All File Changes

v312_base to v313_preview (2015-02-16 to 2015-02-23) v313

• src/hg/cirm/cdw/cdwMakeFileTags/cdwMakeFileTags.c
  • lines changed 135, context: html, text, full: html, text
    Utility to make a cdwFileTags table that is a real but sparse mysql table out of all the tags.
    
  • lines changed 24, context: html, text, full: html, text
    Moving tagListIncludingParents to library.
    
  • lines changed 94, context: html, text, full: html, text
    Making it make purely numeric columns stay that way.
    
• src/hg/cirm/cdw/cdwMakeFileTags/makefile
  • lines changed 4, context: html, text, full: html, text
    Utility to make a cdwFileTags table that is a real but sparse mysql table out of all the tags.
    
• src/hg/cirm/cdw/cdwMakeTrackViz/cdwMakeTrackViz.c
  • lines changed 290, context: html, text, full: html, text
    Starting to build up a track table as well as the file table.
    
• src/hg/cirm/cdw/cdwMakeTrackViz/makefile
  • lines changed 4, context: html, text, full: html, text
    Starting to build up a track table as well as the file table.
    
• src/hg/cirm/cdw/cdwMakeValidFile/cdwMakeValidFile.c
  • lines changed 12, context: html, text, full: html, text
    Providing parent tags from cdwMetaTags.
    
  • lines changed 32, context: html, text, full: html, text
    Starting to process bam.bai and vcf.gz.tbi indexes.
    
• src/hg/cirm/cdw/cdwQuery/cdwQuery.c
  • lines changed 1, context: html, text, full: html, text
    Updating tagTree names to tagStorm names
    
  • lines changed 63, context: html, text, full: html, text
    Adding -format option to control output of cdwQuery. Now can get tab or tags output as well as the original ra.
    
• src/hg/cirm/cdw/cdwReallyRemoveFiles/cdwReallyRemoveFiles.c
  • lines changed 5, context: html, text, full: html, text
    Making this a fraction less hostile on the command line.
    
• src/hg/cirm/cdw/cdwSubmit/cdwSubmit.c
  • lines changed 127, context: html, text, full: html, text
    Permitting bam.bai and vcf.gz.tbi as formats. Getting rid of old unused
    code. Putting in a prefetch check that will catch ungzipped fastqs.
    + "bam.bai", "vcf.gz.tbi",
    
• src/hg/cirm/cdw/cdwWebBrowse/cdwNavBar.html
  • lines changed 60, context: html, text, full: html, text
    Refactoring web.c code so as to have my own menubar. Will hopefully get rid of the nested tables bit soon too.
    
  • lines changed 6, context: html, text, full: html, text
    Got rid of some old Drupal stuff. Everything I need still seems to work.
    
  • lines changed 6, context: html, text, full: html, text
    Refactored part of menuBar function into menuBarAddUiVars for reuse with another menu bar.
    
  • lines changed 25, context: html, text, full: html, text
    Reducing delay before menu drops down.
    
  • lines changed 1, context: html, text, full: html, text
    Putting back most of the delay in hopes of reducing a flickering menu bug.
    
  • lines changed 6, context: html, text, full: html, text
    Rearranging menus.
    
  • lines changed 2, context: html, text, full: html, text
    Adding browseTracks command
    
• src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c
  • lines changed 581, context: html, text, full: html, text
    Refactoring web.c code so as to have my own menubar. Will hopefully get rid of the nested tables bit soon too.
    
  • lines changed 12, context: html, text, full: html, text
    Moving to strict rather than loose transitional HTML 4.01 in DOCTYPE.
    
  • lines changed 12, context: html, text, full: html, text
    Refactored part of menuBar function into menuBarAddUiVars for reuse with another menu bar.
    
  • lines changed 110, context: html, text, full: html, text
    Repositioning menuBar output so that page closes. Breaking page into parts that you see when you select various menu items.
    
  • lines changed 65, context: html, text, full: html, text
    Replacing localMenuBar() with library routine recently refactored in web.c.
    
  • lines changed 100, context: html, text, full: html, text
    Replacing a lot of duplicated code with calls to stuff factored out of existing libraries. SImplifying in general.
    
  • lines changed 92, context: html, text, full: html, text
    Adding implementation for Browse/Files. Adding lab count to home page.
    
