All File Changes

v304_preview to v304_preview2 (2014-07-28 to 2014-08-04) v304

• src/hg/encode3/eap/eapSchedule/eapSchedule.c
  • lines changed 38, context: html, text, full: html, text
    Adding idFile option to restrict action to files in list of IDs.
• src/hg/encode3/encodeDataWarehouse/utils/edwBamFilter/edwBamFilter.c
  • lines changed 2, context: html, text, full: html, text
    Adding 'cen' prefix to what sponge filter takes out.
• src/hg/hgGenome/import.c
  • lines changed 1, context: html, text, full: html, text
    Ugh, forgot to remove external dependencies on jsWriteFunctions in b7b15a261.
• src/hg/hgGenome/mainPage.c
  • lines changed 2, context: html, text, full: html, text
    Ugh, forgot to remove external dependencies on jsWriteFunctions in b7b15a261.
• src/hg/hgLogin/hgLogin.c
  • lines changed 1, context: html, text, full: html, text
    hgLogin evidently needs setUdcCacheDir refs #9859
• src/hg/hgTables/mainPage.c
  • lines changed 1, context: html, text, full: html, text
    Ugh, forgot to remove external dependencies on jsWriteFunctions in b7b15a261.
• src/hg/hgTracks/bamTrack.c
  • lines changed 1, context: html, text, full: html, text
    Two problems noticed by Angie in code review. Redmine #13704.
• src/hg/hgTracks/hgTracks.c
  • lines changed 50, context: html, text, full: html, text
    output the list of visible tracks to error_log #13626
• src/hg/hgTracks/hgTracks.h
  • lines changed 1, context: html, text, full: html, text
    changing jRepeatMethods to rmskJoinedMethods refs #13706
• src/hg/hgTracks/joinedRmskTrack.c
  • lines changed 1182, context: html, text, full: html, text
    rename file to be more consistent refs #13706
• src/hg/hgTracks/makefile
  • lines changed 3, context: html, text, full: html, text
    changing file name from joinedRmskTrack to rmskJoinedTrack refs #13706
• src/hg/hgTracks/rmskJoinedTrack.c
  • lines changed 1182, context: html, text, full: html, text
    rename file to be more consistent refs #13706
  • lines changed 31, context: html, text, full: html, text
    changing methods names to be more consistent and formatting blank space after function calls() refs #13706
  • lines changed 15, context: html, text, full: html, text
    trying a color palette from snakeTrack display refs #13706
• src/hg/hgTracks/simpleTracks.c
  • lines changed 6, context: html, text, full: html, text
    Two problems noticed by Angie in code review. Redmine #13704.
  • lines changed 3, context: html, text, full: html, text
    changing jRepeatMethods to rmskJoinedMethods refs #13706
• src/hg/hgTracks/variation.c
  • lines changed 2, context: html, text, full: html, text
    When showing SNPs' alleles on the reference genome + strand, if the userclicks "reverse" (revCmplDisp) show them on the - strand like other
    base displays (Base Position track, pgSnp/VCF, multiz). refs #13694
    
• src/hg/hgVai/hgVai.c
  • lines changed 4, context: html, text, full: html, text
    Added jsMakeSetClearContainer / jsEndContainer to jsHelper.c, and apppliedthem to a couple long lists of checkboxes in hgVai. While at it, I moved
    jsHelper.c's javascript-inlined-in-HTML out to a new .js file, jsHelper.js.
    
• src/hg/hgc/hgc.c
  • lines changed 6, context: html, text, full: html, text
    Apply ENCODE summary track click handlers more generally to tracks based on root name
• src/hg/hgc/joinedRmskClick.c
  • lines changed 410, context: html, text, full: html, text
    change file name joinedRmskClick to rmskJoinedClick.c refs #13706
• src/hg/hgc/makefile
  • lines changed 3, context: html, text, full: html, text
    change file name joinedRmskClick to rmskJoinedClick.c refs #13706
• src/hg/hgc/rmskJoinedClick.c
  • lines changed 410, context: html, text, full: html, text
    change file name joinedRmskClick to rmskJoinedClick.c refs #13706
• src/hg/hgc/vcfClick.c
  • lines changed 4, context: html, text, full: html, text
    David pointed out how confusing it is to see the 'Haplotype sorting order' optionto change the central variant, when haplotype clustering is disabled. So don't
    show the option unless haplotype clustering is enabled.
