All File Changes
v284_base to v285_preview (2013-05-27 to 2013-06-04) v285
- src/CHANGES
- lines changed 32, context: html, text, full: html, text
Removing old out of date change doc file.
- src/hg/affyTransciptome/nmerParasolGenome.c
- src/hg/altSplice/affySplice/probeMatcher.c
- src/hg/altSplice/affySplice/spliceProbeVis.c
- src/hg/altSplice/altSplice/altSplice.c
- src/hg/altSplice/altSplice/orthoSplice.c
- src/hg/altSplice/altSplice/spliceStats.c
- src/hg/altSplice/axtCountBeds/axtCountBeds.c
- src/hg/altSplice/exonWalk/exonWalk.c
- src/hg/altSplice/inc/mouseAPSetEventMap.h
- src/hg/altSplice/lib/mouseAPSetEventMap.c
- src/hg/altSplice/spliceWalk/spliceWalk.c
- src/hg/autoSql/autoSql.c
- src/hg/autoSql/tests/dbLinkTest.c
- src/hg/autoSql/tests/expected/newTest.c
- src/hg/autoSql/tests/expected/newTest.err
- src/hg/autoSql/tests/expected/newTest.h
- src/hg/autoSql/tests/testSymCols.c
- src/hg/bedItemOverlapCount/bedItemOverlapCount.c
- src/hg/bioImage/bioImageLoad/bioImageLoad.c
- src/hg/bioImage/knownToBioImage/knownToBioImage.c
- src/hg/cgiExample/cgiExample.c
- src/hg/checkHgFindSpec/checkHgFindSpec.c
- src/hg/checkTableCoords/checkTableCoords.c
- src/hg/checkTableCoords/tests/expected/bed12CTCBad.out
- src/hg/checkTableCoords/tests/expected/bed3CTCBad.out
- src/hg/checkTableCoords/tests/expected/bed4CTCBad.out
- src/hg/checkTableCoords/tests/expected/bed8CTCBad.out
- src/hg/checkTableCoords/tests/expected/genePredCTCBad.out
- src/hg/checkTableCoords/tests/expected/pslCTCBad.out
- src/hg/checkTableCoords/tests/makefile
- src/hg/das/das.c
- src/hg/dbTrash/dbTrash.c
- src/hg/dnaGene/dnaGene.c
- src/hg/encode/docId/docIdReport/docIdReport.c
- src/hg/encode/docId/docIdTidy/docIdTidy.c
- src/hg/encode/docId/docIdView/docIdView.c
- src/hg/encode/docId/lib/docIdSub.c
- src/hg/encode/encodeExp/encodeExp.c
- src/hg/encode/encodeRenameObj/encodeRenameObj.c
- src/hg/encode/hgEncodeApi/hgEncodeApi.c
- src/hg/encode/hgEncodeScheduler/hgEncodeScheduler.c
- src/hg/encode/metaCheck/metaCheck.c
- src/hg/encode/metaRename/metaRename.c
- src/hg/encode/regionOrtho/regionOrtho.c
- src/hg/encode3/encodeDataWarehouse/edwAddAssembly/edwAddAssembly.c
- src/hg/encode3/encodeDataWarehouse/edwAddQaEnrichTarget/edwAddQaEnrichTarget.c
- src/hg/encode3/encodeDataWarehouse/edwAddSubscriber/edwAddSubscriber.c
- src/hg/encode3/encodeDataWarehouse/edwChangeFormat/edwChangeFormat.c
- lines changed 8, context: html, text, full: html, text
Making this utility work on other tags too with a command line option.
- src/hg/encode3/encodeDataWarehouse/edwMakeEnrichments/edwMakeEnrichments.c
- src/hg/encode3/encodeDataWarehouse/edwMakeReplicateQa/edwMakeReplicateQa.c
- src/hg/encode3/encodeDataWarehouse/edwMakeValidFile/edwMakeValidFile.c
- src/hg/encode3/encodeDataWarehouse/edwReallyRemoveFiles/edwReallyRemoveFiles.c
- src/hg/encode3/encodeDataWarehouse/edwRunDaemon/edwRunDaemon.c
- src/hg/encode3/encodeDataWarehouse/edwScriptSubmit/edwScriptSubmit.c
- src/hg/encode3/encodeDataWarehouse/edwSubmit/edwSubmit.c
- src/hg/encode3/encodeDataWarehouse/edwWebBrowse/edwWebBrowse.c
- src/hg/encode3/encodeDataWarehouse/edwWebRegisterScript/edwWebRegisterScript.c
- src/hg/encode3/encodeDataWarehouse/edwWebSubmit/edwWebSubmit.c
- src/hg/encode3/encodeDataWarehouse/inc/encodeDataWarehouse.h
- src/hg/encode3/encodeDataWarehouse/lib/edwLib.c
- src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.c
- src/hg/encode3/encodeDataWarehouse/lib/resetEdw
- lines changed 1, context: html, text, full: html, text
Adding Brian Lee to users.
- src/hg/encode3/importEncode2/encode2ExpDumpFlat/encode2ExpDumpFlat.c
- src/hg/encode3/importEncode2/encode2Meta/encode2Meta.c
- src/hg/encode3/importEncode2/encodeExpToCvDb/encodeExpToCvDb.c
- src/hg/estOrient/estOrient.c
- src/hg/featureBits/featureBits.c
- src/hg/fishClones/fishClones.c
- src/hg/geneBounds/assessLibs/assessLibs.c
- src/hg/geneBounds/axtForEst/axtForEst.c
- src/hg/geneBounds/bedCons/bedCons.c
- src/hg/geneBounds/clusterGenes/clusterGenes.c
- src/hg/geneBounds/clusterRna/clusterRna.c
- src/hg/geneBounds/eisenInput/eisenInput.c
- src/hg/geneBounds/estLibStats/estLibStats.c
- src/hg/geneBounds/lib/improbRunInfo.c
- src/hg/geneBounds/promoSeqFromCluster/promoSeqFromCluster.c
- src/hg/getFeatDna/getFeatDna.c
- src/hg/getRna/getRna.c
- src/hg/getRnaPred/getRnaPred.c
- src/hg/getallpep/getallpep.c
- src/hg/gigAssembler/checkDbSync/checkDbSync.c
- src/hg/gisaid/gisaidSample/demog.c
- src/hg/gisaid/gisaidSample/gisaidSample.c
- src/hg/gisaid/gisaidSample/sequence.c
- src/hg/gisaid/gisaidSubj/demog.c
- src/hg/gisaid/gisaidSubj/gisaidSubj.c
- src/hg/gisaid/gisaidSubj/sequence.c
- src/hg/gisaid/gisaidTable/getSeq.c
- src/hg/gisaid/gisaidTable/gisaidSubjInfo.c
- src/hg/gisaid/gisaidTable/gisaidTable.c
- src/hg/gpToGtf/gpToGtf.c
- src/hg/gsid/gsIdXref/gsIdXref.c
- src/hg/gsid/gsidAaMsa/gsidAaMsa.c
- src/hg/gsid/gsidGetConsensus/gsidGetConsensus.c
- src/hg/gsid/gsidMember/gsidMember.c
- src/hg/gsid/gsidMsa/gsidMsa.c
- src/hg/gsid/gsidMsaToTab/gsidMsaToTab.c
- src/hg/gsid/gsidPosSelect/gsidPosSelect.c
- src/hg/gsid/gsidSubj/clinical.c
- src/hg/gsid/gsidSubj/demog.c
- src/hg/gsid/gsidSubj/gsidSubj.c
- src/hg/gsid/gsidSubj/sequence.c
- src/hg/gsid/gsidSubj/vaccine.c
- src/hg/gsid/gsidSubj3/clinical.c
- src/hg/gsid/gsidSubj3/demog.c
- src/hg/gsid/gsidSubj3/gsidSubj3.c
- src/hg/gsid/gsidSubj3/sequence.c
- src/hg/gsid/gsidSubj3/vaccine.c
- src/hg/gsid/gsidTable/getSeq.c
- src/hg/gsid/gsidTable/gsidSubjInfo.c
- src/hg/gsid/gsidTable/gsidTable.c
- src/hg/gsid/pbGsid/pbGsid.c
- src/hg/gsid/pwdtest/members.h
- src/hg/hgApi/hgApi.c
- src/hg/hgBlat/hgBlat.c
- src/hg/hgBlatTest/hgBlatTest.c
- src/hg/hgCoordConv/hgCoordConv.c
- src/hg/hgGateway/hgGateway.c
- src/hg/hgGene/altSplice.c
- src/hg/hgGene/ctd.c
- src/hg/hgGene/dnaBindMotif.c
- src/hg/hgGene/domains.c
- src/hg/hgGene/flyBaseInfo.c
- src/hg/hgGene/gad.c
- src/hg/hgGene/geneReviews.c
- src/hg/hgGene/go.c
- src/hg/hgGene/hgGene.c
- src/hg/hgGene/info.c
- src/hg/hgGene/links.c
- src/hg/hgGene/localization.c
- src/hg/hgGene/microarray.c
- src/hg/hgGene/mrnaDescriptions.c
- src/hg/hgGene/otherOrgs.c
- src/hg/hgGene/pathways.c
- src/hg/hgGene/pseudoGene.c
- src/hg/hgGene/rgdInfo.c
- src/hg/hgGene/rnaStructure.c
- src/hg/hgGene/sequence.c
- src/hg/hgGene/swissProtComments.c
- src/hg/hgGene/synonym.c
- src/hg/hgGene/wikiTrack.c
- src/hg/hgGeneBands/hgGeneBands.c
- src/hg/hgGeneList/hgGeneList.c
- src/hg/hgGeneRing/hgGeneRing.c
- src/hg/hgGeneRing/interaction.c
- src/hg/hgGeneRing/interaction.h
- src/hg/hgGenome/bedList.c
- src/hg/hgGenome/custom.c
- src/hg/hgGenome/hgGenome.c
- src/hg/hgGenome/import.c
- src/hg/hgGenome/sortGenes.c
- src/hg/hgGetAnn/hgGetAnn.c
- src/hg/hgHubConnect/hgHubConnect.c
- src/hg/hgKnownGeneList/hgKnownGeneList.c
- src/hg/hgLogin/gbMembers.c
- src/hg/hgLogin/gbMembers.h
- src/hg/hgLogin/hgLogin.c
- src/hg/hgPcr/hgPcr.c
- src/hg/hgSelect/hgSelect.c
- src/hg/hgSession/hgSession.c
- src/hg/hgSpeciesRna/hgSpeciesRna.c
- src/hg/hgSuggest/hgSuggest.c
- src/hg/hgTables/correlate.c
- src/hg/hgTables/custom.c
- src/hg/hgTables/filterFields.c
- src/hg/hgTables/hgTables.c
- src/hg/hgTables/identifiers.c
- src/hg/hgTables/mainPage.c
- src/hg/hgTables/rangeHistogram.c
- src/hg/hgTables/schema.c
- src/hg/hgTables/seqOut.c
- src/hg/hgTables/wikiTrack.c
- src/hg/hgTablesTest/hgTablesTest.c
- src/hg/hgText/hgText.c
- src/hg/hgText/hgWigText.c
- src/hg/hgTrackUi/cgapSageUi.c
- src/hg/hgTrackUi/hgTrackUi.c
- src/hg/hgTracks/bedTrack.c
- src/hg/hgTracks/cds.c
- src/hg/hgTracks/cgapSageTrack.c
- src/hg/hgTracks/chainTrack.c
- src/hg/hgTracks/chromGraphTrack.c
- src/hg/hgTracks/contigTrack.c
- src/hg/hgTracks/coverageTrack.c
- src/hg/hgTracks/cutterTrack.c
- src/hg/hgTracks/cytoBandTrack.c
- src/hg/hgTracks/expRatioTracks.c
- src/hg/hgTracks/factorSource.c
- src/hg/hgTracks/gencodeTracks.c
- src/hg/hgTracks/hgTracks.c
- src/hg/hgTracks/loweLabTracks.c
- src/hg/hgTracks/makeItemsTrack.c
- src/hg/hgTracks/menu.c
- src/hg/hgTracks/pslTrack.c
- src/hg/hgTracks/pubsTracks.c
- lines changed 1, context: html, text, full: html, text
forgot to remove a debugging printf statement
- src/hg/hgTracks/rmskTrack.c
- src/hg/hgTracks/sampleTracks.c
- src/hg/hgTracks/simpleTracks.c
- src/hg/hgTracks/snakeTrack.c
- src/hg/hgTracks/wabaTrack.c
- src/hg/hgTracks/wigMafTrack.c
- src/hg/hgTracks/wigTrack.c
- src/hg/hgUserSuggestion/hgUserSuggestion.c
- lines changed 406, context: html, text, full: html, text
Feature 9142 suggestion form code checkin for preview1
- src/hg/hgUserSuggestion/hgUserSuggestion.h
- lines changed 15, context: html, text, full: html, text
Feature 9142 suggestion form code checkin for preview1
- src/hg/hgUserSuggestion/makefile
- lines changed 15, context: html, text, full: html, text
Feature 9142 suggestion form code checkin for preview1
- src/hg/hgVai/hgVai.c
- lines changed 1105, context: html, text, full: html, text
New CGI, hgVai (Variant Annotation Integrator): simple checklist-styleUI by which user can select variants that they have uploaded; gene
predictions to identify which part of a gene, if any, is hit by each
variant; several additional sources of annotations/predictions e.g.
