spacedColumn.c
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• src/lib/spacedSeed.c
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• src/lib/synQueue.c
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• src/lib/tabRow.c
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• src/lib/tests/dyStringTester.c
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• src/lib/tests/errCatchTest.c
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• src/lib/tests/fetchUrlTest.c
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• src/lib/tests/gff3Tester.c
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• src/lib/tests/hacTreeTest.c
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• src/lib/tests/htmlExpandUrlTest.c
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• src/lib/tests/htmlMimeTest.c
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• src/lib/tests/htmlPageTest.c
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• src/lib/tests/mimeTester.c
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• src/lib/tests/miniBlat.c
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• src/lib/tests/pipelineTester.c
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• src/lib/tests/safeTester.c
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• src/lib/tests/tabixFetch.c
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• src/lib/tests/testBase64.c
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• src/lib/tests/testHash.c
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• src/lib/tests/testOutOfMem.c
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• src/lib/tests/testQuotedP.c
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• src/lib/tests/testQuotedString.c
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• src/lib/tests/udcTest.c
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• src/lib/tests/vcfParseTest.c
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• src/lib/textOut.c
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• src/lib/tokenizer.c
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• src/lib/trix.c
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• src/lib/twoBit.c
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• src/lib/udc.c
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• src/lib/vGfx.c
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• src/lib/vGfxPrivate.h
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• src/lib/vGif.c
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• src/lib/vPng.c
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• src/lib/vcf.c
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• src/lib/vcfBits.c
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• src/lib/verbose.c
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• src/lib/xmlEscape.c
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/lib/zlibFace.c
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• src/utils/aNotB/aNotB.c
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• src/utils/analyzeCpG/analyzeCpG.c
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    more or less final methylateGenome, and added a new tool analyzeCpG which currently clusters CpG regions in a bed file
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• src/utils/analyzeCpG/makefile
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    more or less final methylateGenome, and added a new tool analyzeCpG which currently clusters CpG regions in a bed file
• src/utils/asCompare/asCompare.c
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• src/utils/bamToFastq/bamToFastq.c
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    converts a bam file to a fastq filesome illumina header data is lost
    
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    Modified comments, camel cased variables
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• src/utils/bbTest/bbTest.c
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• src/utils/bdfToGem/bdfToGem.c
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• src/utils/bedClip/bedClip.c
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• src/utils/bedCommonRegions/bedCommonRegions.c
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• src/utils/bedGeneParts/bedGeneParts.c
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• src/utils/bedGraphPack/bedGraphPack.c
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• src/utils/bedGraphToBigWig/bedGraphToBigWig.c
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• src/utils/bedPileUps/bedPileUps.c
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• src/utils/bedRemoveOverlap/bedRemoveOverlap.c
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• src/utils/bedRestrictToPositions/bedRestrictToPositions.c
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• src/utils/bedScore/bedScore.c
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• src/utils/bedToBigBed/bedToBigBed.c
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• src/utils/bedToClosestPoint/bedToClosestPoint.c
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• src/utils/bestThreshold/bestThreshold.c
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• src/utils/bigBedInfo/bigBedInfo.c
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• src/utils/bigBedNamedItems/bigBedNamedItems.c
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• src/utils/bigBedSummary/bigBedSummary.c
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• src/utils/bigBedToBed/bigBedToBed.c
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• src/utils/bigWigAverageOverBed/bigWigAverageOverBed.c
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• src/utils/bigWigCat/bigWigCat.c
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• src/utils/bigWigCorrelate/bigWigCorrelate.c
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• src/utils/bigWigInfo/bigWigInfo.c
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• src/utils/bigWigMerge/bigWigMerge.c
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• src/utils/bigWigSummary/bigWigSummary.c
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• src/utils/bigWigToBedGraph/bigWigToBedGraph.c
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• src/utils/bigWigToWig/bigWigToWig.c
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• src/utils/cCp/cCp.c
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• src/utils/callGraph/callGraph.c
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• src/utils/catUncomment/catUncomment.c