  • lines changed 60, context: html, text, full: html, text
    Adding initial implementation for browsing labs, data sets, and formats. Moving tables from ascii edge to web 1.0.
    
  • lines changed 355, context: html, text, full: html, text
    Rearranging menus, making summary part of home page. Deleting some old code.
    
  • lines changed 137, context: html, text, full: html, text
    Moving a bunch of code to cdwLib.c, tagStorm.c and even hash.c. Updating version string. Updating help.
    
  • lines changed 17, context: html, text, full: html, text
    Moving limit to separate part of query page
    
  • lines changed 38, context: html, text, full: html, text
    Making a better browseFormats page.
    
  • lines changed 25, context: html, text, full: html, text
    Separating out RQL statement, enforcing it always select from files. The field selector and the where selector are in separate CGI variables.
    
  • lines changed 99, context: html, text, full: html, text
    Switching browseFiles page to using cdwFileTags table rather than building tagStorm.
    
  • lines changed 31, context: html, text, full: html, text
    Making it so you can change sort by clicking on label names in browse files
    
  • lines changed 185, context: html, text, full: html, text
    Refactoring so that use fieldedTable rather than a list of tagStanzas as intermediate part of browse file table redering.
    
  • lines changed 109, context: html, text, full: html, text
    Making browse labs use the showFieldedTable code.
    
  • lines changed 31, context: html, text, full: html, text
    Making doBrowseFormat use new sortable tables.
    
  • lines changed 99, context: html, text, full: html, text
    Making browse tags and the home page use the sortable tables. Making the sortable tables work as expected on numeric fields.
    
  • lines changed 26, context: html, text, full: html, text
    Polishing help text and selected fields.
    
  • lines changed 12, context: html, text, full: html, text
    Sanitizing a supposivedly numerical value before sticking it into a SQL query. Removing lab_quake_markers from default display.
    
  • lines changed 157, context: html, text, full: html, text
    Making it so that you can browse all tags for a file, or all values for a tag.
    
  • lines changed 29, context: html, text, full: html, text
    Adding a free form filter line to file browse (not sure it's a good idea, it's a where clause from SQL. Also making various tags value listers use it to make link to file browseron just files that match given tag value.
    
  • lines changed 5, context: html, text, full: html, text
    Putting in a sanity check on filter. Bumping version.
    
  • lines changed 87, context: html, text, full: html, text
    Adding paging to browse file
    
  • lines changed 51, context: html, text, full: html, text
    MOving paging to under table. Removing free form query.
    
  • lines changed 4, context: html, text, full: html, text
    Removed some unimportant links from home page. Bumped version number.
    
  • lines changed 136, context: html, text, full: html, text
    First cut of browseTracks command, will launch browser with a custom track. Label needs improvement.
    
  • lines changed 38, context: html, text, full: html, text
    Second cut of browseTracks command. Handes VCF this time. Labels are improved but could still be better.
    
  • lines changed 1, context: html, text, full: html, text
    Bumping version (up to 20 since will distribute)
    
• src/hg/cirm/cdw/cdwWebBrowse/makefile
  • lines changed 5, context: html, text, full: html, text
    Adding the menubar html file to makefile. I need to consult with Hiram though, as the .c file needs to get recompiled when the menubar html file is touched and currently it doesn't.
    
• src/hg/cirm/cdw/fix/cdwFix5/cdwFix5.c
  • lines changed 65, context: html, text, full: html, text
    Little fix applied.
    
• src/hg/cirm/cdw/fix/cdwFix5/makefile
  • lines changed 4, context: html, text, full: html, text
    Little fix applied.
    
• src/hg/cirm/cdw/fix/cdwFixInvisibleIndexFiles/cdwFixInvisibleIndexFiles.c
  • lines changed 76, context: html, text, full: html, text
    Utility to link bam and vcf index files to appropriate location.
    
• src/hg/cirm/cdw/inc/cdw.h
  • lines changed 70, context: html, text, full: html, text
    Adding cdwLab table.
    
  • lines changed 72, context: html, text, full: html, text
    Adding cdwTrackViz table to support browseTracks in cdwWebBrowse.
    