dbNSFP scores and conserved elements/scores; and several filters to
constrain output to the variants most likely to have a functional effect.
Along with the new CGI, there are various lib bugfixes and improvements,
a new hg/lib/tests/ testcase, and some test file changes to accomodate
data updates to both knownGene and the pg* tables in knownGene.
refs #6152
- lines changed 2, context: html, text, full: html, text
Added a couple of Galt's new sqlSafef's.
- src/hg/hgVai/libifyMe.c
- lines changed 441, context: html, text, full: html, text
New CGI, hgVai (Variant Annotation Integrator): simple checklist-styleUI by which user can select variants that they have uploaded; gene
predictions to identify which part of a gene, if any, is hit by each
variant; several additional sources of annotations/predictions e.g.
dbNSFP scores and conserved elements/scores; and several filters to
constrain output to the variants most likely to have a functional effect.
Along with the new CGI, there are various lib bugfixes and improvements,
a new hg/lib/tests/ testcase, and some test file changes to accomodate
data updates to both knownGene and the pg* tables in knownGene.
refs #6152
- src/hg/hgVai/libifyMe.h
- lines changed 40, context: html, text, full: html, text
New CGI, hgVai (Variant Annotation Integrator): simple checklist-styleUI by which user can select variants that they have uploaded; gene
predictions to identify which part of a gene, if any, is hit by each
variant; several additional sources of annotations/predictions e.g.
dbNSFP scores and conserved elements/scores; and several filters to
constrain output to the variants most likely to have a functional effect.
Along with the new CGI, there are various lib bugfixes and improvements,
a new hg/lib/tests/ testcase, and some test file changes to accomodate
data updates to both knownGene and the pg* tables in knownGene.
refs #6152
- src/hg/hgVai/makefile
- lines changed 15, context: html, text, full: html, text
New CGI, hgVai (Variant Annotation Integrator): simple checklist-styleUI by which user can select variants that they have uploaded; gene
predictions to identify which part of a gene, if any, is hit by each
variant; several additional sources of annotations/predictions e.g.
dbNSFP scores and conserved elements/scores; and several filters to
constrain output to the variants most likely to have a functional effect.
Along with the new CGI, there are various lib bugfixes and improvements,
a new hg/lib/tests/ testcase, and some test file changes to accomodate
data updates to both knownGene and the pg* tables in knownGene.
refs #6152
- src/hg/hgc/ccdsClick.c
- src/hg/hgc/cgapSageClick.c
- src/hg/hgc/dbRIP.c
- src/hg/hgc/encodeClick.c
- src/hg/hgc/expClick.c
- src/hg/hgc/gencodeClick.c
- src/hg/hgc/gvfClick.c
- src/hg/hgc/hgc.c
- lines changed 4, context: html, text, full: html, text
removing unwanted webEnd calls which caused duplicate ending html and warn handler pop underflow errors
- lines changed 1, context: html, text, full: html, text
fixed bug where it should not use a cgi-var if it is an empty string
- src/hg/hgc/hgdpClick.c
- src/hg/hgc/lowelab.c
- src/hg/hgc/mafClick.c
- src/hg/hgc/makeItemsClick.c
- src/hg/hgc/mgcClick.c
- src/hg/hgc/numtsClick.c
- src/hg/hgc/parClick.c
- src/hg/hgc/peakClusters.c
- src/hg/hgc/pubs.c
- src/hg/hgc/regMotif.c
- src/hg/hgc/retroClick.c
- src/hg/hgc/rnaFoldClick.c
- src/hg/hgc/txCdsInfo.c
- src/hg/hgc/virusClick.c
- src/hg/hgc/wiggleClick.c
- src/hg/hgc/wikiTrack.c
- src/hg/hgcentralTidy/hgcentralTidy.c
- src/hg/htdocs/ENCODE/usageResources.html
- lines changed 7, context: html, text, full: html, text
Add links to April 2013 ENCODE Singapore workshop (Jen Harrow from Sanger organizer, Bob K presenting for UCSC) to ENCODE portal
- src/hg/htdocs/goldenPath/credits.html
- lines changed 90, context: html, text, full: html, text
Added links to papers for zebrafish, coelacanth, rat, plus updated all paper references to current format
- lines changed 105, context: html, text, full: html, text
Re-did the linebreaks and whitespace in some long lines so the html is more easily viewed
- src/hg/htdocs/goldenPath/help/haplotypes.html
- lines changed 7, context: html, text, full: html, text
Changed Pop score definition per Tim in RM 10653#note-38. refs 10653
- lines changed 21, context: html, text, full: html, text
Simplified the intro paragraphs a great deal, cribbing wording from the 1000 Genomes track. If we decide we want to include some of this info after all, perhaps we can bring it back in a different part of the page. refs #10653
- lines changed 16, context: html, text, full: html, text
Removed the textInfo class from several locations and deleted some commented out portions of the page.
- lines changed 86, context: html, text, full: html, text
A lot of rearranging text and a little bit of rewording. Changed the Variant sites, Full sequence and Rare haplotypes sections so that it is easier to tell what any button does without reading a lot of text. Pulled the variant site hover example into its own block. Incorporated the note about the display limit of 100 haplotypes into text.
- src/hg/htdocs/goldenPath/help/hgVaiHelpText.html
- lines changed 7, context: html, text, full: html, text
New CGI, hgVai (Variant Annotation Integrator): simple checklist-styleUI by which user can select variants that they have uploaded; gene
predictions to identify which part of a gene, if any, is hit by each
variant; several additional sources of annotations/predictions e.g.
dbNSFP scores and conserved elements/scores; and several filters to
constrain output to the variants most likely to have a functional effect.
Along with the new CGI, there are various lib bugfixes and improvements,
a new hg/lib/tests/ testcase, and some test file changes to accomodate
data updates to both knownGene and the pg* tables in knownGene.
refs #6152
- src/hg/htdocs/goldenPath/help/trackDb/makefile
- lines changed 27, context: html, text, full: html, text
Adding a makefile for trackDbDoc.html, though it does not need it. This directories contents is already copied from the htdocs dir make.
- src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
- lines changed 20, context: html, text, full: html, text
Minor changes to the detailed explanation of how things work. Also, mentioned the new make file.
- src/hg/htdocs/index.html
- lines changed 2, context: html, text, full: html, text
Feature 9142 suggestion form code checkin for preview1
- src/hg/htdocs/js/staticDoc.js
- lines changed 18, context: html, text, full: html, text
Collapsed staticDoc.js into one file, updated makefile/README to not clobber alpha on make user, refs #10888
- src/hg/inc/affy10K.h
- src/hg/inc/affy10KDetails.h
- src/hg/inc/affy120KDetails.h
- src/hg/inc/affyAllExonProbe.h
- src/hg/inc/affyAtlas.h
- src/hg/inc/affyTranscriptome.h
- src/hg/inc/alleleFreqs.h
- src/hg/inc/altGraph.h
- src/hg/inc/altGraphX.h
- src/hg/inc/annoFormatVep.h
- lines changed 38, context: html, text, full: html, text
New CGI, hgVai (Variant Annotation Integrator): simple checklist-styleUI by which user can select variants that they have uploaded; gene
predictions to identify which part of a gene, if any, is hit by each
variant; several additional sources of annotations/predictions e.g.
dbNSFP scores and conserved elements/scores; and several filters to
constrain output to the variants most likely to have a functional effect.
Along with the new CGI, there are various lib bugfixes and improvements,
a new hg/lib/tests/ testcase, and some test file changes to accomodate
data updates to both knownGene and the pg* tables in knownGene.
refs #6152
- src/hg/inc/annoGratorGpVar.h
- lines changed 23, context: html, text, full: html, text
New CGI, hgVai (Variant Annotation Integrator): simple checklist-styleUI by which user can select variants that they have uploaded; gene
predictions to identify which part of a gene, if any, is hit by each
variant; several additional sources of annotations/predictions e.g.
dbNSFP scores and conserved elements/scores; and several filters to
constrain output to the variants most likely to have a functional effect.