    
  • lines changed 10, context: html, text, full: html, text
    David pointed out that it is inappropriate to show Hardy-Weinberg equilibriumfrequencies on the VCF details page unless the VCF data are from a population
    study -- so at this point, pretty much only 1000 Genomes. So I added a new
    trackDb setting for vcf/vcfTabix, showHardyWeinberg, and added it to the
    1000 Genomes track def.
    
• src/hg/htdocs/FAQ/FAQreleases.html
  • lines changed 2, context: html, text, full: html, text
    Updating docs for rn6 release, refs #13578
  • lines changed 2, context: html, text, full: html, text
    Fixing assembly reelase dates, refs #13578
• src/hg/htdocs/goldenPath/credits.html
  • lines changed 2, context: html, text, full: html, text
    Updating docs for rn6 release, refs #13578
  • lines changed 1, context: html, text, full: html, text
    Fixing assembly version number, refs #13578
• src/hg/htdocs/goldenPath/help/customTrackText.html
  • lines changed 4, context: html, text, full: html, text
    Adding note about Dropbox not working
• src/hg/htdocs/goldenPath/help/gbib.html
  • lines changed 8, context: html, text, full: html, text
    Edits based on code review, refs #13604
• src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.html
  • lines changed 26, context: html, text, full: html, text
    Documentation of new trackDb settings for initial config of VCF tracks.
• src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.html
  • lines changed 26, context: html, text, full: html, text
    Documentation of new trackDb settings for initial config of VCF tracks.
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 68, context: html, text, full: html, text
    Documentation of new trackDb settings for initial config of VCF tracks.
• src/hg/htdocs/goldenPath/help/vcf.html
  • lines changed 14, context: html, text, full: html, text
    Documentation of new trackDb settings for initial config of VCF tracks.
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 33, context: html, text, full: html, text
    Updating docs for rn6 release, refs #13578
• src/hg/htdocs/indexNews.html
  • lines changed 49, context: html, text, full: html, text
    Updating docs for rn6 release, refs #13578
• src/hg/htdocs/staff.html
  • lines changed 12, context: html, text, full: html, text
    removed Tim & Chin. Changed Karen's last name
  • lines changed 4, context: html, text, full: html, text
    removed Morgan. Put everyone in alumni section.
  • lines changed 2, context: html, text, full: html, text
    added GBiB to Max's description
• src/hg/inc/cv.h
  • lines changed 1, context: html, text, full: html, text
    Adding CV_TERM_TREATMENT
  • lines changed 1, context: html, text, full: html, text
    Filling in another metadata type for use by regulation cluster tracks
• src/hg/inc/jsHelper.h
  • lines changed 11, context: html, text, full: html, text
    Removed unused function jsMakeSetClearButton (which should remain unused -- it does a form submit!).
  • lines changed 7, context: html, text, full: html, text
    Added jsMakeSetClearContainer / jsEndContainer to jsHelper.c, and apppliedthem to a couple long lists of checkboxes in hgVai. While at it, I moved
    jsHelper.c's javascript-inlined-in-HTML out to a new .js file, jsHelper.js.
    
  • lines changed 5, context: html, text, full: html, text
    Ugh, forgot to remove external dependencies on jsWriteFunctions in b7b15a261.
• src/hg/inc/mdb.h
  • lines changed 1, context: html, text, full: html, text
    Extend regCluster tools to add metadata to DNase clusters. Update DNase clusters table to include metadata (per Angie request for VAI support). refs #13490
• src/hg/inc/vcfUi.h
  • lines changed 2, context: html, text, full: html, text
    David pointed out that it is inappropriate to show Hardy-Weinberg equilibriumfrequencies on the VCF details page unless the VCF data are from a population
    study -- so at this point, pretty much only 1000 Genomes. So I added a new
    trackDb setting for vcf/vcfTabix, showHardyWeinberg, and added it to the
    1000 Genomes track def.
    
• src/hg/js/jsHelper.js
  • lines changed 121, context: html, text, full: html, text
    Added jsMakeSetClearContainer / jsEndContainer to jsHelper.c, and apppliedthem to a couple long lists of checkboxes in hgVai. While at it, I moved
    jsHelper.c's javascript-inlined-in-HTML out to a new .js file, jsHelper.js.
    
  • lines changed 4, context: html, text, full: html, text
    Oops, left in some console.log calls in jsHelper.js -- removing them.
• src/hg/js/makefile
  • lines changed 1, context: html, text, full: html, text
    Added jsHelper.js.
• src/hg/lib/haplotypes.c
  • lines changed 3, context: html, text, full: html, text
    Addressing Aravinda's concern with text about haplotype phasing being imputed.
• src/hg/lib/hui.c
  • lines changed 5, context: html, text, full: html, text
    be more selective about when calling a javascript routine that isn'talways loaded. Thanks Tim!
    
  • lines changed 1, context: html, text, full: html, text
    super track bigBed was trying to find table info does not exist refs #13713
• src/hg/lib/jsHelper.c
  • lines changed 42, context: html, text, full: html, text
    Removed unused function jsMakeSetClearButton (which should remain unused -- it does a form submit!).
  • lines changed 120, context: html, text, full: html, text
    Added jsMakeSetClearContainer / jsEndContainer to jsHelper.c, and apppliedthem to a couple long lists of checkboxes in hgVai. While at it, I moved
    jsHelper.c's javascript-inlined-in-HTML out to a new .js file, jsHelper.js.
