All File Changes

v302_preview2 to v302_base (2014-06-23 to 2014-06-30) v302

• src/browserbox/root/updateBrowser.sh
  • lines changed 71, context: html, text, full: html, text
    browser update script does not overwrite newer files anymore in automode, refs #13049
    
  • lines changed 5, context: html, text, full: html, text
    previous commit did just update the file, now really adding the -uoption to rsync, refs #13049, note 46
    
• src/hg/hgMirror/hgMirror
  • lines changed 6, context: html, text, full: html, text
    fixing bug refs #11957 note 321
  • lines changed 1, context: html, text, full: html, text
    removing info message on box #11957 note 321
  • lines changed 11, context: html, text, full: html, text
    fixing missing info when clicking on a predefined group in hgMirror, refs #11957, note 321
  • lines changed 1, context: html, text, full: html, text
    newer rsync versions include commas in longer numbers
• src/hg/hgTracks/chainTrack.c
  • lines changed 1, context: html, text, full: html, text
    Making it so that directional arrows are visible more often on chains.
• src/hg/hgTracks/simpleTracks.c
  • lines changed 8, context: html, text, full: html, text
    Hooking up recent dbSNP builds to snp125Methods... really should make a snp125 track type for these.
• src/hg/hgVai/hgVai.c
  • lines changed 313, context: html, text, full: html, text
    Added ENCODE Regulatory summary tracks for clustered DNase and TFBS,with support for filtering based on BED5 score and factor/cellType/treatment.
    refs #11461
    
  • lines changed 1, context: html, text, full: html, text
    Fixing bug found by Jonathan: with clean cart, when showing contents offilter section for Regulatory Elements, the multiselects didn't appear.
    Turns out that the 'force' argument of ddcl.reinit actually makes it do
    nothing! To avoid disrupting anything else, for now I'll just forgo force.
    refs #11461
    
  • lines changed 26, context: html, text, full: html, text
    Adding regulatory region to the functional role filter options.Thanks Jonathan for noticing that I forgot to do that!
    refs #11461
    
• src/hg/hgVai/libifyMe.c
  • lines changed 8, context: html, text, full: html, text
    Added ENCODE Regulatory summary tracks for clustered DNase and TFBS,with support for filtering based on BED5 score and factor/cellType/treatment.
    refs #11461
    
• src/hg/hgVarAnnogrator/hgVarAnnogrator.c
  • lines changed 7, context: html, text, full: html, text
    Removed getFilters method from annoStreamer because it's not needed andit requires annoFilterCloneList, which I'm going to get rid of next because
    it requires too much knowledge about the contents of the filters.
    Also adding addFilters method for incrementally building up filters.
    
• src/hg/hgc/hgc.c
  • lines changed 3, context: html, text, full: html, text
    Now Filter Verdict lines and related subsection will only be displayed on the canFam1 genomicSuperDups details page. Other species with a genomicSuperDups track essentially have no useful information in these lines (just things like NA, etc.), and these extra lines clutter up the aleady busy display, refs #13171
  • lines changed 2, context: html, text, full: html, text
    change "species" to "assembly" in snake hgc clicks
• src/hg/htdocs/FAQ/FAQformat.html
  • lines changed 4, context: html, text, full: html, text
    Editing MAF format FAQ page per comments refs #9083
• src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.html
  • lines changed 7, context: html, text, full: html, text
    fixing "urls" doc
• src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.html
  • lines changed 5, context: html, text, full: html, text
    fixing "urls" doc
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 2, context: html, text, full: html, text
    fixing "urls" doc
• src/hg/inc/annoFormatVep.h
  • lines changed 8, context: html, text, full: html, text
    Added ENCODE Regulatory summary tracks for clustered DNase and TFBS,with support for filtering based on BED5 score and factor/cellType/treatment.
    refs #11461
    
• src/hg/inc/annoStreamDbFactorSource.h
  • lines changed 17, context: html, text, full: html, text
    Added ENCODE Regulatory summary tracks for clustered DNase and TFBS,with support for filtering based on BED5 score and factor/cellType/treatment.
    refs #11461
    