Along with the new CGI, there are various lib bugfixes and improvements,
a new hg/lib/tests/ testcase, and some test file changes to accomodate
data updates to both knownGene and the pg* tables in knownGene.
refs #6152
- src/hg/inc/annoStreamDb.h
- lines changed 1, context: html, text, full: html, text
New CGI, hgVai (Variant Annotation Integrator): simple checklist-styleUI by which user can select variants that they have uploaded; gene
predictions to identify which part of a gene, if any, is hit by each
variant; several additional sources of annotations/predictions e.g.
dbNSFP scores and conserved elements/scores; and several filters to
constrain output to the variants most likely to have a functional effect.
Along with the new CGI, there are various lib bugfixes and improvements,
a new hg/lib/tests/ testcase, and some test file changes to accomodate
data updates to both knownGene and the pg* tables in knownGene.
refs #6152
- src/hg/inc/bed12wSeq.h
- src/hg/inc/chicken13kInfo.h
- src/hg/inc/cnpSebat.h
- src/hg/inc/cnpSharpCutoff.h
- src/hg/inc/cnpSharpSample.h
- src/hg/inc/columnInfo.h
- src/hg/inc/cutter.h
- src/hg/inc/dbRIP.h
- src/hg/inc/dbSnpRs.h
- src/hg/inc/dnaProbe.h
- src/hg/inc/encode/encodeErge.h
- src/hg/inc/encode/encodeExp.h
- src/hg/inc/encode/encodePrimateAlleles.h
- src/hg/inc/encode/encodeRna.h
- src/hg/inc/expRecord.h
- src/hg/inc/gencodeIntron.h
- src/hg/inc/genotype.h
- src/hg/inc/genotypeFreqs.h
- src/hg/inc/ggMrnaAli.h
- src/hg/inc/gv.h
- src/hg/inc/hapmapLd.h
- src/hg/inc/hapmapPrimateAlleles.h
- src/hg/inc/ispyTables.h
- src/hg/inc/jksql.h
- src/hg/inc/jsHelper.h
- lines changed 5, context: html, text, full: html, text
Adjustable font size for collapsible sections.
- src/hg/inc/landmark.h
- src/hg/inc/ld.h
- src/hg/inc/liftOverChain.h
- src/hg/inc/llaInfo.h
- src/hg/inc/mafSummary.h
- src/hg/inc/makeItemsItem.h
- src/hg/inc/mdb.h
- src/hg/inc/omicia.h
- src/hg/inc/oreganno.h
- src/hg/inc/pgSnp.h
- src/hg/inc/polyGenotype.h
- src/hg/inc/protVar.h
- src/hg/inc/pslReader.h
- src/hg/inc/putaInfo.h
- src/hg/inc/retroMrnaInfo.h
- src/hg/inc/rnaHybridization.h
- src/hg/inc/sangerGeneToWBGeneID.h
- src/hg/inc/snp.h
- src/hg/inc/snpExceptions.h
- src/hg/inc/snpMap.h
- src/hg/inc/taxonDivision.h
- src/hg/inc/taxonGeneticCode.h
- src/hg/inc/taxonName.h
- src/hg/inc/taxonNode.h
- src/hg/inc/taxonXref.h
- src/hg/inc/tfbsCons.h
- src/hg/inc/tfbsConsMap.h
- src/hg/inc/tigrCmrGene.h
- src/hg/inc/trackDb.h
- lines changed 1, context: html, text, full: html, text
Added support for multi-view composites of type pgSnp. There are no config options for pgSnp, so disable the config pop-up in configurableByAjax. refs #683
- src/hg/inc/trackVersion.h
- src/hg/inc/ucscRetroInfo.h
- src/hg/inc/ucscRetroOrtho.h
- src/hg/inc/variome.h
- src/hg/inc/wikiTrack.h
- src/hg/intronEnds/intronEnds.c
- src/hg/intronSizes/intronSizes.c
- src/hg/js/README
- lines changed 8, context: html, text, full: html, text
Updated the hg/js README to reflect current make and sandbox behavior
- lines changed 7, context: html, text, full: html, text
Added lines for making static files to makefile, and updated the README accordingly
- lines changed 7, context: html, text, full: html, text
Collapsed staticDoc.js into one file, updated makefile/README to not clobber alpha on make user, refs #10888
- src/hg/js/alleles.js
- lines changed 3, context: html, text, full: html, text
Accidentally lost persistence of variant site highlighting by sort
- src/hg/js/makefile
- lines changed 11, context: html, text, full: html, text
Added lines for making static files to makefile, and updated the README accordingly
- lines changed 1, context: html, text, full: html, text
Collapsed staticDoc.js into one file, updated makefile/README to not clobber alpha on make user, refs #10888
- src/hg/js/staticDoc.js
- lines changed 7, context: html, text, full: html, text
Collapsed staticDoc.js into one file, updated makefile/README to not clobber alpha on make user, refs #10888
- src/hg/lib/affy10K.c
- src/hg/lib/affy10KDetails.c
- src/hg/lib/affy120KDetails.c
- src/hg/lib/affyAllExonProbe.c
- src/hg/lib/affyAtlas.c
- src/hg/lib/affyTranscriptome.c
- src/hg/lib/alleleFreqs.c
- src/hg/lib/altGraph.c
- src/hg/lib/altGraphX.c
- src/hg/lib/annoFormatVep.c
- lines changed 568, context: html, text, full: html, text
New CGI, hgVai (Variant Annotation Integrator): simple checklist-styleUI by which user can select variants that they have uploaded; gene
predictions to identify which part of a gene, if any, is hit by each
variant; several additional sources of annotations/predictions e.g.
dbNSFP scores and conserved elements/scores; and several filters to
constrain output to the variants most likely to have a functional effect.
Along with the new CGI, there are various lib bugfixes and improvements,
a new hg/lib/tests/ testcase, and some test file changes to accomodate
data updates to both knownGene and the pg* tables in knownGene.
refs #6152
- src/hg/lib/annoGratorGpVar.c
- lines changed 131, context: html, text, full: html, text
New CGI, hgVai (Variant Annotation Integrator): simple checklist-styleUI by which user can select variants that they have uploaded; gene
predictions to identify which part of a gene, if any, is hit by each
variant; several additional sources of annotations/predictions e.g.
dbNSFP scores and conserved elements/scores; and several filters to
constrain output to the variants most likely to have a functional effect.
Along with the new CGI, there are various lib bugfixes and improvements,
a new hg/lib/tests/ testcase, and some test file changes to accomodate
data updates to both knownGene and the pg* tables in knownGene.
refs #6152
- src/hg/lib/annoStreamDb.c
- lines changed 5, context: html, text, full: html, text
New CGI, hgVai (Variant Annotation Integrator): simple checklist-styleUI by which user can select variants that they have uploaded; gene
predictions to identify which part of a gene, if any, is hit by each
variant; several additional sources of annotations/predictions e.g.
dbNSFP scores and conserved elements/scores; and several filters to
constrain output to the variants most likely to have a functional effect.
Along with the new CGI, there are various lib bugfixes and improvements,
a new hg/lib/tests/ testcase, and some test file changes to accomodate
data updates to both knownGene and the pg* tables in knownGene.
refs #6152
- src/hg/lib/annoStreamWig.c
- lines changed 1, context: html, text, full: html, text
New CGI, hgVai (Variant Annotation Integrator): simple checklist-styleUI by which user can select variants that they have uploaded; gene
predictions to identify which part of a gene, if any, is hit by each
variant; several additional sources of annotations/predictions e.g.
dbNSFP scores and conserved elements/scores; and several filters to
constrain output to the variants most likely to have a functional effect.
Along with the new CGI, there are various lib bugfixes and improvements,
a new hg/lib/tests/ testcase, and some test file changes to accomodate
data updates to both knownGene and the pg* tables in knownGene.
refs #6152
- src/hg/lib/axtInfo.c
- src/hg/lib/axtLib.c
- src/hg/lib/bed12wSeq.c
- src/hg/lib/bioImage.c
- src/hg/lib/blastzNet.c
- src/hg/lib/blatServers.c
- src/hg/lib/borf.c
- src/hg/lib/borkPseudoHom.c
- src/hg/lib/cart.c
- src/hg/lib/cartDb.c
- src/hg/lib/ccdsGeneMap.c
- src/hg/lib/ccdsInfo.c
- src/hg/lib/ccdsNotes.c
- src/hg/lib/celeraCoverage.c
- src/hg/lib/chainDb.c
- src/hg/lib/chainNetDbLoad.c
- src/hg/lib/chicken13kInfo.c
- src/hg/lib/chr18deletions.c
- src/hg/lib/chromGraph.c
- src/hg/lib/chromGraphFactory.c
- src/hg/lib/chromInfo.c
- src/hg/lib/cnpSebat.c
- src/hg/lib/cnpSharpCutoff.c
- src/hg/lib/cnpSharpSample.c
- src/hg/lib/columnInfo.c
- src/hg/lib/coordConv.c
- src/hg/lib/customFactory.c
- src/hg/lib/customTrack.c
- src/hg/lib/cutter.c
- src/hg/lib/dbRIP.c
- src/hg/lib/dbSnpRs.c
- src/hg/lib/dnaMotifSql.c
- src/hg/lib/dnaProbe.c
- src/hg/lib/ec.c
- src/hg/lib/encode/encodeErge.c
- src/hg/lib/encode/encodeExp.c
- src/hg/lib/encode/encodeRegionInfoCustom.c
- src/hg/lib/encode/encodeRna.c
- src/hg/lib/encode/unused/encodePrimateAlleles.c
- src/hg/lib/ensFace.c
- src/hg/lib/ensPhusionBlast.c
- src/hg/lib/estOrientInfo.c
- src/hg/lib/expData.c
- src/hg/lib/expRecord.c
- src/hg/lib/featureBits.c
- src/hg/lib/findKGAlias.c
- src/hg/lib/findKGProtAlias.c
- src/hg/lib/fosEndPairs.c
- src/hg/lib/genMapDb.c
- src/hg/lib/gencodeIntron.c
- src/hg/lib/geneBands.c
- src/hg/lib/geneGraph.c
- src/hg/lib/genePix.c
- src/hg/lib/genePred.c
- src/hg/lib/genePredReader.c
- src/hg/lib/geneSimilarities.c
- src/hg/lib/genoLay.c
- src/hg/lib/genomicSuperDups.c
- src/hg/lib/genotype.c
- src/hg/lib/genotypeFreqs.c
- src/hg/lib/geoMirror.c
- src/hg/lib/ggCluster.c
- src/hg/lib/ggDbIo.c
- src/hg/lib/ggGraph.c
- src/hg/lib/ggMrnaAli.c
- src/hg/lib/gpFx.c
- lines changed 12, context: html, text, full: html, text
New CGI, hgVai (Variant Annotation Integrator): simple checklist-styleUI by which user can select variants that they have uploaded; gene
predictions to identify which part of a gene, if any, is hit by each
variant; several additional sources of annotations/predictions e.g.
dbNSFP scores and conserved elements/scores; and several filters to
constrain output to the variants most likely to have a functional effect.
