All File Changes

v315_base to v316_preview (2015-04-20 to 2015-04-27) v316

• src/hg/cirm/cdw/cdwWebAuthLogin/cdwWebAuthLogin.c
  • lines changed 110, context: html, text, full: html, text
    Getting rid of old Personna based login/logout
    
• src/hg/cirm/cdw/cdwWebAuthLogin/makefile
  • lines changed 16, context: html, text, full: html, text
    Getting rid of old Personna based login/logout
    
• src/hg/cirm/cdw/cdwWebAuthLogout/cdwWebAuthLogout.c
  • lines changed 18, context: html, text, full: html, text
    Getting rid of old Personna based login/logout
    
• src/hg/cirm/cdw/cdwWebAuthLogout/makefile
  • lines changed 16, context: html, text, full: html, text
    Getting rid of old Personna based login/logout
    
• src/hg/getRnaPred/getRnaPred.c
  • lines changed 3, context: html, text, full: html, text
    don't output peptides in getRnaPred.c if it's non-coding refs #14639
    
• src/hg/hgGene/hgGene.c
  • lines changed 11, context: html, text, full: html, text
    cahnges to browser to support Gencode KnownGene #14639
    
• src/hg/hgIntegrator/hgIntegrator.c
  • lines changed 5, context: html, text, full: html, text
    Moved hgVai's and hgIntegrator's duplicated NO_MAX_ROWS to hAnno.h as ANNO_NO_LIMIT.
    
• src/hg/hgMirror/hgMirror
  • lines changed 64, context: html, text, full: html, text
    fixing hgMirror to handle tracks without a table, refs #15059
    
  • lines changed 8, context: html, text, full: html, text
    adding indexes in hgMirror, refs 15059
    
  • lines changed 4, context: html, text, full: html, text
    hgMirror bacends track fix, refs 15059
    
• src/hg/hgTables/bigBed.c
  • lines changed 6, context: html, text, full: html, text
    Apply some band-aids to fix broken filterFields for bigDataUrl-only bigBed tracks.
    There are still way too many places in hgTables code that use isXyzTable(table, conn)
    even when tdb is available. I think all those places need to be fixed to pass in
    tdb if they have it, or NULL if they don't. The type-testers should use tdb if
    possible, and fall back to using table & conn if tdb is NULL.
    refs #14379, #15059
    
• src/hg/hgTables/filterFields.c
  • lines changed 10, context: html, text, full: html, text
    Apply some band-aids to fix broken filterFields for bigDataUrl-only bigBed tracks.
    There are still way too many places in hgTables code that use isXyzTable(table, conn)
    even when tdb is available. I think all those places need to be fixed to pass in
    tdb if they have it, or NULL if they don't. The type-testers should use tdb if
    possible, and fall back to using table & conn if tdb is NULL.
    refs #14379, #15059
    
• src/hg/hgTables/hgTables.h
  • lines changed 1, context: html, text, full: html, text
    Apply some band-aids to fix broken filterFields for bigDataUrl-only bigBed tracks.
    There are still way too many places in hgTables code that use isXyzTable(table, conn)
    even when tdb is available. I think all those places need to be fixed to pass in
    tdb if they have it, or NULL if they don't. The type-testers should use tdb if
    possible, and fall back to using table & conn if tdb is NULL.
    refs #14379, #15059
    
• src/hg/hgTables/joining.c
  • lines changed 2, context: html, text, full: html, text
    In getBedFieldSlNameList, when parsing the field string from bedSqlFieldsExceptForChrom,
    skip over placeholder field '.' in addition to placeholder 0. Letting the '.' slip through
    was not a problem until 1d8a8611 in which joinerDtfFromDottedTriple was changed to use
    strrchr instead of strchr to separate the field name from the track name, to accommodate
    track hubs with . in the track name.
    refs #15117
    
• src/hg/hgTracks/simpleTracks.c
  • lines changed 3, context: html, text, full: html, text
    cahnges to browser to support Gencode KnownGene #14639
    
• src/hg/hgVai/hgVai.c
  • lines changed 10, context: html, text, full: html, text
    Moved hgVai's and hgIntegrator's duplicated NO_MAX_ROWS to hAnno.h as ANNO_NO_LIMIT.
    
