Commits for braney
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v421_base to v422_preview (2021-09-27 to 2021-10-04) v422
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b30a73b6c5f4aaf404e7b670c0142178b64b6424 Mon Sep 27 17:37:11 2021 -0700
- temporarily remove hg/lib/tests annogratorTest while we consider whether
we're upgrading hg19 knownGene
- src/hg/lib/tests/makefile - lines changed 5, context: html, text, full: html, text
9e4f853136d19ceac7d84170975171e99b7c1552 Tue Sep 28 17:20:40 2021 -0700
- knownGene ids on hg19 have an underbar in them
- src/hg/makeDb/trackDb/human/hg19/knownGene.alpha.ra - lines changed 1, context: html, text, full: html, text
433b7eeaefb4afcb2f61ba4e33311193c63201cc Tue Sep 28 17:21:45 2021 -0700
- hg19 is changing ids to be ENST*
- src/hg/makeDb/schema/all.joiner - lines changed 2, context: html, text, full: html, text
bb2f28c1bff73bfc4732e1298af0b9443079f495 Thu Sep 30 17:02:25 2021 -0700
- making sure each version of knownGene that will appear in a future
archive has its own html
- src/hg/makeDb/trackDb/human/hg19/knownGene.alpha.ra - lines changed 2, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg19/knownGeneV38lift37.html - lines changed 142, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/knownGene.alpha.ra - lines changed 1, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/knownGene.ra - lines changed 1, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/knownGeneV36.html - lines changed 142, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/knownGeneV38.html - lines changed 142, context: html, text, full: html, text
533112afe2a2005e80cdb1f82904ea65032d4302 Sat Oct 2 11:37:34 2021 -0700
- split hg/lib into two separate libaries, one only used by the cgis
- src/hg/cgilib/affy10KDetails.c - lines changed 204, context: html, text, full: html, text
- src/hg/cgilib/affy120KDetails.c - lines changed 587, context: html, text, full: html, text
- src/hg/cgilib/ancientRref.c - lines changed 137, context: html, text, full: html, text
- src/hg/cgilib/annoFormatVep.c - lines changed 1625, context: html, text, full: html, text
- src/hg/cgilib/annoGrateWigDb.c - lines changed 17, context: html, text, full: html, text
- src/hg/cgilib/annoGratorGpVar.c - lines changed 861, context: html, text, full: html, text
- src/hg/cgilib/annoStreamDb.c - lines changed 1342, context: html, text, full: html, text
- src/hg/cgilib/annoStreamDbFactorSource.c - lines changed 213, context: html, text, full: html, text
- src/hg/cgilib/annoStreamDbPslPlus.c - lines changed 256, context: html, text, full: html, text
- src/hg/cgilib/annoStreamWig.c - lines changed 156, context: html, text, full: html, text
- src/hg/cgilib/atomDb.c - lines changed 172, context: html, text, full: html, text
- src/hg/cgilib/axtLib.c - lines changed 192, context: html, text, full: html, text
- src/hg/cgilib/bactigPos.c - lines changed 133, context: html, text, full: html, text
- src/hg/cgilib/barChartData.c - lines changed 174, context: html, text, full: html, text
- src/hg/cgilib/barChartSample.c - lines changed 162, context: html, text, full: html, text
- src/hg/cgilib/bdgpExprLink.c - lines changed 171, context: html, text, full: html, text
- src/hg/cgilib/bdgpGeneInfo.c - lines changed 158, context: html, text, full: html, text
- src/hg/cgilib/bed12Source.c - lines changed 214, context: html, text, full: html, text
- src/hg/cgilib/bed5FloatScore.c - lines changed 146, context: html, text, full: html, text
- src/hg/cgilib/bed6FloatScore.c - lines changed 148, context: html, text, full: html, text
- src/hg/cgilib/bed8Attrs.c - lines changed 213, context: html, text, full: html, text
- src/hg/cgilib/bedCart.c - lines changed 37, context: html, text, full: html, text
- src/hg/cgilib/bgiGeneInfo.c - lines changed 141, context: html, text, full: html, text
- src/hg/cgilib/bgiGeneSnp.c - lines changed 156, context: html, text, full: html, text
- src/hg/cgilib/bgiSnp.c - lines changed 236, context: html, text, full: html, text