• src/hg/cirm/cdw/inc/cdwLib.h
  • lines changed 15, context: html, text, full: html, text
    tagStanzasMatchingQuery function moved to cdwLib from cdwWebBrowse
    
  • lines changed 9, context: html, text, full: html, text
    Adding cdwValidFileFromLicensePlate and cdwFindInSameSubmitDir functinos.
    
• src/hg/cirm/cdw/inc/cdwValid.h
  • lines changed 4, context: html, text, full: html, text
    Adding routine to fetch list of formats and their descriptions.
    
  • lines changed 3, context: html, text, full: html, text
    Adding bam index validation.
    
• src/hg/cirm/cdw/lib/cdw.as
  • lines changed 10, context: html, text, full: html, text
    Adding cdwLab table.
    
  • lines changed 12, context: html, text, full: html, text
    Adding cdwTrackViz table to support browseTracks in cdwWebBrowse.
    
• src/hg/cirm/cdw/lib/cdw.c
  • lines changed 170, context: html, text, full: html, text
    Adding cdwLab table.
    
  • lines changed 175, context: html, text, full: html, text
    Adding cdwTrackViz table to support browseTracks in cdwWebBrowse.
    
• src/hg/cirm/cdw/lib/cdw.sql
  • lines changed 12, context: html, text, full: html, text
    Adding cdwLab table.
    
  • lines changed 13, context: html, text, full: html, text
    Adding cdwTrackViz table to support browseTracks in cdwWebBrowse.
    
• src/hg/cirm/cdw/lib/cdwLib.c
  • lines changed 4, context: html, text, full: html, text
    Ifdeffing out some unused stuff.
    
  • lines changed 23, context: html, text, full: html, text
    Making validator look to cdwMetaTags.tags as well as just tags.
    
  • lines changed 59, context: html, text, full: html, text
    tagStanzasMatchingQuery function moved to cdwLib from cdwWebBrowse
    
  • lines changed 24, context: html, text, full: html, text
    Adding cdwValidFileFromLicensePlate and cdwFindInSameSubmitDir functinos.
    
• src/hg/cirm/cdw/lib/cdwTagStorm.c
  • lines changed 5, context: html, text, full: html, text
    Allowing files without metadata past their own tags into cdwTagStorm.
    
  • lines changed 16, context: html, text, full: html, text
    Adding file_id to storm. Also for some reason changing ef var to cf.
    
• src/hg/cirm/cdw/lib/cdwValid.c
  • lines changed 44, context: html, text, full: html, text
    Adding routine to fetch list of formats and their descriptions.
    
  • lines changed 7, context: html, text, full: html, text
    Adding bam index validation.
    
• src/hg/cirm/quakeLab/quakeFakeMouseManifest/quakeFakeMouseManifest.c
  • lines changed 5, context: html, text, full: html, text
    Making it work with latest cdw tags spec better.
    
• src/hg/hgTables/filterFields.c
  • lines changed 136, context: html, text, full: html, text
    Moving sql where-clause sanity checking to library for reuse in CIRM routines.
    
• src/hg/hgTracks/simpleTracks.c
  • lines changed 1, context: html, text, full: html, text
    let tracks with "itemRgb on" also use codon coloring if the user selects
    it (at least with bigGenePred tracks)
    
• src/hg/hgc/hgc.c
  • lines changed 1, context: html, text, full: html, text
    A little more flexibility with table naming. refs #14731
    
• src/hg/hgc/peakClusters.c
  • lines changed 2, context: html, text, full: html, text
    Renames to fix poor name choice (meta->vocab). refs #14353
    
  • lines changed 9, context: html, text, full: html, text
    Use controlledVocabulary setting for non-ENCODE (table-based) vocabularies (replace briefly used *MetaTables settings)
    
• src/hg/htdocs/goldenPath/help/bigBed.html
  • lines changed 8, context: html, text, full: html, text
    Fixed a couple hard links to hgwdev and added info on making tab-separated BED files, refs #14534
    
• src/hg/htdocs/goldenPath/help/hubQuickStartAssembly.html
  • lines changed 3, context: html, text, full: html, text
    Correcting example about transBlat blat and http.
    