    
  • lines changed 2, context: html, text, full: html, text
    Ugh, forgot to remove external dependencies on jsWriteFunctions in b7b15a261.
• src/hg/makeDb/doc/encodeRegHg19.txt
  • lines changed 12, context: html, text, full: html, text
    Extend regCluster tools to add metadata to DNase clusters. Update DNase clusters table to include metadata (per Angie request for VAI support). refs #13490
• src/hg/makeDb/doc/hg38.txt
  • lines changed 121, context: html, text, full: html, text
    skunk project with vervet.
• src/hg/makeDb/genbank/etc/hgwbeta.dbs
  • lines changed 2, context: html, text, full: html, text
    Adding rn6 to Genbank updates for hgwbeta, moving rn5 down to lower priority list, refs #13578
• src/hg/makeDb/genbank/etc/ignore.idx
  • lines changed 1, context: html, text, full: html, text
    add something new to ignore.idx
  • lines changed 1, context: html, text, full: html, text
    oops, mispelled GenBank
• src/hg/makeDb/genbank/etc/rr.dbs
  • lines changed 2, context: html, text, full: html, text
    Adding rn6 to rr genbank update list, refs #13578
• src/hg/makeDb/trackDb/baboon/papAnu2/defaultPriority.ra
  • lines changed 26, context: html, text, full: html, text
    Made changes to fix track ordering in primate assemblies; tracks visible by default should appear first and in alphabetic order; all other tracks should appear second and in alphabetic order (redmine #7343)
• src/hg/makeDb/trackDb/baboon/papAnu2/trackDb.ra
  • lines changed 7, context: html, text, full: html, text
    Made changes to fix track ordering in primate assemblies; tracks visible by default should appear first and in alphabetic order; all other tracks should appear second and in alphabetic order (redmine #7343)
• src/hg/makeDb/trackDb/baboon/papHam1/defaultPriority.ra
  • lines changed 17, context: html, text, full: html, text
    Made changes to fix track ordering in primate assemblies; tracks visible by default should appear first and in alphabetic order; all other tracks should appear second and in alphabetic order (redmine #7343)
• src/hg/makeDb/trackDb/baboon/papHam1/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    Made changes to fix track ordering in primate assemblies; tracks visible by default should appear first and in alphabetic order; all other tracks should appear second and in alphabetic order (redmine #7343)
• src/hg/makeDb/trackDb/bushbaby/otoGar3/defaultPriority.ra
  • lines changed 20, context: html, text, full: html, text
    Made changes to fix track ordering in primate assemblies; tracks visible by default should appear first and in alphabetic order; all other tracks should appear second and in alphabetic order (redmine #7343)
• src/hg/makeDb/trackDb/bushbaby/otoGar3/trackDb.ra
  • lines changed 11, context: html, text, full: html, text
    Made changes to fix track ordering in primate assemblies; tracks visible by default should appear first and in alphabetic order; all other tracks should appear second and in alphabetic order (redmine #7343)
• src/hg/makeDb/trackDb/chimp/panTro1/defaultPriority.ra
  • lines changed 31, context: html, text, full: html, text
    Made changes to fix track ordering in primate assemblies; tracks visible by default should appear first and in alphabetic order; all other tracks should appear second and in alphabetic order (redmine #7343)
• src/hg/makeDb/trackDb/chimp/panTro1/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    Made changes to fix track ordering in primate assemblies; tracks visible by default should appear first and in alphabetic order; all other tracks should appear second and in alphabetic order (redmine #7343)
• src/hg/makeDb/trackDb/chimp/panTro2/defaultPriority.ra
  • lines changed 41, context: html, text, full: html, text
    Made changes to fix track ordering in primate assemblies; tracks visible by default should appear first and in alphabetic order; all other tracks should appear second and in alphabetic order (redmine #7343)
• src/hg/makeDb/trackDb/chimp/panTro2/trackDb.ra
  • lines changed 4, context: html, text, full: html, text
    Made changes to fix track ordering in primate assemblies; tracks visible by default should appear first and in alphabetic order; all other tracks should appear second and in alphabetic order (redmine #7343)
• src/hg/makeDb/trackDb/chimp/panTro3/defaultPriority.ra
  • lines changed 33, context: html, text, full: html, text
    Made changes to fix track ordering in primate assemblies; tracks visible by default should appear first and in alphabetic order; all other tracks should appear second and in alphabetic order (redmine #7343)
• src/hg/makeDb/trackDb/chimp/panTro3/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    Made changes to fix track ordering in primate assemblies; tracks visible by default should appear first and in alphabetic order; all other tracks should appear second and in alphabetic order (redmine #7343)
• src/hg/makeDb/trackDb/chimp/panTro4/defaultPriority.ra
  • lines changed 30, context: html, text, full: html, text
    Made changes to fix track ordering in primate assemblies; tracks visible by default should appear first and in alphabetic order; all other tracks should appear second and in alphabetic order (redmine #7343)
• src/hg/makeDb/trackDb/chimp/panTro4/trackDb.ra