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• src/utils/ccCp/ccCp.c
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• src/utils/ccCpLock/ccCp.3.c
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• src/utils/ccCpLock/ccCp.c
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• src/utils/ccCpLock/ccCp_rsh.c
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• src/utils/chainDist/chainDist.c
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• src/utils/chopFaLines/chopFaLines.c
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• src/utils/colTransform/colTransform.c
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• src/utils/colorConv/colorConv.c
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• src/utils/combineFiles/combineFiles.c
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• src/utils/convolve/convolve.c
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• src/utils/correlate/correlate.c
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• src/utils/countChars/countChars.c
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• src/utils/cpgIslandExt/cpg.c
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• src/utils/cpgIslandExt/cpg_lh.c
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• src/utils/cpgIslandExt/readseq.h
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• src/utils/detab/detab.c
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• src/utils/dnsInfo/dnsInfo.c
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• src/utils/endsInLf/endsInLf.c
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• src/utils/est2genomeToPsl/est2genomeToPsl.c
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• src/utils/faFlyBaseToUcsc/faFlyBaseToUcsc.c
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• src/utils/faGapLocs/faGapLocs.c
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• src/utils/faGapSizes/faGapSizes.c
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• src/utils/faLowerToN/faLowerToN.c
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• src/utils/faNcbiToUcsc/faNcbiToUcsc.c
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• src/utils/faPolyASizes/faPolyASizes.c
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• src/utils/faRenameRecords/faRenameRecords.c
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• src/utils/faSimplify/faSimplify.c
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• src/utils/faToFastq/faToFastq.c
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• src/utils/faToNib/faToNib.c
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• src/utils/faToTab/faToTab.c
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• src/utils/faToTwoBit/faToTwoBit.c
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• src/utils/faTrans/faTrans.c
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• src/utils/faTrimPolyA/faTrimPolyA.c
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• src/utils/faTrimRead/faTrimRead.c
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• src/utils/faUniqify/faUniqify.c
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    Adding 'addId' to this utility that handles fa files with the same name for multiple records. Needed for sponge.
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• src/utils/fastaToPsl/fastaToPsl.c
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• src/utils/fastqMottTrim/fastqMottTrim.c
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    initial commit for mott trimming
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    updated comments changed a < to <=
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    Modified comments, camel cased variables
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/utils/fastqMottTrim/makefile
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    initial commit for mott trimming
• src/utils/fastqStatsAndSubsample/fastqStatsAndSubsample.c
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• src/utils/fastqToFa/fastqToFa.c
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• src/utils/fileExists/fileExists.c
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• src/utils/findMotif/findMotif.c
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• src/utils/gapSplit/gapSplit.c
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• src/utils/genFedTableDef/genFedTableDef.c
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• src/utils/geneStarts/geneStarts.c
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• src/utils/gffPeek/gffPeek.c
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• src/utils/greedyPack/greedyPack.c
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• src/utils/headRest/headRest.c
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• src/utils/htmlCheck/htmlCheck.c
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• src/utils/htmlPics/htmlPics.c
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• src/utils/lineFileSplit/lineFileSplit.c
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• src/utils/lineRange/lineRange.c
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• src/utils/linesInAllFiles/linesInAllFiles.c
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• src/utils/makeRgbRainbow/makeRgbRainbow.c
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• src/utils/maxEachRow/maxEachRow.c
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• src/utils/methylateGenome/methylateGenome.c
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    more or less final methylateGenome, and added a new tool analyzeCpG which currently clusters CpG regions in a bed file
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    Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
• src/utils/minEachRow/minEachRow.c
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• src/utils/newProg/newProg.c
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• src/utils/nibCheck/nibCheck.c
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• src/utils/nibFrag/nibFrag.c
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• src/utils/nibSize/nibSize.c
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• src/utils/nt4Frag/nt4Frag.c
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• src/utils/paraFetch/paraFetch.c
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• src/utils/paraSync/paraSync.c
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• src/utils/plotDataMatrix/plotDataMatrix.c
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• src/utils/pslLiftSubrangeBlat/pslLiftSubrangeBlat.c