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 11, context: html, text, full: html, text
    Fixed a couple hard links to hgwdev and added info on making tab-separated BED files, refs #14534
    
• src/hg/htdocs/goldenPath/help/trix.html
  • lines changed 1, context: html, text, full: html, text
    Fixed a couple hard links to hgwdev and added info on making tab-separated BED files, refs #14534
    
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 11, context: html, text, full: html, text
    Additional edits to stage announcement of release of new training video. refs #14239
    
• src/hg/htdocs/goldenPath/pubs.html
  • lines changed 18, context: html, text, full: html, text
    Added 2 new pubs. Abridged the author list for Nature pub due to huge number of authors. Nature pub doesn't yet have PMID.
    
• src/hg/htdocs/indexNews.html
  • lines changed 11, context: html, text, full: html, text
    Staging announcement of new training video. refs #14239
    
  • lines changed 48, context: html, text, full: html, text
    Added temporary announcement about power outage. Can remove on Mon.
    
  • lines changed 7, context: html, text, full: html, text
    Additional edits to stage announcement of release of new training video. refs #14239
    
  • lines changed 12, context: html, text, full: html, text
    Removed temporary server outage announcement.
    
• src/hg/htdocs/style/cirm.css
  • lines changed 8194, context: html, text, full: html, text
    These cirm style sheets are no longer used.
    
• src/hg/htdocs/style/cirmUcsc.css
  • lines changed 58, context: html, text, full: html, text
    These cirm style sheets are no longer used.
    
• src/hg/htdocs/style/makefile
  • lines changed 1, context: html, text, full: html, text
    Removing cirm css dependencies.
    
• src/hg/htdocs/training/index.html
  • lines changed 6, context: html, text, full: html, text
    Staging sections for release of training video 6. Also fixing capitalization of html tags. refs #14239
    
• src/hg/htdocs/training/vids/index.html
  • lines changed 4, context: html, text, full: html, text
    Staging sections for release of training video 6. Also fixing capitalization of html tags. refs #14239
    
• src/hg/inc/gtexGeneBed.h
  • lines changed 71, context: html, text, full: html, text
    First cut loader of GTEX gene track. Enough here to test track display. refs #13504
    
• src/hg/inc/hui.h
  • lines changed 4, context: html, text, full: html, text
    Renames to fix poor name choice (meta->vocab). refs #14353
    
  • lines changed 9, context: html, text, full: html, text
    Use controlledVocabulary setting for non-ENCODE (table-based) vocabularies (replace briefly used *MetaTables settings)
    
• src/hg/inc/hvGfx.h
  • lines changed 26, context: html, text, full: html, text
    Libify graphics routine used for GTEX bar graph display. refs #13504
    
• src/hg/inc/sqlSanity.h
  • lines changed 15, context: html, text, full: html, text
    Moving sql where-clause sanity checking to library for reuse in CIRM routines.
    
• src/hg/inc/web.h
  • lines changed 3, context: html, text, full: html, text
    Refactored part of menuBar function into menuBarAddUiVars for reuse with another menu bar.
    
  • lines changed 10, context: html, text, full: html, text
    Refactored a few routines out of the webStartInternal demon for reuse in cdwWebBrowse.
    
  • lines changed 6, context: html, text, full: html, text
    Adding routine to fetch list of formats and their descriptions.
    
• src/hg/lib/encode/wgEncodeTreatment.as
  • lines changed 7, context: html, text, full: html, text
    Add table with info about ENCODE treatment terms (from cv.ra). refs #14353
    
• src/hg/lib/encode/wgEncodeTreatment.sql
  • lines changed 13, context: html, text, full: html, text
    Add table with info about ENCODE treatment terms (from cv.ra). refs #14353
    
• src/hg/lib/gtexGeneBed.as
  • lines changed 15, context: html, text, full: html, text
    First cut loader of GTEX gene track. Enough here to test track display. refs #13504
    
• src/hg/lib/gtexGeneBed.c
  • lines changed 212, context: html, text, full: html, text
    First cut loader of GTEX gene track. Enough here to test track display. refs #13504
    
• src/hg/lib/hui.c
  • lines changed 10, context: html, text, full: html, text
    Fix bad loop over input field meta tables
    
  • lines changed 24, context: html, text, full: html, text
    Renames to fix poor name choice (meta->vocab). refs #14353
    
  • lines changed 3, context: html, text, full: html, text
    Renames to fix poor name choice (meta->vocab). refs #14353
    
  • lines changed 5, context: html, text, full: html, text
    Renames to distinguish ENCODE cv from non-ENCODE table-based vocabularies. refs #14353
    
  • lines changed 9, context: html, text, full: html, text
    Readability changes
    
  • lines changed 31, context: html, text, full: html, text
    Use controlledVocabulary setting for non-ENCODE (table-based) vocabularies (replace briefly used *MetaTables settings)
    
• src/hg/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    Moving sql where-clause sanity checking to library for reuse in CIRM routines.
    