- src/hg/cgilib/bigTransMap.c - lines changed 384, context: html, text, full: html, text
- src/hg/cgilib/borkPseudoHom.c - lines changed 139, context: html, text, full: html, text
- src/hg/cgilib/cartEdit0.c - lines changed 120, context: html, text, full: html, text
- src/hg/cgilib/cartEdit1.c - lines changed 39, context: html, text, full: html, text
- src/hg/cgilib/cartJson.c - lines changed 898, context: html, text, full: html, text
- src/hg/cgilib/cartRewrite.c - lines changed 75, context: html, text, full: html, text
- src/hg/cgilib/cartTrackDb.c - lines changed 447, context: html, text, full: html, text
- src/hg/cgilib/ccdsGeneMap.c - lines changed 270, context: html, text, full: html, text
- src/hg/cgilib/ccdsInfo.c - lines changed 297, context: html, text, full: html, text
- src/hg/cgilib/ccdsNotes.c - lines changed 150, context: html, text, full: html, text
- src/hg/cgilib/cdsSpec.c - lines changed 126, context: html, text, full: html, text
- src/hg/cgilib/celeraCoverage.c - lines changed 141, context: html, text, full: html, text
- src/hg/cgilib/celeraDupPositive.c - lines changed 112, context: html, text, full: html, text
- src/hg/cgilib/chicken13kInfo.c - lines changed 242, context: html, text, full: html, text
- src/hg/cgilib/chr18deletions.c - lines changed 235, context: html, text, full: html, text
- src/hg/cgilib/cnpIafrate.c - lines changed 149, context: html, text, full: html, text
- src/hg/cgilib/cnpIafrate2.c - lines changed 169, context: html, text, full: html, text
- src/hg/cgilib/cnpLocke.c - lines changed 144, context: html, text, full: html, text
- src/hg/cgilib/cnpSebat.c - lines changed 183, context: html, text, full: html, text
- src/hg/cgilib/cnpSebat2.c - lines changed 141, context: html, text, full: html, text
- src/hg/cgilib/cnpSharp.c - lines changed 195, context: html, text, full: html, text
- src/hg/cgilib/cnpSharp2.c - lines changed 144, context: html, text, full: html, text
- src/hg/cgilib/codeBlast.c - lines changed 161, context: html, text, full: html, text
- src/hg/cgilib/contigAcc.c - lines changed 126, context: html, text, full: html, text
- src/hg/cgilib/cpgIslandExt.c - lines changed 166, context: html, text, full: html, text
- src/hg/cgilib/ctgPos2.c - lines changed 148, context: html, text, full: html, text
- src/hg/cgilib/cutter.c - lines changed 791, context: html, text, full: html, text
- src/hg/cgilib/dbRIP.c - lines changed 304, context: html, text, full: html, text
- src/hg/cgilib/dbSnpDetails.c - lines changed 346, context: html, text, full: html, text
- src/hg/cgilib/dbSnpRs.c - lines changed 213, context: html, text, full: html, text
- src/hg/cgilib/delConrad2.c - lines changed 184, context: html, text, full: html, text
- src/hg/cgilib/delHinds2.c - lines changed 141, context: html, text, full: html, text
- src/hg/cgilib/dgvPlus.c - lines changed 258, context: html, text, full: html, text
- src/hg/cgilib/dless.c - lines changed 243, context: html, text, full: html, text
- src/hg/cgilib/dnaProbe.c - lines changed 209, context: html, text, full: html, text
- src/hg/cgilib/dvBed.c - lines changed 136, context: html, text, full: html, text
- src/hg/cgilib/dvXref2.c - lines changed 134, context: html, text, full: html, text
- src/hg/cgilib/ensFace.c - lines changed 152, context: html, text, full: html, text
- src/hg/cgilib/ensInfo.c - lines changed 158, context: html, text, full: html, text
- src/hg/cgilib/ensPhusionBlast.c - lines changed 163, context: html, text, full: html, text
- src/hg/cgilib/factorSource.c - lines changed 222, context: html, text, full: html, text
- src/hg/cgilib/fbTables.c - lines changed 934, context: html, text, full: html, text
- src/hg/cgilib/fileUi.c - lines changed 1201, context: html, text, full: html, text
- src/hg/cgilib/fishClones.c - lines changed 278, context: html, text, full: html, text
- src/hg/cgilib/flyBase2004Xref.c - lines changed 174, context: html, text, full: html, text