  • lines changed 9, context: html, text, full: html, text
    Made changes to fix track ordering in primate assemblies; tracks visible by default should appear first and in alphabetic order; all other tracks should appear second and in alphabetic order (redmine #7343)
• src/hg/makeDb/trackDb/gibbon/nomLeu1/defaultPriority.ra
  • lines changed 21, context: html, text, full: html, text
    Made changes to fix track ordering in primate assemblies; tracks visible by default should appear first and in alphabetic order; all other tracks should appear second and in alphabetic order (redmine #7343)
• src/hg/makeDb/trackDb/gibbon/nomLeu1/trackDb.ra
  • lines changed 6, context: html, text, full: html, text
    Made changes to fix track ordering in primate assemblies; tracks visible by default should appear first and in alphabetic order; all other tracks should appear second and in alphabetic order (redmine #7343)
• src/hg/makeDb/trackDb/gibbon/nomLeu2/defaultPriority.ra
  • lines changed 24, context: html, text, full: html, text
    Made changes to fix track ordering in primate assemblies; tracks visible by default should appear first and in alphabetic order; all other tracks should appear second and in alphabetic order (redmine #7343)
• src/hg/makeDb/trackDb/gibbon/nomLeu2/trackDb.ra
  • lines changed 15, context: html, text, full: html, text
    Made changes to fix track ordering in primate assemblies; tracks visible by default should appear first and in alphabetic order; all other tracks should appear second and in alphabetic order (redmine #7343)
• src/hg/makeDb/trackDb/gibbon/nomLeu3/defaultPriority.ra
  • lines changed 24, context: html, text, full: html, text
    Made changes to fix track ordering in primate assemblies; tracks visible by default should appear first and in alphabetic order; all other tracks should appear second and in alphabetic order (redmine #7343)
• src/hg/makeDb/trackDb/gibbon/nomLeu3/trackDb.ra
  • lines changed 15, context: html, text, full: html, text
    Made changes to fix track ordering in primate assemblies; tracks visible by default should appear first and in alphabetic order; all other tracks should appear second and in alphabetic order (redmine #7343)
• src/hg/makeDb/trackDb/gorilla/gorGor3/defaultPriority.ra
  • lines changed 27, context: html, text, full: html, text
    Made changes to fix track ordering in primate assemblies; tracks visible by default should appear first and in alphabetic order; all other tracks should appear second and in alphabetic order (redmine #7343)
• src/hg/makeDb/trackDb/gorilla/gorGor3/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    Made changes to fix track ordering in primate assemblies; tracks visible by default should appear first and in alphabetic order; all other tracks should appear second and in alphabetic order (redmine #7343)
• src/hg/makeDb/trackDb/human/cloneEnd.trackDb.ra
  • lines changed 185, context: html, text, full: html, text
    first pass at a clone end track refs #13713
  • lines changed 48, context: html, text, full: html, text
    with library identification refs #13713
  • lines changed 24, context: html, text, full: html, text
    now with overlap coverage and indicating multiple mappings refs #13713
• src/hg/makeDb/trackDb/human/cloneEndSuper.html
  • lines changed 16, context: html, text, full: html, text
    adding clone end description refs #13713
• src/hg/makeDb/trackDb/human/hg16/defaultPriority.ra
  • lines changed 53, context: html, text, full: html, text
    Made changes to fix track ordering in human assemblies; tracks visible by default should appear first and in alphabetic order (except for UCSC Genes which should appear first); all other tracks appear second and in alphabetic order (redmine #7343)
• src/hg/makeDb/trackDb/human/hg16/trackDb.encode.ra
  • lines changed 30, context: html, text, full: html, text
    Made changes to fix track ordering in human assemblies; tracks visible by default should appear first and in alphabetic order (except for UCSC Genes which should appear first); all other tracks appear second and in alphabetic order (redmine #7343)
• src/hg/makeDb/trackDb/human/hg16/trackDb.ra
  • lines changed 14, context: html, text, full: html, text
    Made changes to fix track ordering in human assemblies; tracks visible by default should appear first and in alphabetic order (except for UCSC Genes which should appear first); all other tracks appear second and in alphabetic order (redmine #7343)
• src/hg/makeDb/trackDb/human/hg17/defaultPriority.ra
  • lines changed 35, context: html, text, full: html, text
    Made changes to fix track ordering in human assemblies; tracks visible by default should appear first and in alphabetic order (except for UCSC Genes which should appear first); all other tracks appear second and in alphabetic order (redmine #7343)
• src/hg/makeDb/trackDb/human/hg17/trackDb.encode.ra
  • lines changed 48, context: html, text, full: html, text
    Made changes to fix track ordering in human assemblies; tracks visible by default should appear first and in alphabetic order (except for UCSC Genes which should appear first); all other tracks appear second and in alphabetic order (redmine #7343)
• src/hg/makeDb/trackDb/human/hg17/trackDb.instinct.ra
  • lines changed 5, context: html, text, full: html, text