Along with the new CGI, there are various lib bugfixes and improvements,
a new hg/lib/tests/ testcase, and some test file changes to accomodate
data updates to both knownGene and the pg* tables in knownGene.
refs #6152
- src/hg/lib/gv.c
- src/hg/lib/haplotypes.c
- lines changed 3, context: html, text, full: html, text
Minor wording changes only seen when the geneAlleles command-line tool is used.
- lines changed 13, context: html, text, full: html, text
Link on variant to 1000 genomes hgc page will now target a named page/tab. This is the solution that Brooke agreed to for the 'back-button not playing with ajax' problem listed in ref #10653.
- src/hg/lib/hapmapLd.c
- src/hg/lib/hapmapPrimateAlleles.c
- src/hg/lib/hdb.c
- src/hg/lib/hgBam.c
- src/hg/lib/hgExp.c
- src/hg/lib/hgFind.c
- src/hg/lib/hgFindSpecCustom.c
- src/hg/lib/hgRelate.c
- src/hg/lib/hgSeq.c
- src/hg/lib/hubConnect.c
- src/hg/lib/hui.c
- lines changed 1, context: html, text, full: html, text
Added support for multi-view composites of type pgSnp. There are no config options for pgSnp, so disable the config pop-up in configurableByAjax. refs #683
- src/hg/lib/humanParalog.c
- src/hg/lib/ispyTables.c
- src/hg/lib/jaxOrtholog.c
- src/hg/lib/jaxQTL.c
- src/hg/lib/jksql.c
- lines changed 6, context: html, text, full: html, text
fixed bug where it should not use a cgi-var if it is an empty string
- src/hg/lib/jsHelper.c
- lines changed 11, context: html, text, full: html, text
Adjustable font size for collapsible sections.
- src/hg/lib/landmark.c
- src/hg/lib/ld.c
- src/hg/lib/liftOver.c
- src/hg/lib/liftOverChain.c
- src/hg/lib/llaInfo.c
- src/hg/lib/loweutils.c
- src/hg/lib/lsSnpPdbChimera.c
- src/hg/lib/mafFrames.c
- src/hg/lib/mafSummary.c
- src/hg/lib/makeItemsItem.c
- src/hg/lib/mdb.c
- lines changed 115, context: html, text, full: html, text
Three changes to attempt to recover from mysql performace degradation (ref #10910). 1. Added index to val. 2. Replaced subqueries with joins. 3. Replaced ORDER BY query with in code sort.
- src/hg/lib/metaDb.as
- lines changed 2, context: html, text, full: html, text
Three changes to attempt to recover from mysql performace degradation (ref #10910). 1. Added index to val. 2. Replaced subqueries with joins. 3. Replaced ORDER BY query with in code sort.
- src/hg/lib/metaDb.sql
- lines changed 8, context: html, text, full: html, text
Three changes to attempt to recover from mysql performace degradation (ref #10910). 1. Added index to val. 2. Replaced subqueries with joins. 3. Replaced ORDER BY query with in code sort.
- src/hg/lib/mgiID.c
- src/hg/lib/mouseOrtho.c
- src/hg/lib/mouseSynWhd.c
- src/hg/lib/omicia.c
- src/hg/lib/oreganno.c
- src/hg/lib/pal.c
- src/hg/lib/pgPolyphenPred.c
- src/hg/lib/pgSiftPred.c
- src/hg/lib/pgSnp.c
- src/hg/lib/plasEndPairs.c
- src/hg/lib/polyGenotype.c
- src/hg/lib/protVar.c
- src/hg/lib/pslReader.c
- src/hg/lib/putaInfo.c
- src/hg/lib/recombRate.c
- src/hg/lib/retroMrnaInfo.c
- src/hg/lib/rikenBest.c
- src/hg/lib/rikenCluster.c
- src/hg/lib/rnaGroup.c
- src/hg/lib/rnaHybridization.c
- src/hg/lib/sample.c
- src/hg/lib/sangerGeneToWBGeneID.c
- src/hg/lib/scoredRef.c
- src/hg/lib/simpleRepeat.c
- src/hg/lib/snp.c
- src/hg/lib/snp125.c
- src/hg/lib/snp125Exceptions.c
- src/hg/lib/snp132Ext.as
- lines changed 1, context: html, text, full: html, text
Changing the type of strand to match fullBed.as so bedToBigBed willaccept this as 'bed 6 + ' autoSql.
- src/hg/lib/snpExceptions.c
- src/hg/lib/snpFasta.c
- src/hg/lib/snpMap.c
- src/hg/lib/snpTmp.c
- src/hg/lib/spDb.c
- src/hg/lib/stsInfo2.c
- src/hg/lib/stsInfoMouse.c
- src/hg/lib/stsMapMouse.c
- src/hg/lib/synteny100000.c
- src/hg/lib/syntenyBerk.c
- src/hg/lib/syntenySanger.c
- src/hg/lib/targetDb.c
- src/hg/lib/taxonDivision.c
- src/hg/lib/taxonGeneticCode.c
- src/hg/lib/taxonName.c
- src/hg/lib/taxonNode.c
- src/hg/lib/taxonXref.c
- src/hg/lib/tests/annoGratorTester.c
- lines changed 77, context: html, text, full: html, text
New CGI, hgVai (Variant Annotation Integrator): simple checklist-styleUI by which user can select variants that they have uploaded; gene
predictions to identify which part of a gene, if any, is hit by each
variant; several additional sources of annotations/predictions e.g.
dbNSFP scores and conserved elements/scores; and several filters to
constrain output to the variants most likely to have a functional effect.
Along with the new CGI, there are various lib bugfixes and improvements,
a new hg/lib/tests/ testcase, and some test file changes to accomodate
data updates to both knownGene and the pg* tables in knownGene.
refs #6152
- src/hg/lib/tests/annoGratorTests.mk
- lines changed 5, context: html, text, full: html, text
New CGI, hgVai (Variant Annotation Integrator): simple checklist-styleUI by which user can select variants that they have uploaded; gene
predictions to identify which part of a gene, if any, is hit by each
variant; several additional sources of annotations/predictions e.g.
dbNSFP scores and conserved elements/scores; and several filters to
constrain output to the variants most likely to have a functional effect.
Along with the new CGI, there are various lib bugfixes and improvements,
a new hg/lib/tests/ testcase, and some test file changes to accomodate
data updates to both knownGene and the pg* tables in knownGene.
refs #6152
- src/hg/lib/tests/expected/annoGrator/gpFx.txt
- lines changed 26, context: html, text, full: html, text
New CGI, hgVai (Variant Annotation Integrator): simple checklist-styleUI by which user can select variants that they have uploaded; gene
predictions to identify which part of a gene, if any, is hit by each
variant; several additional sources of annotations/predictions e.g.
dbNSFP scores and conserved elements/scores; and several filters to
constrain output to the variants most likely to have a functional effect.
Along with the new CGI, there are various lib bugfixes and improvements,
a new hg/lib/tests/ testcase, and some test file changes to accomodate
data updates to both knownGene and the pg* tables in knownGene.
refs #6152
- src/hg/lib/tests/expected/annoGrator/pgSnpKgDbToGpFx.txt
- lines changed 12, context: html, text, full: html, text
New CGI, hgVai (Variant Annotation Integrator): simple checklist-styleUI by which user can select variants that they have uploaded; gene
predictions to identify which part of a gene, if any, is hit by each
variant; several additional sources of annotations/predictions e.g.
dbNSFP scores and conserved elements/scores; and several filters to
constrain output to the variants most likely to have a functional effect.
Along with the new CGI, there are various lib bugfixes and improvements,
a new hg/lib/tests/ testcase, and some test file changes to accomodate
data updates to both knownGene and the pg* tables in knownGene.
refs #6152
- src/hg/lib/tests/expected/annoGrator/vepOut.txt
- lines changed 14, context: html, text, full: html, text
New CGI, hgVai (Variant Annotation Integrator): simple checklist-styleUI by which user can select variants that they have uploaded; gene
predictions to identify which part of a gene, if any, is hit by each
variant; several additional sources of annotations/predictions e.g.
dbNSFP scores and conserved elements/scores; and several filters to
constrain output to the variants most likely to have a functional effect.
Along with the new CGI, there are various lib bugfixes and improvements,
a new hg/lib/tests/ testcase, and some test file changes to accomodate
data updates to both knownGene and the pg* tables in knownGene.
refs #6152
- src/hg/lib/tests/expected/sqlCheck/sqlCheck.1
- src/hg/lib/tests/expected/sqlCheck/sqlCheck.2
- src/hg/lib/tests/expected/sqlCheck/sqlCheck.3
- src/hg/lib/tests/expected/sqlCheck/sqlCheck.4
- src/hg/lib/tests/expected/sqlCheck/sqlCheck.5
- src/hg/lib/tests/expected/sqlCheck/sqlCheck.6
- src/hg/lib/tests/expected/sqlCheck/sqlCheck.7
- src/hg/lib/tests/expected/sqlCheck/sqlCheck.8
- src/hg/lib/tests/genePredTester.c
- src/hg/lib/tests/input/annoGrator/moreVariants.pgSnp.tab
- lines changed 5, context: html, text, full: html, text
New CGI, hgVai (Variant Annotation Integrator): simple checklist-styleUI by which user can select variants that they have uploaded; gene
predictions to identify which part of a gene, if any, is hit by each
variant; several additional sources of annotations/predictions e.g.
dbNSFP scores and conserved elements/scores; and several filters to
constrain output to the variants most likely to have a functional effect.
Along with the new CGI, there are various lib bugfixes and improvements,
a new hg/lib/tests/ testcase, and some test file changes to accomodate
data updates to both knownGene and the pg* tables in knownGene.
refs #6152
- src/hg/lib/tests/input/annoGrator/pgForTestingGpFx.pgSnp.tab
- lines changed 13, context: html, text, full: html, text
New CGI, hgVai (Variant Annotation Integrator): simple checklist-styleUI by which user can select variants that they have uploaded; gene
predictions to identify which part of a gene, if any, is hit by each
variant; several additional sources of annotations/predictions e.g.
dbNSFP scores and conserved elements/scores; and several filters to
constrain output to the variants most likely to have a functional effect.