• src/hg/inc/factorSource.h
  • lines changed 3, context: html, text, full: html, text
    Added factorSourceAsObj for anno*.
• src/hg/inc/jksql.h
  • lines changed 4, context: html, text, full: html, text
    Added sqlQuickPairList for quick two-column queries.
• src/hg/inc/variant.h
  • lines changed 8, context: html, text, full: html, text
    Added ENCODE Regulatory summary tracks for clustered DNase and TFBS,with support for filtering based on BED5 score and factor/cellType/treatment.
    refs #11461
    
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    New version number v302
• src/hg/js/ddcl.js
  • lines changed 1, context: html, text, full: html, text
    Fixing bug found by Jonathan: with clean cart, when showing contents offilter section for Regulatory Elements, the multiselects didn't appear.
    Turns out that the 'force' argument of ddcl.reinit actually makes it do
    nothing! To avoid disrupting anything else, for now I'll just forgo force.
    refs #11461
    
• src/hg/js/hgTracks.js
  • lines changed 29, context: html, text, full: html, text
    When there are too many tracks, image only reload is slower than full page reload. Now there is a cut-off of 50 tracks, above which only full page reloads will be done. Redmine #13347.
• src/hg/js/utils.js
  • lines changed 3, context: html, text, full: html, text
    In setTableRowVisibility, when changing a row from hide to show,trigger a 'show' event so other JS code can listen and make updates
    if needed (e.g. hgVai.c).
    
  • lines changed 1, context: html, text, full: html, text
    Surprising fallout from jshint changes. Fix for redmine #13492.
• src/hg/lib/annoFormatVep.c
  • lines changed 135, context: html, text, full: html, text
    Added ENCODE Regulatory summary tracks for clustered DNase and TFBS,with support for filtering based on BED5 score and factor/cellType/treatment.
    refs #11461
    
• src/hg/lib/annoGratorGpVar.c
  • lines changed 44, context: html, text, full: html, text
    Added ENCODE Regulatory summary tracks for clustered DNase and TFBS,with support for filtering based on BED5 score and factor/cellType/treatment.
    refs #11461
    
• src/hg/lib/annoStreamDb.c
  • lines changed 28, context: html, text, full: html, text
    Added ENCODE Regulatory summary tracks for clustered DNase and TFBS,with support for filtering based on BED5 score and factor/cellType/treatment.
    refs #11461
    
• src/hg/lib/annoStreamDbFactorSource.c
  • lines changed 221, context: html, text, full: html, text
    Added ENCODE Regulatory summary tracks for clustered DNase and TFBS,with support for filtering based on BED5 score and factor/cellType/treatment.
    refs #11461
    
• src/hg/lib/factorSource.c
  • lines changed 23, context: html, text, full: html, text
    Added factorSourceAsObj for anno*.
• src/hg/lib/googleAnalytics.c
  • lines changed 1, context: html, text, full: html, text
    domain can be 'auto' refs #13120
• src/hg/lib/hdb.c
  • lines changed 6, context: html, text, full: html, text
    some changes in how a missing assembly hub database is announced.
  • lines changed 1, context: html, text, full: html, text
    fix silly bug that resulted in navigation for "other" clade browsers notworking.
    
• src/hg/lib/hui.c
  • lines changed 1, context: html, text, full: html, text
    Add filtering by source count (pick lineage-specific vs. ubiquitous sites). refs #13230
  • lines changed 1, context: html, text, full: html, text
    Revert to previous label; Tim counsels alternate approach
  • lines changed 7, context: html, text, full: html, text
    Suppress spurious 'Minimum' prefix to UI filter box label when using a range filter. refs #13230
• src/hg/lib/jksql.c
  • lines changed 14, context: html, text, full: html, text
    Added sqlQuickPairList for quick two-column queries.
• src/hg/lib/makefile
  • lines changed 2, context: html, text, full: html, text
    Added ENCODE Regulatory summary tracks for clustered DNase and TFBS,with support for filtering based on BED5 score and factor/cellType/treatment.
    refs #11461
    
• src/hg/lib/tests/annoGratorTester.c
  • lines changed 3, context: html, text, full: html, text
    Added ENCODE Regulatory summary tracks for clustered DNase and TFBS,with support for filtering based on BED5 score and factor/cellType/treatment.
    refs #11461
    
• src/hg/lib/variant.c
  • lines changed 28, context: html, text, full: html, text
    Added ENCODE Regulatory summary tracks for clustered DNase and TFBS,with support for filtering based on BED5 score and factor/cellType/treatment.
    refs #11461
    
• src/hg/lib/web.c
  • lines changed 2, context: html, text, full: html, text
    some changes in how a missing assembly hub database is announced.
  • lines changed 1, context: html, text, full: html, text
    fix silly bug that resulted in navigation for "other" clade browsers notworking.
    