  • lines changed 1, context: html, text, full: html, text
    First cut loader of GTEX gene track. Enough here to test track display. refs #13504
    
• src/hg/lib/sqlSanity.c
  • lines changed 149, context: html, text, full: html, text
    Moving sql where-clause sanity checking to library for reuse in CIRM routines.
    
• src/hg/lib/web.c
  • lines changed 54, context: html, text, full: html, text
    Refactored part of menuBar function into menuBarAddUiVars for reuse with another menu bar.
    
  • lines changed 70, context: html, text, full: html, text
    Refactored a few routines out of the webStartInternal demon for reuse in cdwWebBrowse.
    
  • lines changed 23, context: html, text, full: html, text
    Adding routine to fetch list of formats and their descriptions.
    
• src/hg/makeDb/doc/hg19.txt
  • lines changed 33, context: html, text, full: html, text
    snp142 for hg19 & hg38: User reported missing validation info (#14836);
    Jonathan found that SNP.bcp.gz had been updated 1/30/15, argh. Rebuilt
    snp142{,Common,Flagged,Mult,ExceptionDesc} with changes.
    refs #14836, #14189
    
• src/hg/makeDb/doc/hg38/lastzRuns.txt
  • lines changed 137, context: html, text, full: html, text
    completed capHir1 triMan1 conCri1 apaSpi1 redone rn6 micOch1 swapping criGri1 sorAra2 macEug2 sarhar1 pelSin1 ornAna1 allMis1 colLiv1 anaPla1 melGal1 falChe1 amaVit refs #14560
    
  • lines changed 1268, context: html, text, full: html, text
    finished: rn6 criGri1 mesAur1 sorAra2 sarHar1 alMis1 colLiv1 galGal4 melGal1 falChe1 falPer1 running micOch1 macEug2 apaSpi1 ornAna1 anaPla1 amaVit1 araMac1 pseHum1 melUnd1 ficAlb2 zonAlb1 geoFor1 taeGut2 gadMor1 gasAcu1 oreNil2 tetNig2 neoBri1 takFla1 hapBur1 fr3 astMex refs #14560
    
  • lines changed 178, context: html, text, full: html, text
    begin reruns on chrAsi1 criGri1 eleEdw1 eriEur2 jacJac1 macEug2 mesAur1 sorAra2 tupChi1 refs #14560
    
  • lines changed 286, context: html, text, full: html, text
    done with araMac1 gasAcu1 tetNig2 neoBri1 takFla1 hapBur1 fr3 continuing oreNil2 xenTro7 latCha1 lepOcu1 refs #14560
    
  • lines changed 199, context: html, text, full: html, text
    rerun alignments for chrAsi1 eptFus1 tupChi1 equCab2 eleEdw1 jacJac1 eriEur2 echTel2 mesAur1 sorAra2 macEug2 and done with sarHar1 ornAna1 melGal1 pseHum1 melUnd1 ficAlb2 zonAlb1 geoFor1 taeGut2 gadMor1 gasAcu1 tetNig2 xenTro7 latCha1 lepOcu1refs #14560
    
  • lines changed 13, context: html, text, full: html, text
    done with rerun of criGri1 and done with macEug2 refs #14560
    
• src/hg/makeDb/doc/hg38/reg.txt
  • lines changed 20, context: html, text, full: html, text
    Testing for data issue
    
  • lines changed 12, context: html, text, full: html, text
    Merge branch 'master' into dnase38
    
  • lines changed 23, context: html, text, full: html, text
    Add table with info about ENCODE treatment terms (from cv.ra). refs #14353
    
  • lines changed 40, context: html, text, full: html, text
    Prep for renames. refs #14353
    
  • lines changed 134, context: html, text, full: html, text
    Rename tables for consistency with hg19. refs #14353
    
  • lines changed 26, context: html, text, full: html, text
    Move new DNase tracks to ENCODE Reg supertrack. Compare to CHris' lifted track. refs #14353
    