Along with the new CGI, there are various lib bugfixes and improvements,
a new hg/lib/tests/ testcase, and some test file changes to accomodate
data updates to both knownGene and the pg* tables in knownGene.
refs #6152
- src/hg/lib/tests/makefile
- src/hg/lib/tests/sqlCheck.c
- src/hg/lib/tests/sqlCheck.mk
- src/hg/lib/tfbsCons.c
- src/hg/lib/tfbsConsMap.c
- src/hg/lib/tigrCmrGene.c
- src/hg/lib/tilingPath.c
- src/hg/lib/trackDb.c
- src/hg/lib/trackDbCustom.c
- lines changed 4, context: html, text, full: html, text
Added support for multi-view composites of type pgSnp. There are no config options for pgSnp, so disable the config pop-up in configurableByAjax. refs #683
- src/hg/lib/trackVersion.c
- src/hg/lib/ucscRetroInfo.c
- src/hg/lib/ucscRetroOrtho.c
- src/hg/lib/variome.c
- src/hg/lib/visiGene.c
- src/hg/lib/web.c
- src/hg/lib/wigDataStream.c
- src/hg/lib/wiggleCart.c
- src/hg/lib/wiggleUtils.c
- src/hg/lib/wikiTrack.c
- src/hg/makeDb/doc/echTel2.txt
- lines changed 1985, context: html, text, full: html, text
masked sequence done, ready for genbank and other tracks refs #9693
- src/hg/makeDb/doc/hg18.txt
- lines changed 16, context: html, text, full: html, text
A couple data updates for hg18 Genome Variants -- much less extensive than hg19.
- src/hg/makeDb/doc/hg19.txt
- lines changed 80, context: html, text, full: html, text
Updated Personal Genome Variants with new data, trackDb and description from Belinda Giardine at PSU. refs #683
- lines changed 191, context: html, text, full: html, text
Documented adding Retroposed Genes 5.0 track.
- lines changed 2, context: html, text, full: html, text
Minor edit of Retroposed Genes track description.
- lines changed 13, context: html, text, full: html, text
adding doc and trackDb entry for hgmd
- lines changed 7, context: html, text, full: html, text
A couple more updates for hg19 Personal Genome Variant tables. refs #683
- lines changed 7, context: html, text, full: html, text
New CGI, hgVai (Variant Annotation Integrator): simple checklist-styleUI by which user can select variants that they have uploaded; gene
predictions to identify which part of a gene, if any, is hit by each
variant; several additional sources of annotations/predictions e.g.
dbNSFP scores and conserved elements/scores; and several filters to
constrain output to the variants most likely to have a functional effect.
Along with the new CGI, there are various lib bugfixes and improvements,
a new hg/lib/tests/ testcase, and some test file changes to accomodate
data updates to both knownGene and the pg* tables in knownGene.
refs #6152
- src/hg/makeDb/doc/mm10.txt
- lines changed 113, context: html, text, full: html, text
Documented adding Retroposed Genes track V2.0.
- src/hg/makeDb/doc/sorAra2.txt
- lines changed 2029, context: html, text, full: html, text
initial browser built refs #9348
- src/hg/makeDb/doc/ucscGenes/hg19.ucscGenes14.csh
- lines changed 16, context: html, text, full: html, text
adding BrianL's method of cleaning knowToLocusLink to make a new table knowToWikipedia so we don't make bad links anymore. refs #10707
- src/hg/makeDb/genbank/src/ccds/ccdsCommon.c
- src/hg/makeDb/genbank/src/ccds/ccdsImport.c
- src/hg/makeDb/genbank/src/ccds/ccdsMkTables.c
- src/hg/makeDb/genbank/src/dbload/gbAlignTbl.c
- src/hg/makeDb/genbank/src/dbload/gbBuildState.c
- src/hg/makeDb/genbank/src/dbload/gbGeneTbl.c
- src/hg/makeDb/genbank/src/dbload/gbIgnoreDelete.c
- src/hg/makeDb/genbank/src/dbload/gbLoadRna.c
- src/hg/makeDb/genbank/src/dbload/gbMetaData.c
- src/hg/makeDb/genbank/src/extFileUpdate/extFileUpdate.c
- src/hg/makeDb/genbank/src/gbSanity/chkAlignTbls.c
- src/hg/makeDb/genbank/src/gbSanity/chkMetaDataTbls.c
- src/hg/makeDb/genbank/src/gbSanity/chkSeqTbl.c
- src/hg/makeDb/genbank/src/gbSanity/gbSanity.c
- src/hg/makeDb/genbank/src/lib/extFileTbl.c
- src/hg/makeDb/genbank/src/lib/gbLoadedTbl.c
- src/hg/makeDb/genbank/src/lib/gbSql.c
- src/hg/makeDb/genbank/src/lib/gbStatusTbl.c
- src/hg/makeDb/genbank/src/lib/imageCloneTbl.c
- src/hg/makeDb/genbank/src/lib/mgcStatusTbl.c
- src/hg/makeDb/genbank/src/lib/seqTbl.c
- src/hg/makeDb/genbank/src/lib/sqlDeleter.c
- src/hg/makeDb/genbank/src/lib/sqlUpdater.c
- src/hg/makeDb/genbank/src/lib/uniqueStrTbl.c
- src/hg/makeDb/genbank/src/repair/refPepRepair.c
- src/hg/makeDb/hgAddLiftOverChain/hgAddLiftOverChain.c
- src/hg/makeDb/hgBbiDbLink/hgBbiDbLink.c
- src/hg/makeDb/hgCalStat/hgCalStat.c
- src/hg/makeDb/hgClonePos/hgClonePos.c
- src/hg/makeDb/hgCtgPos/hgCtgPos.c
- src/hg/makeDb/hgCutters/hgCutters.c
- src/hg/makeDb/hgDeleteChrom/hgDeleteChrom.c
- src/hg/makeDb/hgDropSplitTable/hgDropSplitTable.c
- src/hg/makeDb/hgExtFileCheck/hgExtFileCheck.c
- src/hg/makeDb/hgFindSpec/hgFindSpec.c
- src/hg/makeDb/hgGcPercent/hgGcPercent.c
- src/hg/makeDb/hgGeneBands/hgGeneBands.c
- src/hg/makeDb/hgGetKgUrls/hgGetKgUrls.c
- src/hg/makeDb/hgGetNrOmimGene/hgGetNrOmimGene.c
- src/hg/makeDb/hgGoldGapGl/hgGoldGapGl.c
- src/hg/makeDb/hgGoldGapGl/hgLoadGap.c
- src/hg/makeDb/hgKgGetText/hgKgGetText.c
- src/hg/makeDb/hgKgMrna/hgKgMrna.c
- src/hg/makeDb/hgKnownMore.oo21/hgKnownMore.c
- src/hg/makeDb/hgKnownMore/hgKnownMore.c
- src/hg/makeDb/hgLoadBed/hgLoadBed.c
- src/hg/makeDb/hgLoadBlastTab/hgLoadBlastTab.c
- src/hg/makeDb/hgLoadCdsEvidence/hgLoadCdsEvidence.c
- src/hg/makeDb/hgLoadChain/hgLoadChain.c
- src/hg/makeDb/hgLoadChromGraph/hgLoadChromGraph.c
- src/hg/makeDb/hgLoadItemAttr/hgLoadItemAttr.c
- src/hg/makeDb/hgLoadNet/hgLoadNet.c
- src/hg/makeDb/hgLoadOut/hgLoadOut.c
- src/hg/makeDb/hgLoadPsl/hgLoadPsl.c
- src/hg/makeDb/hgLoadSample/hgLoadSample.c
- src/hg/makeDb/hgLoadSeq/hgLoadSeq.c
- src/hg/makeDb/hgLoadSqlTab/hgLoadSqlTab.c
- src/hg/makeDb/hgLoadWiggle/hgDumpWiggle.c
- src/hg/makeDb/hgLoadWiggle/hgLoadWiggle.c
- src/hg/makeDb/hgMapMicroarray/hgMapMicroarray.c
- src/hg/makeDb/hgMedianMicroarray/hgMedianMicroarray.c
- src/hg/makeDb/hgMrnaRefseq/hgMrnaRefseq.c
- src/hg/makeDb/hgNibSeq/hgNibSeq.c
- src/hg/makeDb/hgPar/hgPar.c
- src/hg/makeDb/hgPepPred/hgPepPred.c
- src/hg/makeDb/hgRatioMicroarray/hgRatioMicroarray.c
- src/hg/makeDb/hgRenameSplitTable/hgRenameSplitTable.c
- src/hg/makeDb/hgSanger20/hgSanger20.c
- src/hg/makeDb/hgSanger22/hgSanger22.c
- src/hg/makeDb/hgStanfordMicroarray/hgStanfordMicroarray.c
- src/hg/makeDb/hgStsAlias/hgStsAlias.c
- src/hg/makeDb/hgStsMarkers/hgStsMarkers.c
- src/hg/makeDb/hgTomRough/hgTomRough.c
- src/hg/makeDb/hgTpf/hgTpf.c
- src/hg/makeDb/hgTraceInfo/hgTraceInfo.c
- src/hg/makeDb/hgTrackDb/hgTrackDb.c
- src/hg/makeDb/hgWaba/hgWaba.c
- src/hg/makeDb/makefile
- lines changed 2, context: html, text, full: html, text
adding to the userUtils build refs #9149
- src/hg/makeDb/outside/hgExonerate/hgExonerate.c
- src/hg/makeDb/outside/hgFiberglass/hgFiberglass.c
- src/hg/makeDb/outside/hgFlyBase/hgFlyBase.c
- src/hg/makeDb/outside/hgJaxQtl/hgJaxQtl.c
- src/hg/makeDb/outside/hgKegg/hgKegg.c
- src/hg/makeDb/outside/hgKegg2/hgKegg2.c
- src/hg/makeDb/outside/hgKegg3/hgKegg3.c
- src/hg/makeDb/outside/hgLoadEranModules/hgLoadEranModules.c
- src/hg/makeDb/outside/hgLsSnpPdbLoad/hgLsSnpPdbLoad.c
- src/hg/makeDb/outside/hgPhMouse/hgPhMouse.c
- src/hg/makeDb/outside/hgRnaGenes/hgRnaGenes.c
- src/hg/makeDb/outside/hgSoftPromoter/hgSoftPromoter.c
- src/hg/makeDb/outside/hgSoftberryHom/hgSoftberryHom.c
- src/hg/makeDb/outside/hgSuperfam/hgSuperfam.c
- src/hg/makeDb/outside/yeast/fixHarbisonMotifs/fixHarbisonMotifs.c
- src/hg/makeDb/outside/yeast/hgSgdGfp/hgSgdGfp.c
- src/hg/makeDb/schema/dbFindFieldsWith/dbFindFieldsWith.c
- src/hg/makeDb/schema/dbSnoop/dbSnoop.c
- src/hg/makeDb/schema/joinTwoInfo/joinTwoInfo.c
- src/hg/makeDb/schema/joinerCheck/joinerCheck.c
- src/hg/makeDb/schema/makeTableDescriptions/makeTableDescriptions.c
- src/hg/makeDb/trackDb/human/hg18/pgSnp.html
- lines changed 15, context: html, text, full: html, text
A couple data updates for hg18 Genome Variants -- much less extensive than hg19.