• src/hg/makeDb/doc/encodeAwgHg19.txt
  • lines changed 16, context: html, text, full: html, text
    Changes to doc and labels after review by Bob Thurman. Fix to loader program. Log transform scores for better spectrum display. refs #13230
  • lines changed 14, context: html, text, full: html, text
    Fix cell types to match ENCODE controlled vocab. refs #13230
• src/hg/makeDb/doc/encodeRegHg19.txt
  • lines changed 36, context: html, text, full: html, text
    V3 of DNase clusters track. Restores lineage-specific clusters. refs #13490
• src/hg/makeDb/doc/hg38.txt
  • lines changed 13, context: html, text, full: html, text
    document GRC Incident ottomate refs #12407
• src/hg/makeDb/hgBedSources/hgBedSources.c
  • lines changed 2, context: html, text, full: html, text
    Changes to doc and labels after review by Bob Thurman. Fix to loader program. Log transform scores for better spectrum display. refs #13230
• src/hg/makeDb/schema/all.joiner
  • lines changed 2, context: html, text, full: html, text
    Adding tables to all.joiner for animalQtl and facebase tracks refs #10954 and #12606
• src/hg/makeDb/trackDb/animalQtl.html
  • lines changed 27, context: html, text, full: html, text
    Edited description section; made some minor corrections (redmine #10954)
• src/hg/makeDb/trackDb/baboon/papAnu2/description.html
  • lines changed 2, context: html, text, full: html, text
    Changing links on baboon (papAnu2) track description pages
• src/hg/makeDb/trackDb/baboon/papAnu2/gap.html
  • lines changed 3, context: html, text, full: html, text
    Changing links on baboon (papAnu2) track description pages
• src/hg/makeDb/trackDb/baboon/papAnu2/gold.html
  • lines changed 3, context: html, text, full: html, text
    Changing links on baboon (papAnu2) track description pages
• src/hg/makeDb/trackDb/blatFr1.html
  • lines changed 2, context: html, text, full: html, text
    Changing links on chicken (galGal2) track description pages
• src/hg/makeDb/trackDb/cat/felCat4/cons6way.html
  • lines changed 53, context: html, text, full: html, text
    Changing links on cat (felCat4 and felCat5) track description pages
• src/hg/makeDb/trackDb/cat/felCat4/description.html
  • lines changed 1, context: html, text, full: html, text
    Changing links on cat (felCat4 and felCat5) track description pages
• src/hg/makeDb/trackDb/cat/felCat5/description.html
  • lines changed 2, context: html, text, full: html, text
    Changing links on cat (felCat4 and felCat5) track description pages
• src/hg/makeDb/trackDb/cat/felCat5/gap.html
  • lines changed 3, context: html, text, full: html, text
    Changing links on cat (felCat4 and felCat5) track description pages
• src/hg/makeDb/trackDb/cat/felCat5/gold.html
  • lines changed 3, context: html, text, full: html, text
    Changing links on cat (felCat4 and felCat5) track description pages
• src/hg/makeDb/trackDb/chicken/galGal2/description.html
  • lines changed 1, context: html, text, full: html, text
    Changing links on chicken (galGal2) track description pages
• src/hg/makeDb/trackDb/chicken/galGal2/ecoresTetraodon.html
  • lines changed 13, context: html, text, full: html, text
    Changing links on chicken (galGal2) track description pages
• src/hg/makeDb/trackDb/chicken/galGal2/isochore.html
  • lines changed 9, context: html, text, full: html, text
    Changing links on chicken (galGal2) track description pages
• src/hg/makeDb/trackDb/chicken/galGal2/multiz7way.html
  • lines changed 104, context: html, text, full: html, text
    Changing links on chicken (galGal2) track description pages
• src/hg/makeDb/trackDb/chicken/galGal2/phastConsElements7way.html