• src/hg/makeDb/doc/hg38/variation.txt
  • lines changed 31, context: html, text, full: html, text
    snp142 for hg19 & hg38: User reported missing validation info (#14836);
    Jonathan found that SNP.bcp.gz had been updated 1/30/15, argh. Rebuilt
    snp142{,Common,Flagged,Mult,ExceptionDesc} with changes.
    refs #14836, #14189
    
• src/hg/makeDb/doc/nasLar1/initialBuild.txt
  • lines changed 546, context: html, text, full: html, text
    nasLar1 in the pushQ refs #14437
    
• src/hg/makeDb/doc/nasLar1/ucscCompositeAgp.pl
  • lines changed 62, context: html, text, full: html, text
    nasLar1 in the pushQ refs #14437
    
• src/hg/makeDb/doc/nasLar1/unplaced.pl
  • lines changed 48, context: html, text, full: html, text
    nasLar1 in the pushQ refs #14437
    
• src/hg/makeDb/genbank/etc/align.dbs
  • lines changed 1, context: html, text, full: html, text
    Added nasLar1 - Proboscis monkey refs #14437
    
  • lines changed 1, context: html, text, full: html, text
    Added rhiRox1 - Golden snub-nosed monkey refs #14438
    
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 22, context: html, text, full: html, text
    Added rhiRox1; refs #14438
    
• src/hg/makeDb/genbank/etc/hgwdev.dbs
  • lines changed 1, context: html, text, full: html, text
    Added nasLar1 - Proboscis monkey refs #14437
    
  • lines changed 1, context: html, text, full: html, text
    Added rhiRox1 - Golden snub-nosed monkey refs #14438
    
• src/hg/makeDb/genbank/src/lib/gbGenome.c
  • lines changed 2, context: html, text, full: html, text
    Added rhiRox Rhinopithecus roxellana refs #14438
    
• src/hg/makeDb/outside/hgGtexGeneBed/hgGtexGeneBed.c
  • lines changed 242, context: html, text, full: html, text
    First cut loader of GTEX gene track. Enough here to test track display. refs #13504
    
  • lines changed 1, context: html, text, full: html, text
    First cut loader of GTEX gene track. Enough here to test track display. refs #13504
    
  • lines changed 8, context: html, text, full: html, text
    Compute max score, will need this in trackDb. refs #13504
    
• src/hg/makeDb/outside/hgGtexGeneBed/makefile
  • lines changed 4, context: html, text, full: html, text
    First cut loader of GTEX gene track. Enough here to test track display. refs #13504
    
• src/hg/makeDb/schema/all.joiner
  • lines changed 11, context: html, text, full: html, text
    adding nasLar1 refs #14437
    
  • lines changed 3, context: html, text, full: html, text
    add newSequences track tables to tables ignored for eboVir3 refs #14278
    
  • lines changed 7, context: html, text, full: html, text
    add rules for hg38Patch2 tracks refs #14167
    
  • lines changed 3, context: html, text, full: html, text
    Added tables to hg38 tablesIgnored list for GRC patch release; refs #14167
    
• src/hg/makeDb/trackDb/cow/trackDb.chainNet.ra
  • lines changed 6, context: html, text, full: html, text
    override to make matrix match getMatrixLines output
    
• src/hg/makeDb/trackDb/ebola/eboVir3/newSeqs.html
  • lines changed 65, context: html, text, full: html, text
    Adding display conventions section to newSequences track. refs #14278
    
• src/hg/makeDb/trackDb/ebola/eboVir3/trackDb.newSequences.ra
  • lines changed 2, context: html, text, full: html, text
    Changing capitalization of GenBank
    
• src/hg/makeDb/trackDb/ebola/eboVir3/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    removing release tag from newSequences.ra include, refs #14278
    
• src/hg/makeDb/trackDb/horse/trackDb.chainNet.ra
  • lines changed 4, context: html, text, full: html, text
    override to make matrix match getMatrixLines output
    
• src/hg/makeDb/trackDb/human/chainNetPlacental.ra
  • lines changed 6, context: html, text, full: html, text
    replacing bosTau7 chain/net with bosTau8
    
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    More renames for consistency with hg19. refs #14353
    