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• src/utils/pslPosTarget/pslPosTarget.c
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• src/utils/pslToPslx/pslToPslx.c
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• src/utils/pslToXa/pslToXa.c
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• src/utils/qa/bamToBedGraph.csh
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    made utils to convert BAM files to bedGraph and bigWig, using kent tools and bedTools
• src/utils/qa/bamToBigWig.csh
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    made utils to convert BAM files to bedGraph and bigWig, using kent tools and bedTools
• src/utils/qa/makefile
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    made utils to convert BAM files to bedGraph and bigWig, using kent tools and bedTools
• src/utils/qa/weeklybld/buildEnv.csh
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    v301 preview1
• src/utils/raFromTab/raFromTab.c
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• src/utils/raMerge/raMerge.c
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• src/utils/raSqlQuery/raRecord.c
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• src/utils/raSqlQuery/raRecord.h
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• src/utils/raSqlQuery/raSqlQuery.c
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• src/utils/raToLines/linesToRa/linesToRa.c
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• src/utils/raToLines/raToLines/raToLines.c
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• src/utils/raToStructGen/raToStructGen.c
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• src/utils/raToStructGen/testOut/testRaToStruct.c
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• src/utils/raToSvmLight/raToSvmLight.c
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• src/utils/raToTab/raToTab.c
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• src/utils/replaceTextBetween/replaceTextBetween.c
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• src/utils/reverseLineOrder/reverseLineOrder.c
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• src/utils/rmFaDups/rmFaDups.c
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• src/utils/rowsToCols/rowsToCols.c
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• src/utils/sampleIndexes/sampleIndexes.c
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• src/utils/scaffoldFaToAgp/scaffoldFaToAgp.c
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• src/utils/scrambleFa/scrambleFa.c
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• src/utils/sets/sets.c
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• src/utils/shuffleLines/shuffleLines.c
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• src/utils/sizeof/sizeof.c
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• src/utils/sortFa/sortFa.c
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• src/utils/spacedToTab/spacedToTab.c
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• src/utils/splitFileByColumn/splitFileByColumn.c
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    fixed a couple of bugs in splitFileByColumn #13297
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• src/utils/subChar/subChar.c
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• src/utils/subColumn/subColumn.c
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• src/utils/tTestTwo/tTestTwo.c
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• src/utils/tableSum/tableSum.c
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• src/utils/tailLines/tailLines.c
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• src/utils/textBetween/textBetween.c
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• src/utils/textHist2/textHist2.c
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• src/utils/textHistogram/textHistogram.c
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• src/utils/tickToDate/tickToDate.c
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• src/utils/timing/gmtime.c
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• src/utils/timing/gmtime/gmtime.c
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• src/utils/timing/localtime.c
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• src/utils/timing/localtime/localtime.c
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• src/utils/timing/mktime.c
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• src/utils/timing/mktime/mktime.c
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• src/utils/toLower/toLower.c
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• src/utils/twoBitDup/twoBitDup.c
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• src/utils/twoBitInfo/twoBitInfo.c
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• src/utils/twoBitToFa/twoBitToFa.c
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• src/utils/udcCleanup/udcCleanup.c
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• src/utils/undupFa/undupFa.c
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• src/utils/venn/venn.c
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• src/utils/vennIds/vennIds.c
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• src/utils/verticalSplitSqlTable/verticalSplitSqlTable.c
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• src/utils/vulgarToPsl/vulgarToPsl.c
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• src/utils/wgetMd5/wgetMd5.c
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• src/utils/wigAsciiCrunch/wigAsciiCrunch.c
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• src/utils/wigAsciiToBinary/wigAsciiToBinary.c
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• src/utils/wigAsciiToBinary/wigBedToBinary.c
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• src/utils/wigAsciiToBinary/wigZoom.c
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• src/utils/wigCorrelate/wigCorrelate.c
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• src/utils/wigSetSpanOrStep/wigSetSpanOrStep.c
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• src/utils/wigSort/wigSort.c
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• src/utils/wigTestMaker/wigTestMaker.c
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• src/utils/wigToBed/wigToBed.c
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• src/utils/wigToBedGraph/wigToBedGraph.c
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• src/utils/wigToBigWig/wigToBigWig.c
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• src/utils/wordsInEachLine/wordsInEachLine.c
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