- src/hg/cgilib/flyBaseSwissProt.c - lines changed 142, context: html, text, full: html, text
- src/hg/cgilib/flyreg.c - lines changed 149, context: html, text, full: html, text
- src/hg/cgilib/flyreg2.c - lines changed 154, context: html, text, full: html, text
- src/hg/cgilib/gbMiscDiff.c - lines changed 151, context: html, text, full: html, text
- src/hg/cgilib/gbProtAnn.c - lines changed 147, context: html, text, full: html, text
- src/hg/cgilib/gbWarn.c - lines changed 128, context: html, text, full: html, text
- src/hg/cgilib/genMapDb.c - lines changed 221, context: html, text, full: html, text
- src/hg/cgilib/gencodeAnnotationRemark.c - lines changed 126, context: html, text, full: html, text
- src/hg/cgilib/gencodeExonSupport.c - lines changed 160, context: html, text, full: html, text
- src/hg/cgilib/gencodeGeneSource.c - lines changed 126, context: html, text, full: html, text
- src/hg/cgilib/gencodeIntron.c - lines changed 226, context: html, text, full: html, text
- src/hg/cgilib/gencodeTag.c - lines changed 126, context: html, text, full: html, text
- src/hg/cgilib/gencodeToEntrezGene.c - lines changed 123, context: html, text, full: html, text
- src/hg/cgilib/gencodeToPdb.c - lines changed 126, context: html, text, full: html, text
- src/hg/cgilib/gencodeToPubMed.c - lines changed 123, context: html, text, full: html, text
- src/hg/cgilib/gencodeToUniProt.c - lines changed 145, context: html, text, full: html, text
- src/hg/cgilib/gencodeTranscriptSource.c - lines changed 126, context: html, text, full: html, text
- src/hg/cgilib/gencodeTranscriptSupport.c - lines changed 134, context: html, text, full: html, text
- src/hg/cgilib/gencodeTranscriptionSupportLevel.c - lines changed 126, context: html, text, full: html, text
- src/hg/cgilib/geneSimilarities.c - lines changed 213, context: html, text, full: html, text
- src/hg/cgilib/genoLay.c - lines changed 564, context: html, text, full: html, text
- src/hg/cgilib/genomicDups.c - lines changed 151, context: html, text, full: html, text
- src/hg/cgilib/genomicSuperDups.c - lines changed 286, context: html, text, full: html, text
- src/hg/cgilib/growthCondition.c - lines changed 134, context: html, text, full: html, text
- src/hg/cgilib/gtexBoxplot.c - lines changed 161, context: html, text, full: html, text
- src/hg/cgilib/gtexEqtlCluster.c - lines changed 327, context: html, text, full: html, text
- src/hg/cgilib/gwasCatalog.c - lines changed 280, context: html, text, full: html, text
- src/hg/cgilib/hAnno.c - lines changed 434, context: html, text, full: html, text
- src/hg/cgilib/hCytoBand.c - lines changed 170, context: html, text, full: html, text
- src/hg/cgilib/haplotypes.c - lines changed 3644, context: html, text, full: html, text
- src/hg/cgilib/hapmapAllelesSummary.c - lines changed 282, context: html, text, full: html, text
- src/hg/cgilib/hashJoin.c - lines changed 312, context: html, text, full: html, text
- src/hg/cgilib/hgBam.c - lines changed 247, context: html, text, full: html, text
- src/hg/cgilib/hgExp.c - lines changed 328, context: html, text, full: html, text
- src/hg/cgilib/hgSeq.c - lines changed 811, context: html, text, full: html, text
- src/hg/cgilib/hgdpGeo.c - lines changed 173, context: html, text, full: html, text
- src/hg/cgilib/hubPublic.c - lines changed 259, context: html, text, full: html, text
- src/hg/cgilib/humanParalog.c - lines changed 164, context: html, text, full: html, text
- src/hg/cgilib/hvGfx.c - lines changed 301, context: html, text, full: html, text
- src/hg/cgilib/isochores.c - lines changed 101, context: html, text, full: html, text
- src/hg/cgilib/itemConf.c - lines changed 128, context: html, text, full: html, text
- src/hg/cgilib/itemDetailsHtml.c - lines changed 126, context: html, text, full: html, text
- src/hg/cgilib/jaxOrtholog.c - lines changed 171, context: html, text, full: html, text
- src/hg/cgilib/jaxQTL.c - lines changed 182, context: html, text, full: html, text