    Made changes to fix track ordering in human assemblies; tracks visible by default should appear first and in alphabetic order (except for UCSC Genes which should appear first); all other tracks appear second and in alphabetic order (redmine #7343)
• src/hg/makeDb/trackDb/human/hg17/trackDb.ra
  • lines changed 23, context: html, text, full: html, text
    Made changes to fix track ordering in human assemblies; tracks visible by default should appear first and in alphabetic order (except for UCSC Genes which should appear first); all other tracks appear second and in alphabetic order (redmine #7343)
• src/hg/makeDb/trackDb/human/hg18/defaultPriority.ra
  • lines changed 23, context: html, text, full: html, text
    Made changes to fix track ordering in human assemblies; tracks visible by default should appear first and in alphabetic order (except for UCSC Genes which should appear first); all other tracks appear second and in alphabetic order (redmine #7343)
• src/hg/makeDb/trackDb/human/hg18/trackDb.encodeCompAndVar.ra
  • lines changed 3, context: html, text, full: html, text
    Made changes to fix track ordering in human assemblies; tracks visible by default should appear first and in alphabetic order (except for UCSC Genes which should appear first); all other tracks appear second and in alphabetic order (redmine #7343)
• src/hg/makeDb/trackDb/human/hg18/trackDb.encodeGenes.ra
  • lines changed 2, context: html, text, full: html, text
    Made changes to fix track ordering in human assemblies; tracks visible by default should appear first and in alphabetic order (except for UCSC Genes which should appear first); all other tracks appear second and in alphabetic order (redmine #7343)
• src/hg/makeDb/trackDb/human/hg18/trackDb.encodeTxLevels.ra
  • lines changed 1, context: html, text, full: html, text
    Made changes to fix track ordering in human assemblies; tracks visible by default should appear first and in alphabetic order (except for UCSC Genes which should appear first); all other tracks appear second and in alphabetic order (redmine #7343)
• src/hg/makeDb/trackDb/human/hg18/trackDb.ra
  • lines changed 9, context: html, text, full: html, text
    Made changes to fix track ordering in human assemblies; tracks visible by default should appear first and in alphabetic order (except for UCSC Genes which should appear first); all other tracks appear second and in alphabetic order (redmine #7343)
• src/hg/makeDb/trackDb/human/hg19/defaultPriority.ra
  • lines changed 46, context: html, text, full: html, text
    Made changes to fix track ordering in human assemblies; tracks visible by default should appear first and in alphabetic order (except for UCSC Genes which should appear first); all other tracks appear second and in alphabetic order (redmine #7343)
• src/hg/makeDb/trackDb/human/hg19/peptideAtlas.html
  • lines changed 3, context: html, text, full: html, text
    Committing last year's exploratory work for proteomics, expecting updates ahead of HUPO 2014 in October
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    David pointed out that it is inappropriate to show Hardy-Weinberg equilibriumfrequencies on the VCF details page unless the VCF data are from a population
    study -- so at this point, pretty much only 1000 Genomes. So I added a new
    trackDb setting for vcf/vcfTabix, showHardyWeinberg, and added it to the
    1000 Genomes track def.
    
  • lines changed 9, context: html, text, full: html, text
    Made changes to fix track ordering in human assemblies; tracks visible by default should appear first and in alphabetic order (except for UCSC Genes which should appear first); all other tracks appear second and in alphabetic order (redmine #7343)
  • lines changed 12, context: html, text, full: html, text
    Committing last year's exploratory work for proteomics, expecting updates ahead of HUPO 2014 in October
• src/hg/makeDb/trackDb/human/hg38/defaultPriority.ra
  • lines changed 38, context: html, text, full: html, text
    Made changes to fix track ordering in human assemblies; tracks visible by default should appear first and in alphabetic order (except for UCSC Genes which should appear first); all other tracks appear second and in alphabetic order (redmine #7343)
• src/hg/makeDb/trackDb/human/hg38/trackDb.7way.ra
  • lines changed 1, context: html, text, full: html, text
    Made changes to fix track ordering in human assemblies; tracks visible by default should appear first and in alphabetic order (except for UCSC Genes which should appear first); all other tracks appear second and in alphabetic order (redmine #7343)
  • lines changed 3, context: html, text, full: html, text
    shorter shor labels refs #13300
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 13, context: html, text, full: html, text
    Made changes to fix track ordering in human assemblies; tracks visible by default should appear first and in alphabetic order (except for UCSC Genes which should appear first); all other tracks appear second and in alphabetic order (redmine #7343)
• src/hg/makeDb/trackDb/human/trackDb.encode.ra
  • lines changed 27, context: html, text, full: html, text
    Made changes to fix track ordering in human assemblies; tracks visible by default should appear first and in alphabetic order (except for UCSC Genes which should appear first); all other tracks appear second and in alphabetic order (redmine #7343)