- src/hg/makeDb/trackDb/human/hg19/pgSnp.html
- lines changed 229, context: html, text, full: html, text
Updated Personal Genome Variants with new data, trackDb and description from Belinda Giardine at PSU. refs #683
- src/hg/makeDb/trackDb/human/hg19/pgSnpHgwdev.html
- lines changed 331, context: html, text, full: html, text
Updated Personal Genome Variants with new data, trackDb and description from Belinda Giardine at PSU. refs #683
- src/hg/makeDb/trackDb/human/hg19/snp137Flagged.html
- lines changed 2, context: html, text, full: html, text
made the caveat about Flagged SNPs not being risk alleles BOLD
- src/hg/makeDb/trackDb/human/hg19/snp137FlaggedMention.html
- lines changed 1, context: html, text, full: html, text
made the caveat about Flagged SNPs not being risk alleles BOLD
- src/hg/makeDb/trackDb/human/hg19/ucscRetroAli5.html
- lines changed 1, context: html, text, full: html, text
Minor edit to correct retrogene type.
- src/hg/makeDb/trackDb/human/hg19/wgEncodeReg.ra
- lines changed 1, context: html, text, full: html, text
Adding beta release tag to test new CGI for v284 new TFBS Clustered V3 refs #10097
- src/hg/makeDb/trackDb/human/hg19/wgEncodeRegTfbsClusteredV3.html
- lines changed 17, context: html, text, full: html, text
Editing _blank links and unifying HTML tags for new Clustered V3 TFBS html, CR refs #10914 #10097
- lines changed 7, context: html, text, full: html, text
Adding new link to Sherman lab, link to Supertrack page, line about cell abbreviations to TFBS Clustered html refs #10097
- src/hg/makeDb/trackDb/human/hgmd.html
- src/hg/makeDb/trackDb/human/spMut.html
- src/hg/makeDb/trackDb/human/trackDb.pgSnp.ra
- lines changed 463, context: html, text, full: html, text
Updated Personal Genome Variants with new data, trackDb and description from Belinda Giardine at PSU. refs #683
- src/hg/makeDb/trackDb/human/trackDb.ra
- lines changed 16, context: html, text, full: html, text
adding doc and trackDb entry for hgmd
- src/hg/makeDb/trackDb/makefile
- lines changed 1, context: html, text, full: html, text
adding sorAra2 to the build refs #9348
- lines changed 1, context: html, text, full: html, text
adding echTel2 to the build refs #9693
- src/hg/makeDb/trackDb/mouse/mm10/ucscRetroAli2.html
- lines changed 1, context: html, text, full: html, text
Minor edit to correct retrogene type.
- src/hg/makeDb/trackDb/shrew/sorAra2/description.html
- lines changed 63, context: html, text, full: html, text
initial set of trackDb files from makeGenomeDb.pl refs #9348
- src/hg/makeDb/trackDb/shrew/sorAra2/gap.html
- lines changed 30, context: html, text, full: html, text
initial set of trackDb files from makeGenomeDb.pl refs #9348
- src/hg/makeDb/trackDb/shrew/sorAra2/gold.html
- lines changed 33, context: html, text, full: html, text
initial set of trackDb files from makeGenomeDb.pl refs #9348
- src/hg/makeDb/trackDb/shrew/sorAra2/trackDb.ra
- lines changed 8, context: html, text, full: html, text
initial set of trackDb files from makeGenomeDb.pl refs #9348
- src/hg/makeDb/trackDb/tagTypes.tab
- lines changed 3, context: html, text, full: html, text
pgSnp tracks are now declared as 'type pgSnp', so add pgSnp to theacceptable types for pgSnp-related tags.
- src/hg/makeDb/trackDb/tenrec/echTel2/description.html
- lines changed 63, context: html, text, full: html, text
initial files from makeGenomeDb.pl refs #9693
- src/hg/makeDb/trackDb/tenrec/echTel2/gap.html
- lines changed 30, context: html, text, full: html, text
initial files from makeGenomeDb.pl refs #9693
- src/hg/makeDb/trackDb/tenrec/echTel2/gold.html
- lines changed 34, context: html, text, full: html, text
initial files from makeGenomeDb.pl refs #9693
- src/hg/makeDb/trackDb/tenrec/echTel2/trackDb.ra
- lines changed 8, context: html, text, full: html, text
initial files from makeGenomeDb.pl refs #9693
- src/hg/makefile
- lines changed 1, context: html, text, full: html, text
include pslToChain in builds
- lines changed 4, context: html, text, full: html, text
adding to the userUtils build refs #9149
- lines changed 2, context: html, text, full: html, text
adding pslToChain to the userApps refs #9149
- lines changed 1, context: html, text, full: html, text
New CGI, hgVai (Variant Annotation Integrator): simple checklist-styleUI by which user can select variants that they have uploaded; gene
predictions to identify which part of a gene, if any, is hit by each
variant; several additional sources of annotations/predictions e.g.
dbNSFP scores and conserved elements/scores; and several filters to
constrain output to the variants most likely to have a functional effect.
Along with the new CGI, there are various lib bugfixes and improvements,
a new hg/lib/tests/ testcase, and some test file changes to accomodate
data updates to both knownGene and the pg* tables in knownGene.
refs #6152
- lines changed 1, context: html, text, full: html, text
Feature 9142 suggestion form code checkin for preview1
- src/hg/mouseStuff/bedCoverage/bedCoverage.c
- src/hg/mouseStuff/chainDbToFile/chainDbToFile.c
- src/hg/mouseStuff/knownVsBlat/knownVsBlat.c
- src/hg/mouseStuff/libScan/libScan.c
- src/hg/mouseStuff/mafCoverage/mafCoverage.c
- src/hg/mouseStuff/makefile
- lines changed 6, context: html, text, full: html, text
adding to the userUtils build refs #9149
- src/hg/mouseStuff/mousePoster/mousePoster.c
- src/hg/mouseStuff/netClass/netClass.c
- src/hg/mouseStuff/orthologBySynteny/orthologBySynteny.c
- src/hg/mouseStuff/regionPicker/regionPicker.c
- src/hg/mouseStuff/rikenBestInCluster/rikenBestInCluster.c
- src/hg/mouseStuff/xmfaToMaf/xmfaToMaf.c
- src/hg/mrnaToGene/mrnaToGene.c
- src/hg/nci60/findStanAlignments.c
- src/hg/near/hgCeOrfToGene/hgCeOrfToGene.c
- src/hg/near/hgClusterGenes/hgClusterGenes.c
- src/hg/near/hgExpDistance/diffDistTables.c
- src/hg/near/hgExpDistance/hgExpDistance.c
- src/hg/near/hgExpDistance/hgExpDistance_fm.c
- src/hg/near/hgExpDistance/hgExpDistance_fm_tm.c
- src/hg/near/hgExpDistance/hgExpDistance_fq.c
- src/hg/near/hgExpDistance/hgExpDistance_fq_tm.c
- src/hg/near/hgExpDistance/hgExpDistance_tm.c
- src/hg/near/hgGoAssociation/hgGoAssociation.c
- src/hg/near/hgKnownToSuper/hgKnownToSuper.c
- src/hg/near/hgMapToGene/hgMapToGene.c
- src/hg/near/hgMapViaSwissProt/hgMapViaSwissProt.c
- src/hg/near/hgNear/afiAli.c
- src/hg/near/hgNear/association.c
- src/hg/near/hgNear/colTemplate.c
- src/hg/near/hgNear/expRatio.c
- src/hg/near/hgNear/getSeq.c
- src/hg/near/hgNear/go.c
- src/hg/near/hgNear/hgNear.c
- src/hg/near/hgNear/intronSize.c
- src/hg/near/hgNear/knownGene.c
- src/hg/near/hgNear/order.c
- src/hg/near/hgNear/pfam.c
- src/hg/near/hgNear/search.c
- src/hg/near/hgNetDist/hgLoadNetDist.c
- src/hg/near/hgProtIdToGenePred/hgProtIdToGenePred.c
- src/hg/near/knownToHprd/knownToHprd.c
- src/hg/near/pepPredToFa/pepPredToFa.c
- src/hg/oneShot/bed15To3Col/bed15To3Col.c
- src/hg/oneShot/cacheMergedRanges/cacheMergedRanges.c
- src/hg/oneShot/cartSim/cartSim.c
- src/hg/oneShot/cartSimNoInsert/cartSimNoInsert.c
- src/hg/oneShot/clonePos/clonePos.c
- src/hg/oneShot/doEvoFold/doEvoFold.c
- src/hg/oneShot/doEvoFoldV2/doEvoFoldV2.c
- src/hg/oneShot/doOmimDisorders/doOmimDisorders.c
- src/hg/oneShot/doRgdGene2/doRgdGene2.c
- src/hg/oneShot/doRgdGene2UniProt/doRgdGene2UniProt.c
- src/hg/oneShot/doRgdGene2Xref/doRgdGene2Xref.c
- src/hg/oneShot/dupedInTable/dupedInTable.c
- src/hg/oneShot/fakeHomozygousity/fakeHomozygousity.c
- src/hg/oneShot/fakeLinkage/fakeLinkage.c
- src/hg/oneShot/fakeSeqDiffs/fakeSeqDiffs.c
- src/hg/oneShot/findToFixBedGraphLimits/findToFixBedGraphLimits.c
- src/hg/oneShot/findToFixBedGraphViewLimits/findToFixBedGraphViewLimits.c
- src/hg/oneShot/getHumanBrainRna/getHumanBrainRna.c
- src/hg/oneShot/getRgdGeneCds/getRgdGeneCds.c
- src/hg/oneShot/kgName/fbName.c
- src/hg/oneShot/kgName/kgName.c
- src/hg/oneShot/kgName/sgName.c
- src/hg/oneShot/makeOrthoAtgTable/makeOrthoAtgTable.c
- src/hg/oneShot/musAliAt/musAliAt.c
- src/hg/oneShot/parseOmimDisorder/parseOmimDisorder.c
- src/hg/oneShot/patchDir/patchDir.c
- src/hg/oneShot/randomEst/randomEst.c
- src/hg/oneShot/rcvs/rcvs.c
- src/hg/oneShot/somePsls/somePsls.c
- src/hg/oneShot/tempLift/tempLift.c
- src/hg/oneShot/tempLower/tempLower.c
- src/hg/oneShot/testCart/cart.c
- src/hg/oneShot/testTableExists/testTableExists.c
- src/hg/oneShot/tetDensity/tetDensity.c
- src/hg/oneShot/tetFilter/tetFilter.c
- src/hg/oneShot/timeMysqlHandler/timeMysqlHandler.c
- src/hg/oneShot/weedKnownBlastTab/weedKnownBlastTab.c
- src/hg/oneShot/wgEncodeRegGenRa/wgEncodeRegGenRa.c