  • lines changed 50, context: html, text, full: html, text
    Changing links on chicken (galGal2) track description pages
• src/hg/makeDb/trackDb/chicken/galGal2/rnaGene.html
  • lines changed 46, context: html, text, full: html, text
    Changing links on chicken (galGal2) track description pages
• src/hg/makeDb/trackDb/chicken/galGal2/uniGene_gg.html
  • lines changed 2, context: html, text, full: html, text
    Changing links on chicken (galGal2) track description pages
• src/hg/makeDb/trackDb/cpgIslandGgfAndy.html
  • lines changed 6, context: html, text, full: html, text
    Changing links on chicken (galGal2) track description pages
• src/hg/makeDb/trackDb/dolphin/turTru2/description.html
  • lines changed 2, context: html, text, full: html, text
    Changing links on dolphin (turTru2) track description pages
• src/hg/makeDb/trackDb/dolphin/turTru2/gap.html
  • lines changed 3, context: html, text, full: html, text
    Changing links on dolphin (turTru2) track description pages
• src/hg/makeDb/trackDb/dolphin/turTru2/gold.html
  • lines changed 3, context: html, text, full: html, text
    Changing links on dolphin (turTru2) track description pages
• src/hg/makeDb/trackDb/drosophila/droEre1/description.html
  • lines changed 1, context: html, text, full: html, text
    Changing links on Drosphila (droYak2 and droEre1) track description pages
• src/hg/makeDb/trackDb/drosophila/droEre1/gap.html
  • lines changed 2, context: html, text, full: html, text
    Changing links on Drosphila (droYak2 and droEre1) track description pages
• src/hg/makeDb/trackDb/drosophila/droYak2/description.html
  • lines changed 4, context: html, text, full: html, text
    Changing links on Drosphila (droYak2 and droEre1) track description pages
• src/hg/makeDb/trackDb/fugu/est.html
  • lines changed 17, context: html, text, full: html, text
    Changing links on fugu (fr2) track description pages
• src/hg/makeDb/trackDb/fugu/fr2/gap.html
  • lines changed 8, context: html, text, full: html, text
    Changing links on fugu (fr2) track description pages
• src/hg/makeDb/trackDb/fugu/fr2/multiz5way.html
  • lines changed 80, context: html, text, full: html, text
    Changing links on fugu (fr2) track description pages
• src/hg/makeDb/trackDb/fugu/fr2/phastConsElements5way.html
  • lines changed 49, context: html, text, full: html, text
    Changing links on fugu (fr2) track description pages
• src/hg/makeDb/trackDb/fugu/gap.html
  • lines changed 9, context: html, text, full: html, text
    Changing links on fugu (fr2) track description pages
• src/hg/makeDb/trackDb/fugu/intronEst.html
  • lines changed 20, context: html, text, full: html, text
    Changing links on fugu (fr2) track description pages
• src/hg/makeDb/trackDb/fugu/mrna.html
  • lines changed 17, context: html, text, full: html, text
    Changing links on fugu (fr2) track description pages
• src/hg/makeDb/trackDb/fugu/xenoMrna.html
  • lines changed 20, context: html, text, full: html, text
    Changing links on fugu (fr2) track description pages
• src/hg/makeDb/trackDb/human/cytoBand.html
  • lines changed 1, context: html, text, full: html, text
    Fixing small typo in page numbering reported by user.
• src/hg/makeDb/trackDb/human/hg17/trackDb.ra
  • lines changed 12, context: html, text, full: html, text
    I noticed searchMethod and searchType were in tagTypes.tab for trackDbsettings -- they shouldn't be. They're only for search specs. I removed
    those settings from track stanzas (where they're ignored) and added
    search specs where necessary. Also moved some shared definitions up to
    human/trackDb.ra.
    