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    first pass at a clone end track refs #13713
• src/hg/makeDb/trackDb/joinedRmsk.html
  • lines changed 17, context: html, text, full: html, text
    trying a color palette from snakeTrack display refs #13706
• src/hg/makeDb/trackDb/marmoset/calJac1/defaultPriority.ra
  • lines changed 38, context: html, text, full: html, text
    Made changes to fix track ordering in primate assemblies; tracks visible by default should appear first and in alphabetic order; all other tracks should appear second and in alphabetic order (redmine #7343)
• src/hg/makeDb/trackDb/marmoset/calJac1/trackDb.ra
  • lines changed 7, context: html, text, full: html, text
    Made changes to fix track ordering in primate assemblies; tracks visible by default should appear first and in alphabetic order; all other tracks should appear second and in alphabetic order (redmine #7343)
• src/hg/makeDb/trackDb/marmoset/calJac3/defaultPriority.ra
  • lines changed 32, context: html, text, full: html, text
    Made changes to fix track ordering in primate assemblies; tracks visible by default should appear first and in alphabetic order; all other tracks should appear second and in alphabetic order (redmine #7343)
• src/hg/makeDb/trackDb/marmoset/calJac3/trackDb.ra
  • lines changed 11, context: html, text, full: html, text
    Made changes to fix track ordering in primate assemblies; tracks visible by default should appear first and in alphabetic order; all other tracks should appear second and in alphabetic order (redmine #7343)
• src/hg/makeDb/trackDb/mouse/FaceBase24SampleTypesAvg.html
  • lines changed 2, context: html, text, full: html, text
    removed <body> tags per code review #13708
• src/hg/makeDb/trackDb/mouse/mm10/defaultPriority.ra
  • lines changed 6, context: html, text, full: html, text
    Fixed ordering of mm9 default gene tracks; fixed organization in mm10 file (redmine #7343)
  • lines changed 23, context: html, text, full: html, text
    Made changes to fix track ordering in mouse assemblies; tracks visible by default should appear first and in alphabetic order (except for UCSC Genes which appears first); all other tracks appear second and in alphabetic order (redmine #7343)
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
  • lines changed 53, context: html, text, full: html, text
    Added Retroposed Genes V5 track.
  • lines changed 8, context: html, text, full: html, text
    Made changes to fix track ordering in mouse assemblies; tracks visible by default should appear first and in alphabetic order (except for UCSC Genes which appears first); all other tracks appear second and in alphabetic order (redmine #7343)
• src/hg/makeDb/trackDb/mouse/mm10/ucscRetroAli5.html
  • lines changed 147, context: html, text, full: html, text
    Added RetroFinder V5 track description.
• src/hg/makeDb/trackDb/mouse/mm7/defaultPriority.ra
  • lines changed 41, context: html, text, full: html, text
    Made changes to fix track ordering in mouse assemblies; tracks visible by default should appear first and in alphabetic order (except for UCSC Genes which appears first); all other tracks appear second and in alphabetic order (redmine #7343)
• src/hg/makeDb/trackDb/mouse/mm7/trackDb.ra
  • lines changed 4, context: html, text, full: html, text
    Made changes to fix track ordering in mouse assemblies; tracks visible by default should appear first and in alphabetic order (except for UCSC Genes which appears first); all other tracks appear second and in alphabetic order (redmine #7343)
• src/hg/makeDb/trackDb/mouse/mm8/defaultPriority.ra
  • lines changed 47, context: html, text, full: html, text
    Made changes to fix track ordering in mouse assemblies; tracks visible by default should appear first and in alphabetic order (except for UCSC Genes which appears first); all other tracks appear second and in alphabetic order (redmine #7343)
• src/hg/makeDb/trackDb/mouse/mm8/trackDb.ra
  • lines changed 10, context: html, text, full: html, text
    Made changes to fix track ordering in mouse assemblies; tracks visible by default should appear first and in alphabetic order (except for UCSC Genes which appears first); all other tracks appear second and in alphabetic order (redmine #7343)
• src/hg/makeDb/trackDb/mouse/mm9/defaultPriority.ra
  • lines changed 28, context: html, text, full: html, text
    Fixed ordering of mm9 default gene tracks; fixed organization in mm10 file (redmine #7343)
  • lines changed 6, context: html, text, full: html, text
    Made some additional mm9 ordering changes (redmine #7343)
  • lines changed 18, context: html, text, full: html, text
    Made changes to fix track ordering in mouse assemblies; tracks visible by default should appear first and in alphabetic order (except for UCSC Genes which appears first); all other tracks appear second and in alphabetic order (redmine #7343)
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    Fixed ordering of mm9 default gene tracks; fixed organization in mm10 file (redmine #7343)
  • lines changed 21, context: html, text, full: html, text