- src/hg/cgilib/jaxQTL3.c - lines changed 203, context: html, text, full: html, text
- src/hg/cgilib/joinMixer.c - lines changed 363, context: html, text, full: html, text
- src/hg/cgilib/kg1ToKg2.c - lines changed 160, context: html, text, full: html, text
- src/hg/cgilib/lsSnpPdbChimera.c - lines changed 185, context: html, text, full: html, text
- src/hg/cgilib/makefile - lines changed 59, context: html, text, full: html, text
- src/hg/cgilib/mammalPsg.c - lines changed 295, context: html, text, full: html, text
- src/hg/cgilib/mapSts.c - lines changed 135, context: html, text, full: html, text
- src/hg/cgilib/mathWig.c - lines changed 268, context: html, text, full: html, text
- src/hg/cgilib/mcnBreakpoints.c - lines changed 168, context: html, text, full: html, text
- src/hg/cgilib/mouseOrtho.c - lines changed 164, context: html, text, full: html, text
- src/hg/cgilib/mouseSyn.c - lines changed 101, context: html, text, full: html, text
- src/hg/cgilib/mouseSynWhd.c - lines changed 171, context: html, text, full: html, text
- src/hg/cgilib/ncRna.c - lines changed 179, context: html, text, full: html, text
- src/hg/cgilib/ncbiRefSeqLink.c - lines changed 262, context: html, text, full: html, text
- src/hg/cgilib/nonCodingUi.c - lines changed 67, context: html, text, full: html, text
- src/hg/cgilib/omicia.c - lines changed 690, context: html, text, full: html, text
- src/hg/cgilib/omimTitle.c - lines changed 138, context: html, text, full: html, text
- src/hg/cgilib/oreganno.c - lines changed 531, context: html, text, full: html, text
- src/hg/cgilib/oregannoUi.c - lines changed 62, context: html, text, full: html, text
- src/hg/cgilib/pcrResult.c - lines changed 214, context: html, text, full: html, text
- src/hg/cgilib/peptideAtlasPeptide.c - lines changed 141, context: html, text, full: html, text
- src/hg/cgilib/pgPolyphenPred.c - lines changed 222, context: html, text, full: html, text
- src/hg/cgilib/pgSiftPred.c - lines changed 261, context: html, text, full: html, text
- src/hg/cgilib/polyGenotype.c - lines changed 193, context: html, text, full: html, text
- src/hg/cgilib/protVar.c - lines changed 695, context: html, text, full: html, text
- src/hg/cgilib/protobuf.c - lines changed 324, context: html, text, full: html, text
- src/hg/cgilib/pscreen.c - lines changed 176, context: html, text, full: html, text
- src/hg/cgilib/pseudoGeneLink.c - lines changed 405, context: html, text, full: html, text
- src/hg/cgilib/pslWScore.c - lines changed 226, context: html, text, full: html, text
- src/hg/cgilib/putaInfo.c - lines changed 347, context: html, text, full: html, text
- src/hg/cgilib/recombRate.c - lines changed 186, context: html, text, full: html, text
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- src/hg/cgilib/recombRateRat.c - lines changed 146, context: html, text, full: html, text
- src/hg/cgilib/rhMapZfishInfo.c - lines changed 184, context: html, text, full: html, text
- src/hg/cgilib/rmskAlign.c - lines changed 212, context: html, text, full: html, text
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- src/hg/cgilib/roughAli.c - lines changed 137, context: html, text, full: html, text
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- src/hg/cgilib/search.c - lines changed 356, context: html, text, full: html, text
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- src/hg/cgilib/sgdDescription.c - lines changed 134, context: html, text, full: html, text
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- src/hg/cgilib/simpleRepeat.c - lines changed 204, context: html, text, full: html, text
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cbae92acc5a892119e74986a827ffb3b459ab987 Sat Oct 2 12:20:30 2021 -0700
- some clean up of the library split to handle hubPublic having a new
function that the utilities use
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- src/hg/lib/hubPublic.c - lines changed 275, context: html, text, full: html, text
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