• src/hg/makeDb/trackDb/human/hg38/uwDnase.html
  • lines changed 2, context: html, text, full: html, text
    Refer to local ENCODE page. refs #14353
    
  • lines changed 51, context: html, text, full: html, text
    Move new DNase tracks to ENCODE Reg supertrack. Compare to CHris' lifted track. refs #14353
    
• src/hg/makeDb/trackDb/human/hg38/uwDnase.ra
  • lines changed 10, context: html, text, full: html, text
    Testing for data issue
    
  • lines changed 1, context: html, text, full: html, text
    Add treatment vocab table
    
  • lines changed 95, context: html, text, full: html, text
    Eliminate unneeded duplicate tables. refs #14353
    
  • lines changed 1, context: html, text, full: html, text
    Fix vocab setting. refs #14353
    
  • lines changed 6, context: html, text, full: html, text
    Use controlledVocabulary setting for non-ENCODE (table-based) vocabularies (replace briefly used *MetaTables settings)
    
  • lines changed 868, context: html, text, full: html, text
    Rename tables for consistency with hg19. refs #14353
    
  • lines changed 290, context: html, text, full: html, text
    Change default ordering of views (Peak, Hotspot, Signal). refs #14733
    
  • lines changed 3246, context: html, text, full: html, text
    Move new DNase tracks to ENCODE Reg supertrack. Compare to CHris' lifted track. refs #14353
    
• src/hg/makeDb/trackDb/human/hg38/uwDnaseClusters.html
  • lines changed 1, context: html, text, full: html, text
    Refer to local ENCODE page. refs #14353
    
  • lines changed 37, context: html, text, full: html, text
    Move new DNase tracks to ENCODE Reg supertrack. Compare to CHris' lifted track. refs #14353
    
• src/hg/makeDb/trackDb/human/hg38/uwDnaseSignal.html
  • lines changed 2, context: html, text, full: html, text
    Refer to local ENCODE page. refs #14353
    
  • lines changed 45, context: html, text, full: html, text
    Move new DNase tracks to ENCODE Reg supertrack. Compare to CHris' lifted track. refs #14353
    
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg.ra
  • lines changed 211, context: html, text, full: html, text
    Added TFBS and DNase stanzas to correspond to lifted tracks
    
  • lines changed 21, context: html, text, full: html, text
    More renames for consistency with hg19. refs #14353
    
  • lines changed 23, context: html, text, full: html, text
    Tweak DNase lifted track config.
    
  • lines changed 2, context: html, text, full: html, text
    Tweak priorities and label.
    
  • lines changed 1, context: html, text, full: html, text
    Tweak pri
    
• src/hg/makeDb/trackDb/human/hg38/wgEncodeRegDnase.html
  • lines changed 51, context: html, text, full: html, text
    Move new DNase tracks to ENCODE Reg supertrack. Compare to CHris' lifted track. refs #14353
    
• src/hg/makeDb/trackDb/human/hg38/wgEncodeRegDnase.ra
  • lines changed 3243, context: html, text, full: html, text
    Move new DNase tracks to ENCODE Reg supertrack. Compare to CHris' lifted track. refs #14353
    
  • lines changed 3, context: html, text, full: html, text
    Tweak priorities and label.
    
  • lines changed 1, context: html, text, full: html, text
    Label tweak.
    
• src/hg/makeDb/trackDb/human/hg38/wgEncodeRegDnaseClustered.html
  • lines changed 37, context: html, text, full: html, text
    Move new DNase tracks to ENCODE Reg supertrack. Compare to CHris' lifted track. refs #14353
    
• src/hg/makeDb/trackDb/human/hg38/wgEncodeRegDnaseSignal.html
  • lines changed 45, context: html, text, full: html, text
    Move new DNase tracks to ENCODE Reg supertrack. Compare to CHris' lifted track. refs #14353
    
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.placentalsChainNet.ra
  • lines changed 6, context: html, text, full: html, text
    replacing bosTau7 chain/net with bosTau8
    
• src/hg/makeDb/trackDb/rhinopithecus/rhiRox1/gap.html
  • lines changed 1, context: html, text, full: html, text
    now using the correct sequence for this build refs #14438
    
• src/hg/makeDb/trackDb/rhinopithecus/rhiRox1/gold.html
  • lines changed 2, context: html, text, full: html, text
    now using the correct sequence for this build refs #14438
    
• src/hg/oneShot/getVersionedCssJs/getVersionedCssJs.c
  • lines changed 73, context: html, text, full: html, text
    Utility to help transport versioned .css and .js to cirm-01.
    