- src/hg/orthoMap/orthoEvaluate.c
- src/hg/orthoMap/orthoMap.c
- src/hg/perf/hgTracksRandom.c
- src/hg/poster/finPoster/finPoster.c
- src/hg/poster/foldDb/foldDb.c
- src/hg/protein/dv2/dv2.c
- src/hg/protein/fixMd/fixMd.c
- src/hg/protein/gadPos/gadPos.c
- src/hg/protein/getInterProFa/getInterProFa.c
- src/hg/protein/kgAliasKgXref/kgAliasKgXref.c
- src/hg/protein/kgAliasM/kgAliasM.c
- src/hg/protein/kgAliasRefseq/kgAliasRefseq.c
- src/hg/protein/kgAttachKegg/kgAttachKegg.c
- src/hg/protein/kgBestMrna/kgPrepBestMrna.c
- src/hg/protein/kgBestMrna/kgPrepBestMrna2.c
- src/hg/protein/kgBestMrna/kgResultBestMrna.c
- src/hg/protein/kgBestMrna2/kgPrepBestMrna2.c
- src/hg/protein/kgBestMrna2/kgResultBestMrna2.c
- src/hg/protein/kgBestRef2/kgPrepBestRef2.c
- src/hg/protein/kgBestRef2/kgResultBestRef2.c
- src/hg/protein/kgBioCyc0/kgBioCyc0.c
- src/hg/protein/kgBioCyc1/kgBioCyc1.c
- src/hg/protein/kgCheck/kgCheck.c
- src/hg/protein/kgCheck2/kgCheck2.c
- src/hg/protein/kgGetCds/kgGetCds.c
- src/hg/protein/kgGetPep/kgGetPep.c
- src/hg/protein/kgPepMrna/kgPepMrna.c
- src/hg/protein/kgPick/kgPick.c
- src/hg/protein/kgPick0/kgPickPrep.c
- src/hg/protein/kgProtAlias/kgProtAlias.c
- src/hg/protein/kgProtAliasNCBI/kgProtAliasNCBI.c
- src/hg/protein/kgPutBack/kgPutBack.c
- src/hg/protein/kgSelect/kgSelect.c
- src/hg/protein/kgUniq/kgUniq.c
- src/hg/protein/kgXref/kgXref.c
- src/hg/protein/kgXref2/kgXref2.c
- src/hg/protein/lib/doSam.c
- src/hg/protein/lib/doStamps.c
- src/hg/protein/lib/doTracks.c
- src/hg/protein/lib/domains.c
- src/hg/protein/lib/pbUtil.c
- src/hg/protein/lib/spKgMap.c
- src/hg/protein/omimCheckAv/omimCheckAv.c
- src/hg/protein/omimParseAv/omimParseAv.c
- src/hg/protein/pbCalDist/pbCalDist.c
- src/hg/protein/pbCalDistGlobal/pbCalDistGlobal.c
- src/hg/protein/pbCalPi/pbCalPi.c
- src/hg/protein/pbCalResStd/pbCalResStd.c
- src/hg/protein/pbCalResStdGlobal/pbCalResStdGlobal.c
- src/hg/protein/pbGlobal/pbGlobal.c
- src/hg/protein/pbHgnc/pbHgnc.c
- src/hg/protein/pfamXref/pfamXref.c
- src/hg/protein/rmKGPepMrna/rmKGPepMrna.c
- src/hg/protein/spDbAddVarSplice/spDbAddVarSplice.c
- src/hg/protein/spLoadPsiBlast/spLoadPsiBlast.c
- src/hg/protein/spLoadRankProp/spLoadRankProp.c
- src/hg/protein/spToProteins/spToProteins.c
- src/hg/protein/spToProteinsVar/spToProteinsVar.c
- src/hg/protein/spToSpXref2/spToSpXref2.c
- src/hg/protein/spXref2/spXref2.c
- src/hg/protein/spXref3/spXref3.c
- src/hg/protein/spm3/spm3.c
- src/hg/protein/spm6/spm6.c
- src/hg/protein/spm7/spm7.c
- src/hg/pslAnal/pslAnal.c
- src/hg/pslCheck/pslCheck.c
- src/hg/pslToChain/makefile
- lines changed 14, context: html, text, full: html, text
adding to the userUtils build refs #9149
- src/hg/qa/apacheMonitor.c
- src/hg/qa/checkCardinality.c
- src/hg/qa/gbSeqCheck.c
- src/hg/qa/getChroms.c
- src/hg/qa/reviewIndexes.c
- src/hg/qa/seqCheck.c
- src/hg/qa/timePosTable.c
- src/hg/qaPushQ/qaPushQ.c
- src/hg/ratStuff/mafGene/mafGene.c
- src/hg/ratStuff/mafSplitPos/mafSplitPos.c
- src/hg/ratStuff/mafToProtein/mafToProtein.c
- src/hg/recycleDb/bedDown/bedDown.c
- src/hg/recycleDb/bedUp/bedUp.c
- src/hg/regulate/regClusterAttachMetadataToTableOfTables/regClusterAttachMetadataToTableOfTables.c
- src/hg/regulate/regStartSampleEmbl/regStartSampleEmbl.c
- src/hg/rnaStructure/hgLoadRnaFold/hgLoadRnaFold.c
- src/hg/sageVisCGI/sageVisCGI.c
- src/hg/snp/details/dbSnp.c
- src/hg/snp/fixedDiffs/fixedDiffs.c
- src/hg/snp/snpLoad/affyCheck.c
- src/hg/snp/snpLoad/affyLookup.c
- src/hg/snp/snpLoad/cnpLookup.c
- src/hg/snp/snpLoad/hapmap2.c
- src/hg/snp/snpLoad/hapmapLookup.c
- src/hg/snp/snpLoad/hapmapMixed.c
- src/hg/snp/snpLoad/hapmapOrtho.c
- src/hg/snp/snpLoad/hapmapSummary.c
- src/hg/snp/snpLoad/hapmapValidate.c
- src/hg/snp/snpLoad/illuminaLookup.c
- src/hg/snp/snpLoad/illuminaLookup1M.c
- src/hg/snp/snpLoad/illuminaLookup2.c
- src/hg/snp/snpLoad/snpCheckAlleles.c
- src/hg/snp/snpLoad/snpCheckClassAndObserved.c
- src/hg/snp/snpLoad/snpCheckCluster.c
- src/hg/snp/snpLoad/snpCheckCluster2.c
- src/hg/snp/snpLoad/snpCheckLocTypeSize.c
- src/hg/snp/snpLoad/snpClassAndObserved.c
- src/hg/snp/snpLoad/snpCompare.c
- src/hg/snp/snpLoad/snpCompareLoctype.c
- src/hg/snp/snpLoad/snpCompareWeight.c
- src/hg/snp/snpLoad/snpContigLocFilter.c
- src/hg/snp/snpLoad/snpContigLocFilter125.c
- src/hg/snp/snpLoad/snpContigLocusIdCondense.c
- src/hg/snp/snpLoad/snpContigLocusIdFilter.c
- src/hg/snp/snpLoad/snpContigLocusIdFilter125.c
- src/hg/snp/snpLoad/snpExceptionCheck.c
- src/hg/snp/snpLoad/snpExceptions.c
- src/hg/snp/snpLoad/snpExpandAllele.c
- src/hg/snp/snpLoad/snpFinalTable.c
- src/hg/snp/snpLoad/snpFreq.c
- src/hg/snp/snpLoad/snpFunction.c
- src/hg/snp/snpLoad/snpFunctionCheck.c
- src/hg/snp/snpLoad/snpGetDeletions.c
- src/hg/snp/snpLoad/snpGetInsertions.c
- src/hg/snp/snpLoad/snpGetSimple.c
- src/hg/snp/snpLoad/snpLoad.c
- src/hg/snp/snpLoad/snpLoadFasta.c
- src/hg/snp/snpLoad/snpLoadFromTmp.c
- src/hg/snp/snpLoad/snpLocType.c
- src/hg/snp/snpLoad/snpLocType125.c
- src/hg/snp/snpLoad/snpMissing.c
- src/hg/snp/snpLoad/snpMoltype.c
- src/hg/snp/snpLoad/snpMultiple.c
- src/hg/snp/snpLoad/snpOrtho.c
- src/hg/snp/snpLoad/snpOrthoJoin.c
- src/hg/snp/snpLoad/snpOrthoLookup.c
- src/hg/snp/snpLoad/snpOrthoStats.c
- src/hg/snp/snpLoad/snpPAR.c
- src/hg/snp/snpLoad/snpReadFasta.c
- src/hg/snp/snpLoad/snpRefUCSC.c
- src/hg/snp/snpLoad/snpSNP.c
- src/hg/snp/snpLoad/snpSort.c
- src/hg/snp/snpLoad/snpSplit.c
- src/hg/snp/snpLoad/snpSplitByChrom.c
- src/hg/snp/snpLoad/snpSplitByChrom2.c
- src/hg/snp/snpLoad/snpSplitSimple.c
- src/hg/snp/snpLoad/subSnpCondense.c
- src/hg/snp/snpMask/seqWithInsertions.c
- src/hg/snp/snpMask/seqWithoutDeletions.c
- src/hg/snp/snpMask/snpMapToExon.c
- src/hg/snp/snpMask/snpMask.c
- src/hg/snp/snpMask/snpMaskChrom.c
- src/hg/snp/snpMask/snpMaskFlank.c
- src/hg/snp/snpMask/snpMaskFlankSubset.c
- src/hg/snp/snpMask/snpMaskGenes.c
- src/hg/snp/snpValid/snpValid.c
- src/hg/snp/snpValid/snpValidOld.c
- src/hg/snpException/snpException.c
- src/hg/sqlToXml/sqlToXml.c
- src/hg/synMap/createSlamParaSpec.c
- src/hg/test/otest/test1.c
- src/hg/tutorial/affyVsIlluminaCommon/affyVsIlluminaCommon.c
- src/hg/tutorial/bigGene/bigGene.c
- src/hg/txCds/txCdsBadBed/txCdsBadBed.c
- src/hg/txCds/txCdsGoodBed/txCdsGoodBed.c
- src/hg/txGene/txGeneAlias/txGeneAlias.c
- src/hg/txGene/txGeneXref/txGeneXref.c
- src/hg/txGraph/txAbFragFind/txAbFragFind.c
- src/hg/ultras/sqlAddCol/sqlAddCol.c
- src/hg/ultras/ultraPlateau/ultraPlateau.c
- src/hg/useCount/useCount.c
- src/hg/utils/bedExtendRanges/bedExtendRanges.c
- src/hg/utils/bedMergeExpData/bedMergeExpData.c
- src/hg/utils/gapToLift/gapToLift.c
- src/hg/utils/geoMirrorNode/geoMirrorNode.c
- src/hg/utils/hubPublicCheck/hubPublicCheck.c
- src/hg/utils/lovd/download.sh
- lines changed 2, context: html, text, full: html, text
trying to suppress non-error messages from lovd otto jobs
- src/hg/utils/makeTableList/makeTableList.c
- src/hg/utils/makeTrackIndex/makeTrackIndex.c
- src/hg/utils/motifFinder/motifFinder.c
- src/hg/utils/mutationClassifier/mutationClassifier.c
- src/hg/utils/omim/doOmimAv/doOmimAv.c
- src/hg/utils/omim/doOmimGene2/doOmimGene2.c
- src/hg/utils/omim/doOmimGeneSymbols/doOmimGeneSymbols.c
- src/hg/utils/omim/doOmimLocation/doOmimLocation.c
- src/hg/utils/phyloTrees/103way.commonNames.nh
- lines changed 103, context: html, text, full: html, text
adding mesAur1, lepWed1, zonAlb1, anaPla1, apaSpi1, astMex1 refs #10272
- src/hg/utils/phyloTrees/103way.nh
- lines changed 103, context: html, text, full: html, text
adding mesAur1, lepWed1, zonAlb1, anaPla1, apaSpi1, astMex1 refs #10272
- src/hg/utils/phyloTrees/103way.scientificNames.nh
- lines changed 103, context: html, text, full: html, text
adding mesAur1, lepWed1, zonAlb1, anaPla1, apaSpi1, astMex1 refs #10272
- src/hg/utils/phyloTrees/104way.commonNames.nh
- lines changed 104, context: html, text, full: html, text
adding panHod1 Tibetan antelop refs 0272
- src/hg/utils/phyloTrees/104way.nh
- lines changed 104, context: html, text, full: html, text
adding panHod1 Tibetan antelop refs 0272
- src/hg/utils/phyloTrees/104way.scientificNames.nh
- lines changed 104, context: html, text, full: html, text
adding panHod1 Tibetan antelop refs 0272
- src/hg/utils/phyloTrees/commonNames.sh
- lines changed 6, context: html, text, full: html, text
adding mesAur1, lepWed1, zonAlb1, anaPla1, apaSpi1, astMex1 refs #10272
- lines changed 1, context: html, text, full: html, text
adding panHod1 Tibetan antelop refs 0272
- src/hg/utils/phyloTrees/makefile