• src/hg/makeDb/trackDb/human/hg18/trackDb.ra
  • lines changed 14, context: html, text, full: html, text
    I noticed searchMethod and searchType were in tagTypes.tab for trackDbsettings -- they shouldn't be. They're only for search specs. I removed
    those settings from track stanzas (where they're ignored) and added
    search specs where necessary. Also moved some shared definitions up to
    human/trackDb.ra.
    
• src/hg/makeDb/trackDb/human/hg19/allHg19RS_BW.html
  • lines changed 3, context: html, text, full: html, text
    Adding clarification of spp used for GERP calculations. refs #12334
• src/hg/makeDb/trackDb/human/hg19/cons100way.html
  • lines changed 1, context: html, text, full: html, text
    Updating link in html of 100 way page to correct path refs MLQ #13508
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra
  • lines changed 3, context: html, text, full: html, text
    Fix controlIds in HAIB TFBS metadata. refs #13476
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeRegDnaseClustered.ra
  • lines changed 8, context: html, text, full: html, text
    Adding metadata for V3 DNase clusters. refs #13490
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 16, context: html, text, full: html, text
    I noticed searchMethod and searchType were in tagTypes.tab for trackDbsettings -- they shouldn't be. They're only for search specs. I removed
    those settings from track stanzas (where they're ignored) and added
    search specs where necessary. Also moved some shared definitions up to
    human/trackDb.ra.
    
• src/hg/makeDb/trackDb/human/hg19/wgEncodeAwg.ra
  • lines changed 3, context: html, text, full: html, text
    Add filtering by source count (pick lineage-specific vs. ubiquitous sites). refs #13230
  • lines changed 4, context: html, text, full: html, text
    Changes to doc and labels after review by Bob Thurman. Fix to loader program. Log transform scores for better spectrum display. refs #13230
• src/hg/makeDb/trackDb/human/hg19/wgEncodeAwgDnaseCombinedSites.html
  • lines changed 64, context: html, text, full: html, text
    Changes to doc and labels after review by Bob Thurman. Fix to loader program. Log transform scores for better spectrum display. refs #13230
• src/hg/makeDb/trackDb/human/hg19/wgEncodeAwgDnaseMasterSites.html
  • lines changed 91, context: html, text, full: html, text
    Changes to doc and labels after review by Bob Thurman. Fix to loader program. Log transform scores for better spectrum display. refs #13230
• src/hg/makeDb/trackDb/human/hg19/wgEncodeAwgSegmentation.html
  • lines changed 3, context: html, text, full: html, text
    Adding note about prefixes to Segmentation Track for Segway elements per MLQ #13514
• src/hg/makeDb/trackDb/human/hg19/wgEncodeReg.ra
  • lines changed 29, context: html, text, full: html, text
    V3 of DNase clusters track. Restores lineage-specific clusters. refs #13490
  • lines changed 1, context: html, text, full: html, text
    refs #13490
  • lines changed 24, context: html, text, full: html, text
    Add V3 update of DNase Clusters. refs #13490
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 14, context: html, text, full: html, text
    I noticed searchMethod and searchType were in tagTypes.tab for trackDbsettings -- they shouldn't be. They're only for search specs. I removed
    those settings from track stanzas (where they're ignored) and added
    search specs where necessary. Also moved some shared definitions up to
    human/trackDb.ra.
    
• src/hg/makeDb/trackDb/kangarooRat/dipOrd1/description.html
  • lines changed 2, context: html, text, full: html, text
    Changing links on kangaroo rat (dipOrd1) track description pages
• src/hg/makeDb/trackDb/kangarooRat/dipOrd1/gap.html
  • lines changed 3, context: html, text, full: html, text
    Changing links on kangaroo rat (dipOrd1) track description pages
• src/hg/makeDb/trackDb/kangarooRat/dipOrd1/gold.html
  • lines changed 3, context: html, text, full: html, text
    Changing links on kangaroo rat (dipOrd1) track description pages
• src/hg/makeDb/trackDb/mouse/FaceBase24SampleTypesAvg.html
  • lines changed 69, context: html, text, full: html, text
    Edits to FaceBase microarray track description page, refs #12606
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhHist.ra
  • lines changed 15, context: html, text, full: html, text
    Fixed filenames in two fastq tarballs. refs #13404
• src/hg/makeDb/trackDb/opossum/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    I noticed searchMethod and searchType were in tagTypes.tab for trackDbsettings -- they shouldn't be. They're only for search specs. I removed
    those settings from track stanzas (where they're ignored) and added
    search specs where necessary. Also moved some shared definitions up to
    human/trackDb.ra.
    