• src/hg/oneShot/getVersionedCssJs/makefile
  • lines changed 3, context: html, text, full: html, text
    Utility to help transport versioned .css and .js to cirm-01.
    
• src/hg/oneShot/tryGtexBoxPlot/tryGtexBoxPlot.c
  • lines changed 29, context: html, text, full: html, text
    Libify graphics routine used for GTEX bar graph display. refs #13504
    
• src/hg/utils/automation/makeDownloads.pl
  • lines changed 6, context: html, text, full: html, text
    adding <db>.chrom.sizes to the bigZips downloads refs #11248
    
• src/inc/common.h
  • lines changed 3, context: html, text, full: html, text
    Adding isNumericString function.
    
• src/inc/hash.h
  • lines changed 4, context: html, text, full: html, text
    Adding routine for sorting elements from a hashInt type hash.
    
• src/inc/rql.h
  • lines changed 3, context: html, text, full: html, text
    Adding a helper function to parse from a string as opposed to a file.
    
• src/inc/tagStorm.h
  • lines changed 1, context: html, text, full: html, text
    Updating comment.
    
  • lines changed 4, context: html, text, full: html, text
    Added the option to append new information to the existing stanza for tagStormJoinTab.c
    
  • lines changed 8, context: html, text, full: html, text
    Updating some old tagTree names to be tagStorm. Adding tagStormCountTagVals function that summarizes values of a given tag in storm.
    
  • lines changed 3, context: html, text, full: html, text
    Moving tagListIncludingParents to library.
    
  • lines changed 1, context: html, text, full: html, text
    Fixed transposed words in symbol in comment.
    
• src/lib/bbiWrite.c
  • lines changed 2, context: html, text, full: html, text
    In bbiChromSizesFromFile, use netLineFileOpen instead of lineFileOpen so we can open URLs as well as files.
    refs #14857
    
• src/lib/common.c
  • lines changed 8, context: html, text, full: html, text
    Adding isNumericString function.
    
• src/lib/hash.c
  • lines changed 9, context: html, text, full: html, text
    Adding routine for sorting elements from a hashInt type hash.
    
• src/lib/rqlParse.c
  • lines changed 4, context: html, text, full: html, text
    Fixing bug in inequalities.
    
  • lines changed 9, context: html, text, full: html, text
    Adding a helper function to parse from a string as opposed to a file.
    
• src/lib/tagStorm.c
  • lines changed 13, context: html, text, full: html, text
    Added the option to append new information to the existing stanza for tagStormJoinTab.c
    
  • lines changed 32, context: html, text, full: html, text
    Updating some old tagTree names to be tagStorm. Adding tagStormCountTagVals function that summarizes values of a given tag in storm.
    
  • lines changed 23, context: html, text, full: html, text
    Moving tagListIncludingParents to library.
    
• src/lib/udc.c
  • lines changed 45, context: html, text, full: html, text
    fix a bug in UDC cache when strings between slashes in a URL are longer
    than 255 characters so they can't be made into a directory. In this
    case we know make a SHA1 hash of the long string and use that instead.
    
• src/oneShot/randString/makefile
  • lines changed 3, context: html, text, full: html, text
    using dev/random to generate seed to drand48 to obtain random strings refs #14863
    
• src/oneShot/randString/randString.c
  • lines changed 82, context: html, text, full: html, text
    using dev/random to generate seed to drand48 to obtain random strings refs #14863
    
• src/tagStorm/tagStormJoinTab/tagStormJoinTab.c
  • lines changed 20, context: html, text, full: html, text
    Added the option to append new information to the existing stanza for tagStormJoinTab.c
    
• src/utils/qa/qaAutoTrack.sh
  • lines changed 283, context: html, text, full: html, text
    New script to QA autopushed tracks. QA inlucdes last update and coverage info. refs #12561
    
  • lines changed 10, context: html, text, full: html, text
    Fixing output for multi-table tracks like isca. Fixing issues with if statement where it would fail if there was more that one prevLogFile
    
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    v313 preview1 refs #14821
    

• lines changed: 26249
• files changed: 211