    Made changes to fix track ordering in mouse assemblies; tracks visible by default should appear first and in alphabetic order (except for UCSC Genes which appears first); all other tracks appear second and in alphabetic order (redmine #7343)
• src/hg/makeDb/trackDb/mouseLemur/micMur1/defaultPriority.ra
  • lines changed 15, context: html, text, full: html, text
    Made changes to fix track ordering in primate assemblies; tracks visible by default should appear first and in alphabetic order; all other tracks should appear second and in alphabetic order (redmine #7343)
• src/hg/makeDb/trackDb/mouseLemur/micMur1/trackDb.ra
  • lines changed 11, context: html, text, full: html, text
    Made changes to fix track ordering in primate assemblies; tracks visible by default should appear first and in alphabetic order; all other tracks should appear second and in alphabetic order (redmine #7343)
• src/hg/makeDb/trackDb/orangutan/ponAbe2/defaultPriority.ra
  • lines changed 32, context: html, text, full: html, text
    Made changes to fix track ordering in primate assemblies; tracks visible by default should appear first and in alphabetic order; all other tracks should appear second and in alphabetic order (redmine #7343)
• src/hg/makeDb/trackDb/orangutan/ponAbe2/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    Made changes to fix track ordering in primate assemblies; tracks visible by default should appear first and in alphabetic order; all other tracks should appear second and in alphabetic order (redmine #7343)
• src/hg/makeDb/trackDb/pika/ochPri3/description.html
  • lines changed 1, context: html, text, full: html, text
    Updated usage link per code review (redmine #13645)
• src/hg/makeDb/trackDb/rat/rn3/defaultPriority.ra
  • lines changed 46, context: html, text, full: html, text
    Made changes to fix track ordering in rat assemblies; tracks visible by default should appear first and in alphabetic order; all other tracks should appear second and in alphabetic order (redmine #7343)
• src/hg/makeDb/trackDb/rat/rn3/trackDb.ra
  • lines changed 5, context: html, text, full: html, text
    Made changes to fix track ordering in rat assemblies; tracks visible by default should appear first and in alphabetic order; all other tracks should appear second and in alphabetic order (redmine #7343)
• src/hg/makeDb/trackDb/rat/rn4/defaultPriority.ra
  • lines changed 59, context: html, text, full: html, text
    Made changes to fix track ordering in rat assemblies; tracks visible by default should appear first and in alphabetic order; all other tracks should appear second and in alphabetic order (redmine #7343)
• src/hg/makeDb/trackDb/rat/rn4/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    Made changes to fix track ordering in rat assemblies; tracks visible by default should appear first and in alphabetic order; all other tracks should appear second and in alphabetic order (redmine #7343)
• src/hg/makeDb/trackDb/rat/rn5/cons13way.ra
  • lines changed 1, context: html, text, full: html, text
    Made changes to fix track ordering in rat assemblies; tracks visible by default should appear first and in alphabetic order; all other tracks should appear second and in alphabetic order (redmine #7343)
• src/hg/makeDb/trackDb/rat/rn5/defaultPriority.ra
  • lines changed 38, context: html, text, full: html, text
    Made changes to fix track ordering in rat assemblies; tracks visible by default should appear first and in alphabetic order; all other tracks should appear second and in alphabetic order (redmine #7343)
• src/hg/makeDb/trackDb/rat/rn5/trackDb.ra
  • lines changed 11, context: html, text, full: html, text
    Made changes to fix track ordering in rat assemblies; tracks visible by default should appear first and in alphabetic order; all other tracks should appear second and in alphabetic order (redmine #7343)
• src/hg/makeDb/trackDb/rat/rn6/defaultPriority.ra
  • lines changed 26, context: html, text, full: html, text
    Made changes to fix track ordering in rat assemblies; tracks visible by default should appear first and in alphabetic order; all other tracks should appear second and in alphabetic order (redmine #7343)
• src/hg/makeDb/trackDb/rat/rn6/trackDb.ra
  • lines changed 6, context: html, text, full: html, text
    Made changes to fix track ordering in rat assemblies; tracks visible by default should appear first and in alphabetic order; all other tracks should appear second and in alphabetic order (redmine #7343)
• src/hg/makeDb/trackDb/rat/trackDb.ra
  • lines changed 7, context: html, text, full: html, text
    Made changes to fix track ordering in rat assemblies; tracks visible by default should appear first and in alphabetic order; all other tracks should appear second and in alphabetic order (redmine #7343)
• src/hg/makeDb/trackDb/rhesus/rheMac2/defaultPriority.ra
  • lines changed 46, context: html, text, full: html, text
    Made changes to fix track ordering in primate assemblies; tracks visible by default should appear first and in alphabetic order; all other tracks should appear second and in alphabetic order (redmine #7343)
• src/hg/makeDb/trackDb/rhesus/rheMac2/trackDb.ra
  • lines changed 13, context: html, text, full: html, text
    Made changes to fix track ordering in primate assemblies; tracks visible by default should appear first and in alphabetic order; all other tracks should appear second and in alphabetic order (redmine #7343)