- lines changed 8, context: html, text, full: html, text
adding mesAur1, lepWed1, zonAlb1, anaPla1, apaSpi1, astMex1 refs #10272
- lines changed 8, context: html, text, full: html, text
adding panHod1 Tibetan antelop refs 0272
- src/hg/utils/phyloTrees/placentals.txt
- lines changed 5, context: html, text, full: html, text
adding mesAur1, lepWed1, zonAlb1, anaPla1, apaSpi1, astMex1 refs #10272
- lines changed 3, context: html, text, full: html, text
adding panHod1 Tibetan antelop refs 0272
- src/hg/utils/phyloTrees/scientificNames.sh
- lines changed 6, context: html, text, full: html, text
adding mesAur1, lepWed1, zonAlb1, anaPla1, apaSpi1, astMex1 refs #10272
- lines changed 1, context: html, text, full: html, text
adding panHod1 Tibetan antelop refs 0272
- src/hg/utils/phyloTrees/vertebrates.txt
- lines changed 13, context: html, text, full: html, text
adding mesAur1, lepWed1, zonAlb1, anaPla1, apaSpi1, astMex1 refs #10272
- src/hg/utils/positionalTblCheck/positionalTblCheck.c
- src/hg/utils/refSeqGet/refSeqGet.c
- src/hg/utils/refSeqGet/refSeqVerInfo.c
- src/hg/utils/refreshNamedSessionCustomTracks/refreshNamedSessionCustomTracks.c
- src/hg/utils/rgdGeneXref2/rgdGeneXref2.c
- src/hg/utils/safePush/safePush.c
- src/hg/utils/toDev64/toDev64.c
- src/hg/utils/uniprotMutations/liftUniprotMut.py
- lines changed 3, context: html, text, full: html, text
tiny change to uniprot lifter to take care of this incredibly rare amino acid
- src/hg/visiGene/gensat/gensatFixFull/gensatFixFull.c
- src/hg/visiGene/hgVisiGene/fullTextExperiment.c
- src/hg/visiGene/hgVisiGene/hgVisiGene.c
- src/hg/visiGene/hgVisiGene/printCaption.c
- src/hg/visiGene/hgVisiGene/probePage.c
- src/hg/visiGene/hgVisiGene/visiSearch.c
- src/hg/visiGene/knownToVisiGene/knownToVisiGene.c
- src/hg/visiGene/vgChangeContributors/vgChangeContributors.c
- src/hg/visiGene/vgGetText/vgGetText.c
- src/hg/visiGene/vgLoadJax/vgLoadJax.c
- src/hg/visiGene/vgLoadMahoney/vgLoadMahoney.c
- src/hg/visiGene/vgPatchJax/vgPatchJax.c
- src/hg/visiGene/vgProbeTrack/vgPrb.h
- src/hg/visiGene/vgProbeTrack/vgPrbAli.h
- src/hg/visiGene/vgProbeTrack/vgPrbAliAll.h
- src/hg/visiGene/vgProbeTrack/vgPrbMap.h
- src/hg/visiGene/vgProbeTrack/vgProbeTrack.c
- src/hg/visiGene/vgRemoveSubmission/vgRemoveSubmission.c
- src/hg/visiGene/visiGeneLoad/visiGeneLoad.c
- src/hg/visiGene/visiGeneSearch/visiGeneSearch.c
- src/inc/annoGrator.h
- lines changed 1, context: html, text, full: html, text
oops, forgot to clean up qLm -- added now. for #6152
- src/inc/annoStreamBigBed.h
- lines changed 1, context: html, text, full: html, text
Fixed implementation of maxItems. To reduce the delay before getting thefirst item in range, now bbi queries are limited to 100,000 items at a time,
so now there is a series of "chunk" queries instead of one query per region
or chromosome. for #6152
- src/inc/psl.h
- src/inc/vcf.h
- lines changed 5, context: html, text, full: html, text
New CGI, hgVai (Variant Annotation Integrator): simple checklist-styleUI by which user can select variants that they have uploaded; gene
predictions to identify which part of a gene, if any, is hit by each
variant; several additional sources of annotations/predictions e.g.
dbNSFP scores and conserved elements/scores; and several filters to
constrain output to the variants most likely to have a functional effect.
Along with the new CGI, there are various lib bugfixes and improvements,
a new hg/lib/tests/ testcase, and some test file changes to accomodate
data updates to both knownGene and the pg* tables in knownGene.
refs #6152
- src/lib/annoGrator.c
- lines changed 13, context: html, text, full: html, text
oops, forgot to clean up qLm -- added now. for #6152
- src/lib/annoStreamBigBed.c
- lines changed 97, context: html, text, full: html, text
Fixed implementation of maxItems. To reduce the delay before getting thefirst item in range, now bbi queries are limited to 100,000 items at a time,
so now there is a series of "chunk" queries instead of one query per region
or chromosome. for #6152
- src/lib/annoStreamVcf.c
- lines changed 44, context: html, text, full: html, text
New CGI, hgVai (Variant Annotation Integrator): simple checklist-styleUI by which user can select variants that they have uploaded; gene
predictions to identify which part of a gene, if any, is hit by each
variant; several additional sources of annotations/predictions e.g.
dbNSFP scores and conserved elements/scores; and several filters to
constrain output to the variants most likely to have a functional effect.
Along with the new CGI, there are various lib bugfixes and improvements,
a new hg/lib/tests/ testcase, and some test file changes to accomodate
data updates to both knownGene and the pg* tables in knownGene.
refs #6152
- src/lib/cheapcgi.c
- lines changed 4, context: html, text, full: html, text
When running from command line, SCRIPT_NAME is undefined (unless one purposefully sets it). Avoid segv.
- src/lib/genomeRangeTree.c
- lines changed 4, context: html, text, full: html, text
Improving misleading comment.
- src/lib/psl.c
- src/lib/vcf.c
- lines changed 38, context: html, text, full: html, text
New CGI, hgVai (Variant Annotation Integrator): simple checklist-styleUI by which user can select variants that they have uploaded; gene
predictions to identify which part of a gene, if any, is hit by each
variant; several additional sources of annotations/predictions e.g.
dbNSFP scores and conserved elements/scores; and several filters to
constrain output to the variants most likely to have a functional effect.
Along with the new CGI, there are various lib bugfixes and improvements,
a new hg/lib/tests/ testcase, and some test file changes to accomodate
data updates to both knownGene and the pg* tables in knownGene.
refs #6152
- src/makefile
- lines changed 2, context: html, text, full: html, text
adding to the userUtils build refs #9149
- lines changed 1, context: html, text, full: html, text
Adding bigWigCorrelate to UTILS_APPLIST
- src/oneShot/jksql/jksql.c
- src/oneShot/newSang6/newSang6.c
- src/oneShot/tabTable/tabTable.c
- src/parasol/lib/machSpec.c
- src/parasol/makefile
- lines changed 2, context: html, text, full: html, text
make sure bin exists before any of the builds start here refs #9149
- src/parasol/para/jobResult.c
- src/userApps/Makefile
- lines changed 8, context: html, text, full: html, text
add the update of the actual userApps bits during an update refs #9149
- src/userApps/README
- lines changed 4, context: html, text, full: html, text
add note about contacting UCSC refs #9149
- src/userApps/fetchKentSource.sh
- lines changed 1, context: html, text, full: html, text
adding pslToChain to the build refs #9149
- src/utils/addCols/addCols.c
- lines changed 4, context: html, text, full: html, text
improve usage message to include with userUtils refs #9149
- lines changed 3, context: html, text, full: html, text
correct usage message to include with userUtils refs #9149
- lines changed 0, context: html, text, full: html, text
improve usage message to include with userUtils refs #9149
- src/utils/aveCols/aveCols.c
- lines changed 3, context: html, text, full: html, text
improve usage message to include with userUtils refs #9149
- src/utils/bedScore/bedScore.c
- src/utils/bigWigCorrelate/bigWigCorrelate.c
- lines changed 132, context: html, text, full: html, text
Making a utility that will restrict correlation to something defined by a bigBed. Easier to do that than to add to wigCorrelate.
- src/utils/bigWigCorrelate/makefile
- lines changed 3, context: html, text, full: html, text
Making a utility that will restrict correlation to something defined by a bigBed. Easier to do that than to add to wigCorrelate.
- src/utils/geneStarts/geneStarts.c
- src/utils/makefile
- lines changed 1, context: html, text, full: html, text
Making a utility that will restrict correlation to something defined by a bigBed. Easier to do that than to add to wigCorrelate.
- lines changed 2, context: html, text, full: html, text
adding addCols and aveCols to the userUtils build refs #9149
- lines changed 12, context: html, text, full: html, text
adding to the userUtils build refs #9149
- src/utils/qa/weeklybld/buildEnv.csh
- src/utils/toLower/toLower.c
- lines changed 2, context: html, text, full: html, text
adding to the userUtils build refs #9149
- src/utils/toUpper/toUpper.c
- lines changed 2, context: html, text, full: html, text
adding to the userUtils build refs #9149
- lines changed: 21537
- files changed: 1015