• src/hg/makeDb/trackDb/platypus/ornAna1/description.html
  • lines changed 11, context: html, text, full: html, text
    Changing links on platypus (ornAna1) track description pages
• src/hg/makeDb/trackDb/platypus/ornAna1/gold.html
  • lines changed 8, context: html, text, full: html, text
    Changing links on platypus (ornAna1) track description pages
• src/hg/makeDb/trackDb/platypus/ornAna1/multiz6way.html
  • lines changed 74, context: html, text, full: html, text
    Changing links on platypus (ornAna1) track description pages
• src/hg/makeDb/trackDb/platypus/ornAna1/phastConsElements6way.html
  • lines changed 43, context: html, text, full: html, text
    Changing links on platypus (ornAna1) track description pages
• src/hg/makeDb/trackDb/platypus/ornAna1/wssdCoverage.html
  • lines changed 23, context: html, text, full: html, text
    Changing links on platypus (ornAna1) track description pages
• src/hg/makeDb/trackDb/tagTypes.tab
  • lines changed 2, context: html, text, full: html, text
    I noticed searchMethod and searchType were in tagTypes.tab for trackDbsettings -- they shouldn't be. They're only for search specs. I removed
    those settings from track stanzas (where they're ignored) and added
    search specs where necessary. Also moved some shared definitions up to
    human/trackDb.ra.
    
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    no longer need the nonBedFieldsLabel entry for GRC Incident refs #12407
• src/hg/makeDb/trackDb/worm/caePb1/ctgPos2.html
  • lines changed 2, context: html, text, full: html, text
    Changing links on C. brenneri (caePb1) track description pages
• src/hg/makeDb/trackDb/worm/caePb1/description.html
  • lines changed 4, context: html, text, full: html, text
    Changing links on C. brenneri (caePb1) track description pages
• src/hg/makeDb/trackDb/worm/caePb1/gap.html
  • lines changed 2, context: html, text, full: html, text
    Changing links on C. brenneri (caePb1) track description pages
• src/hg/makeDb/trackDb/worm/caePb1/gold.html
  • lines changed 2, context: html, text, full: html, text
    Changing links on C. brenneri (caePb1) track description pages
• src/hg/makeDb/trackDb/xenTro/xenTro1/trackDb.ra
  • lines changed 4, context: html, text, full: html, text
    I noticed searchMethod and searchType were in tagTypes.tab for trackDbsettings -- they shouldn't be. They're only for search specs. I removed
    those settings from track stanzas (where they're ignored) and added
    search specs where necessary. Also moved some shared definitions up to
    human/trackDb.ra.
    
• src/hg/makeDb/trackDb/zebraFinch/nscanGene.html
  • lines changed 22, context: html, text, full: html, text
    Changing links on zebrafinch (taeGut1) track description pages
• src/hg/makeDb/trackDb/zebraFinch/taeGut1/description.html
  • lines changed 4, context: html, text, full: html, text
    Changing links on zebrafinch (taeGut1) track description pages
• src/hg/pslPairs/pslPairs.c
  • lines changed 3, context: html, text, full: html, text
    pslPairs has a memory trashing bug. These changes avoid the problem,without incurring any real cost.
    