• src/hg/makeDb/trackDb/rhesus/rheMac3/defaultPriority.ra
  • lines changed 19, context: html, text, full: html, text
    Made changes to fix track ordering in primate assemblies; tracks visible by default should appear first and in alphabetic order; all other tracks should appear second and in alphabetic order (redmine #7343)
• src/hg/makeDb/trackDb/rhesus/rheMac3/trackDb.ra
  • lines changed 9, context: html, text, full: html, text
    Made changes to fix track ordering in primate assemblies; tracks visible by default should appear first and in alphabetic order; all other tracks should appear second and in alphabetic order (redmine #7343)
• src/hg/makeDb/trackDb/saiBol/saiBol1/defaultPriority.ra
  • lines changed 24, context: html, text, full: html, text
    Made changes to fix track ordering in primate assemblies; tracks visible by default should appear first and in alphabetic order; all other tracks should appear second and in alphabetic order (redmine #7343)
• src/hg/makeDb/trackDb/saiBol/saiBol1/trackDb.ra
  • lines changed 15, context: html, text, full: html, text
    Made changes to fix track ordering in primate assemblies; tracks visible by default should appear first and in alphabetic order; all other tracks should appear second and in alphabetic order (redmine #7343)
• src/hg/makeDb/trackDb/shrew/sorAra2/description.html
  • lines changed 1, context: html, text, full: html, text
    Updated usage link per code review (redmine #13645)
• src/hg/makeDb/trackDb/tagTypes.tab
  • lines changed 9, context: html, text, full: html, text
    David pointed out that it is inappropriate to show Hardy-Weinberg equilibriumfrequencies on the VCF details page unless the VCF data are from a population
    study -- so at this point, pretty much only 1000 Genomes. So I added a new
    trackDb setting for vcf/vcfTabix, showHardyWeinberg, and added it to the
    1000 Genomes track def.
    
  • lines changed 1, context: html, text, full: html, text
    now with overlap coverage and indicating multiple mappings refs #13713
• src/hg/makeDb/trackDb/tarsier/tarSyr1/defaultPriority.ra
  • lines changed 24, context: html, text, full: html, text
    Made changes to fix track ordering in primate assemblies; tracks visible by default should appear first and in alphabetic order; all other tracks should appear second and in alphabetic order (redmine #7343)
• src/hg/makeDb/trackDb/tarsier/tarSyr1/trackDb.ra
  • lines changed 14, context: html, text, full: html, text
    Made changes to fix track ordering in primate assemblies; tracks visible by default should appear first and in alphabetic order; all other tracks should appear second and in alphabetic order (redmine #7343)
• src/hg/makeDb/trackDb/treeShrew/tupBel1/defaultPriority.ra
  • lines changed 24, context: html, text, full: html, text
    Made changes to fix track ordering in primate assemblies; tracks visible by default should appear first and in alphabetic order; all other tracks should appear second and in alphabetic order (redmine #7343)
• src/hg/makeDb/trackDb/treeShrew/tupBel1/trackDb.ra
  • lines changed 14, context: html, text, full: html, text
    Made changes to fix track ordering in primate assemblies; tracks visible by default should appear first and in alphabetic order; all other tracks should appear second and in alphabetic order (redmine #7343)
• src/hg/regulate/regCluster/regCluster.c
  • lines changed 30, context: html, text, full: html, text
    Extend regCluster tools to add metadata to DNase clusters. Update DNase clusters table to include metadata (per Angie request for VAI support). refs #13490
• src/hg/regulate/regClusterMakeTableOfTables/makefile
  • lines changed 2, context: html, text, full: html, text
    Extend regCluster tools to add metadata to DNase clusters. Update DNase clusters table to include metadata (per Angie request for VAI support). refs #13490
• src/hg/regulate/regClusterMakeTableOfTables/regClusterMakeTableOfTables.c
  • lines changed 48, context: html, text, full: html, text
    Extend regCluster tools to add metadata to DNase clusters. Update DNase clusters table to include metadata (per Angie request for VAI support). refs #13490
• src/hg/utils/automation/makeGenomeDb.pl
  • lines changed 1, context: html, text, full: html, text
    poing to credits _use instead of _credits refs #13645
• src/inc/gff3.h
  • lines changed 2, context: html, text, full: html, text
    allow underbars in gff3. Grok Is_circular. #13673
• src/lib/gff3.c
  • lines changed 10, context: html, text, full: html, text
    allow underbars in gff3. Grok Is_circular. #13673
• src/makefile
  • lines changed 1, context: html, text, full: html, text
    makeing cscope use absolute pathnames
  • lines changed 2, context: html, text, full: html, text
    changing cscope target again for older versions
• src/product/README.building.source
  • lines changed 9, context: html, text, full: html, text
    indicate PDF format not available error message solved refs #13744
• src/utils/bigWigCorrelate/bigWigCorrelate.c
  • lines changed 47, context: html, text, full: html, text
    Adding option to do correlations between list of files, not just a pair.
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    v304 preview2 refs #13703

• lines changed: 6306
• files changed: 169