• src/hg/htdocs/images/freeStemCell.jpg
  • lines changed 0, context: html, text, full: html, text
    A stem cell image with clear free usage rights from creative commons.
    
• src/hg/htdocs/images/transparent.gif
  • lines changed 0, context: html, text, full: html, text
    Adding a decent looking so far color picker.
    
• src/hg/htdocs/indexNews.html
  • lines changed 23, context: html, text, full: html, text
    Removing redundant danRer10 announcement (no redmine)
    
• src/hg/htdocs/style/HGStyle.css
  • lines changed 27, context: html, text, full: html, text
    Fixing some style inconsistencies that Matt noted.
    refs #14579
    
• src/hg/htdocs/style/jquery.ui.colorPicker.css
  • lines changed 67, context: html, text, full: html, text
    Adding a decent looking so far color picker.
    
• src/hg/htdocs/training/index.html
  • lines changed 14, context: html, text, full: html, text
    removing completed workshops from the list
    
• src/hg/inc/hAnno.h
  • lines changed 4, context: html, text, full: html, text
    Moved hgVai's and hgIntegrator's duplicated NO_MAX_ROWS to hAnno.h as ANNO_NO_LIMIT.
    
• src/hg/inc/trackDb.h
  • lines changed 6, context: html, text, full: html, text
    Apply some band-aids to fix broken filterFields for bigDataUrl-only bigBed tracks.
    There are still way too many places in hgTables code that use isXyzTable(table, conn)
    even when tdb is available. I think all those places need to be fixed to pass in
    tdb if they have it, or NULL if they don't. The type-testers should use tdb if
    possible, and fall back to using table & conn if tdb is NULL.
    refs #14379, #15059
    
• src/hg/js/external/.gitattributes
  • lines changed 1, context: html, text, full: html, text
    Adding .gitattributes files in directories that contain only compiled JS
    that is not going to be hand-edited, only replaced with newly compiled JS.
    
• src/hg/js/jquery.ui.colorPicker.js
  • lines changed 400, context: html, text, full: html, text
    Adding a decent looking so far color picker.
    
• src/hg/js/react/hgIntegrator/hgIntegrator.jsx
  • lines changed 7, context: html, text, full: html, text
    Fixing some style inconsistencies that Matt noted.
    refs #14579
    
• src/hg/js/react/lib/Section.jsx
  • lines changed 1, context: html, text, full: html, text
    Fixing some style inconsistencies that Matt noted.
    refs #14579
    
• src/hg/lib/genePred.c
  • lines changed 3, context: html, text, full: html, text
    Improve error message from gff3ToGenePred to make it easier to determine
    where bad GFF3 annotations created an invalid genePred. (no redmine)
    
• src/hg/lib/hAnno.c
  • lines changed 30, context: html, text, full: html, text
    cleanup: variable renaming, getting rid of unnecessary second conn,
    use bigDataUrl if it's present regardless of hub/db, use existing
    lib function instead of ad-hoc copy-paste.
    
• src/hg/makeDb/doc/hg19.txt
  • lines changed 62, context: html, text, full: html, text
    Loaded 1000 Genomes Phase 3 variants and accessible regions & added to trackDb.
    Still need to write descriptions.
    refs #14325
    
• src/hg/makeDb/doc/hg38/hg38.txt
  • lines changed 1, context: html, text, full: html, text
    Fixed GENCODE V22 section to say V22; refs #15115
    
• src/hg/makeDb/doc/hg38/hg38Patch3.txt
  • lines changed 90, context: html, text, full: html, text
    wrapping up patch3 build refs #15413
    
• src/hg/makeDb/doc/hg38/lastzRuns.txt
  • lines changed 464, context: html, text, full: html, text
    rerunning old lastz runs mm10 canFam3 rheMac3 to fix problems and new run for tupBel1 and rerunning some others to get better coverage with default parameters refs #15144
    
• src/hg/makeDb/doc/hg38/multiz17way.txt
  • lines changed 270, context: html, text, full: html, text
    done with 17-way then upgraded to 20-way refs #14970
    