• src/hg/utils/hubPublicCheck/hubPublicCheck.c
  • lines changed 2, context: html, text, full: html, text
    add descriptionUrl to add hub command. Thanks Angie!
• src/hg/utils/phyloTrees/171way.commonNames.nh
  • lines changed 171, context: html, text, full: html, text
    adding five new birds chaVoc1 cucCan1 apaVit1 phaCar1 nipNip1 refs #10272
  • lines changed 4, context: html, text, full: html, text
    looks better with colLiv1 on top of the group refs #10272
• src/hg/utils/phyloTrees/171way.nh
  • lines changed 171, context: html, text, full: html, text
    adding five new birds chaVoc1 cucCan1 apaVit1 phaCar1 nipNip1 refs #10272
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    looks better with colLiv1 on top of the group refs #10272
• src/hg/utils/phyloTrees/171way.scientificNames.nh
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    adding five new birds chaVoc1 cucCan1 apaVit1 phaCar1 nipNip1 refs #10272
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    looks better with colLiv1 on top of the group refs #10272
• src/hg/utils/phyloTrees/172way.commonNames.nh
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    adding balPav1 Crowned crain refs #10272
• src/hg/utils/phyloTrees/172way.nh
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    adding balPav1 Crowned crain refs #10272
• src/hg/utils/phyloTrees/172way.scientificNames.nh
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    adding balPav1 Crowned crain refs #10272
• src/hg/utils/phyloTrees/174way.commonNames.nh
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    adding tinGut1 and tauEry1 refs #10272
• src/hg/utils/phyloTrees/174way.nh
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    adding tinGut1 and tauEry1 refs #10272
• src/hg/utils/phyloTrees/174way.scientificNames.nh
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    adding tinGut1 and tauEry1 refs #10272
• src/hg/utils/phyloTrees/commonNames.sh
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    adding five new birds chaVoc1 cucCan1 apaVit1 phaCar1 nipNip1 refs #10272
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    adding balPav1 Crowned crain refs #10272
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    adding tinGut1 and tauEry1 refs #10272
• src/hg/utils/phyloTrees/db.ncbiTaxId.tab
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    fixup to UCSC db names refs #10272
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    fix the Sus scrofa name refs #10272
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    adding balPav Balearica pavonina gibbericeps refs #10272
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    adding tinGut1 and tauEry1 refs #10272
• src/hg/utils/phyloTrees/dbCommonScientificCladeOrderkey.tab
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    add the five new birds chaVoc1 cucCan1 apaVit1 nipNip1 phaCar1 refs #10272
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    correct sci names for bosMut1 and apaVit1 refs #10272
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    adding balPav1 Crowned crain refs #10272
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    adding tinGut1 and tauEry1 refs #10272
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    correct cotJap sciName refs #10272
• src/hg/utils/phyloTrees/makefile
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    adding five new birds chaVoc1 cucCan1 apaVit1 phaCar1 nipNip1 refs #10272
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    adding balPav1 Crowned crain refs #10272
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    adding tinGut1 and tauEry1 refs #10272
• src/hg/utils/phyloTrees/scientificNames.sh
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    adding five new birds chaVoc1 cucCan1 apaVit1 phaCar1 nipNip1 refs #10272
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    adding balPav1 Crowned crain refs #10272
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    adding tinGut1 and tauEry1 refs #10272
• src/inc/annoAssembly.h
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    Adding sequence cache to annoAssembly (moving up from annoGratorGpVar).
• src/inc/annoFilter.h
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    Added ENCODE Regulatory summary tracks for clustered DNase and TFBS,with support for filtering based on BED5 score and factor/cellType/treatment.
    refs #11461
    
• src/inc/annoStreamer.h
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    Removed getFilters method from annoStreamer because it's not needed andit requires annoFilterCloneList, which I'm going to get rid of next because
    it requires too much knowledge about the contents of the filters.
    Also adding addFilters method for incrementally building up filters.
    
• src/lib/annoAssembly.c
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    Adding sequence cache to annoAssembly (moving up from annoGratorGpVar).
• src/lib/annoFilter.c
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    Added ENCODE Regulatory summary tracks for clustered DNase and TFBS,with support for filtering based on BED5 score and factor/cellType/treatment.
    refs #11461
    
• src/lib/annoGrator.c
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    Removed getFilters method from annoStreamer because it's not needed andit requires annoFilterCloneList, which I'm going to get rid of next because
    it requires too much knowledge about the contents of the filters.
    Also adding addFilters method for incrementally building up filters.
    
• src/lib/annoStreamer.c
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    Removed getFilters method from annoStreamer because it's not needed andit requires annoFilterCloneList, which I'm going to get rid of next because
    it requires too much knowledge about the contents of the filters.
    Also adding addFilters method for incrementally building up filters.
    
• src/makefile
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    adding cscope to makefile, extension of ctags
• src/utils/qa/weeklybld/buildEnv.csh
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    v302 final build refs #13327

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• files changed: 162