• src/hg/makeDb/doc/hg38/patchDescr.pl
  • lines changed 164, context: html, text, full: html, text
    used to construct the description page for patch release 3 refs #15413
    
• src/hg/makeDb/doc/tarSyr2/multiz20way.txt
  • lines changed 36, context: html, text, full: html, text
    show comparison tree length estimates between this 20-way and the hg38 reference 20-way refs #15112
    
• src/hg/makeDb/makeGencodeKnownGene/makeGencodeKnownGene.c
  • lines changed 113, context: html, text, full: html, text
    more work on makeGencodeKnownGene which builds knownGene, and kgXref,
    and some other tables #14639
    
• src/hg/makeDb/schema/all.joiner
  • lines changed 3, context: html, text, full: html, text
    Changed some minCheck values to allow joinerCheck to run without errors; refs #15115
    
• src/hg/makeDb/trackDb/human/chainNetBosTau7.ra
  • lines changed 17, context: html, text, full: html, text
    trying bosTau7 in a beta public tag refs #11681
    
• src/hg/makeDb/trackDb/human/chainNetPlacental.ra
  • lines changed 16, context: html, text, full: html, text
    Adding bosTau7 stanza back to chainNetPlacental.ra so will build for hg19, hg38 will build bosTau8 refs# 11681
    
  • lines changed 15, context: html, text, full: html, text
    trying bosTau7 in a beta public tag refs #11681
    
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 33, context: html, text, full: html, text
    Loaded 1000 Genomes Phase 3 variants and accessible regions & added to trackDb.
    Still need to write descriptions.
    refs #14325
    
• src/hg/makeDb/trackDb/human/hg38/defaultPriority.ra
  • lines changed 2, context: html, text, full: html, text
    trackDb changes to switch to Gencode UCSC Genes on hg38 refs #14639
    
• src/hg/makeDb/trackDb/human/hg38/hg38Patch3.html
  • lines changed 236, context: html, text, full: html, text
    adding description page for hg38Patch3 refs #15413
    
• src/hg/makeDb/trackDb/human/hg38/knownGene.ra.alpha
  • lines changed 19, context: html, text, full: html, text
    trackDb changes to switch to Gencode UCSC Genes on hg38 refs #14639
    
• src/hg/makeDb/trackDb/human/hg38/knownGene.ra.beta
  • lines changed 18, context: html, text, full: html, text
    trackDb changes to switch to Gencode UCSC Genes on hg38 refs #14639
    
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    trackDb changes to switch to Gencode UCSC Genes on hg38 refs #14639
    
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV22.html
  • lines changed 8, context: html, text, full: html, text
    Made corrections to GENCODE V22 description page; refs #15115
    
• src/hg/makeDb/trackDb/tagTypes.tab
  • lines changed 1, context: html, text, full: html, text
    add isGencode to acceptable tagTypes. refs #14639
    
• src/hg/makeDb/trackDb/tarsier/tarSyr2/trackDb.20way.ra
  • lines changed 4, context: html, text, full: html, text
    Fixing species number in longLabels, refs #15112
    
• src/hg/mouseStuff/lavToPsl/lavToPsl.c
  • lines changed 6, context: html, text, full: html, text
    new version 66 of lastz outputs lav records with zero length, ignore them refs #12502
    
• src/hg/txGraph/txBedToGraph/makeGraph.c
  • lines changed 3, context: html, text, full: html, text
    make txToBedGraph a little more tolerant #14639
    
• src/hg/utils/gff3ToGenePred/gff3ToGenePred.c
  • lines changed 10, context: html, text, full: html, text
    Improve error message from gff3ToGenePred to make it easier to determine
    where bad GFF3 annotations created an invalid genePred. (no redmine)
    
• src/inc/htmlPage.h
  • lines changed 1, context: html, text, full: html, text
    Improving comment.
    
• src/utils/makefile
  • lines changed 1, context: html, text, full: html, text
    Adding bigWigCluster to utilities compilation.
    
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    v316 preview1
    

• lines changed: 2467
• files changed: 57