All File Changes

v274_base to v275_preview (2012-10-09 to 2012-10-16) v275

• src/hg/hgFileUi/hgFileUi.c
  • lines changed 8, context: html, text, full: html, text
    Added 'Contact' link that jumps to Credits section so users can more easily locate lab contacts (reduce load on mailing list). #9328
• src/hg/hgLogin/hgLogin.c
  • lines changed 1, context: html, text, full: html, text
    redmine #9151 note #10 -- missing 'the' in the confirm message fixed.
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 13, context: html, text, full: html, text
    Add Contacts link to top of hgTrackUi and hgFileUi ENCODE pages, to encourage users to contact labs directly
• src/hg/hgTracks/hgTracks.c
  • lines changed 3, context: html, text, full: html, text
    this resolves the '+' in track names problem (#9254) by modifying all hub track names by changing all characters that aren't alphanumeric or dash or underbar into underbars. I also added code to check for track name overlaps, and confirmed that none of the hubs in hgcentral.hubStatus would end up with duplicated track names because of this munging. I also changed the udcTimeout in hubCheck to be 1 second.
  • lines changed 1, context: html, text, full: html, text
    Fix for strict compiler warning: warn() needs a proper format string, not char * variable.
• src/hg/hgc/encodeClick.c
  • lines changed 1, context: html, text, full: html, text
    bug fix for #9287 - hgc click handler for encode bed plus should handle encode custom track clickthrough properly
• src/hg/hgc/hgc.c
  • lines changed 1, context: html, text, full: html, text
    bug fix for #9287 - hgc click handler for encode bed plus should handle encode custom track clickthrough properly
• src/hg/hgc/pubs.c
  • lines changed 3, context: html, text, full: html, text
    correction after code review #9300
• src/hg/hgc/vcfClick.c
  • lines changed 9, context: html, text, full: html, text
    HTML-encode VCF alternate alleles in case they're symbolic like "<DEL>" (but don't encode twice :).
• src/hg/htdocs/ENCODE/contacts.html
  • lines changed 1, context: html, text, full: html, text
    Add eng
• src/hg/htdocs/ENCODE/index.html
  • lines changed 2, context: html, text, full: html, text
    Retire Jobs link on ENCODE portal
• src/hg/htdocs/cite.html
  • lines changed 26, context: html, text, full: html, text
    changed refs to latest update
• src/hg/htdocs/goldenPath/help/customTrackText.html
  • lines changed 16, context: html, text, full: html, text
    Changed the labels here for better clarity and added a definition. Some users thought that <track_name> meant our short label. See redmine #4875.
• src/hg/htdocs/goldenPath/pubs.html
  • lines changed 2, context: html, text, full: html, text
    changed refs to latest update
• src/hg/inc/trackHub.h
  • lines changed 2, context: html, text, full: html, text
    this resolves the '+' in track names problem (#9254) by modifying all hub track names by changing all characters that aren't alphanumeric or dash or underbar into underbars. I also added code to check for track name overlaps, and confirmed that none of the hubs in hgcentral.hubStatus would end up with duplicated track names because of this munging. I also changed the udcTimeout in hubCheck to be 1 second.
• src/hg/lib/customFactory.c
  • lines changed 2, context: html, text, full: html, text
    Check for NULL in errAbort arguments, or else we can SEGV and see blank screen.
• src/hg/lib/ensFace.c
  • lines changed 7, context: html, text, full: html, text
    Fixed bug #9299 Broken speTri2 ensGene link to ensembl.org.
• src/hg/lib/hubConnect.c
  • lines changed 10, context: html, text, full: html, text
    this resolves the '+' in track names problem (#9254) by modifying all hub track names by changing all characters that aren't alphanumeric or dash or underbar into underbars. I also added code to check for track name overlaps, and confirmed that none of the hubs in hgcentral.hubStatus would end up with duplicated track names because of this munging. I also changed the udcTimeout in hubCheck to be 1 second.
• src/hg/lib/liftOver.c
  • lines changed 1, context: html, text, full: html, text
    Fixing liftOver of bedPlus, copy-paste-forget-edit bug introduced inb224dbbd -- important arguments of liftOverBedPlus were discarded,
    like bedPlus(!), hasBin and tabSep.
    
• src/hg/lib/trackHub.c
  • lines changed 60, context: html, text, full: html, text
    this resolves the '+' in track names problem (#9254) by modifying all hub track names by changing all characters that aren't alphanumeric or dash or underbar into underbars. I also added code to check for track name overlaps, and confirmed that none of the hubs in hgcentral.hubStatus would end up with duplicated track names because of this munging. I also changed the udcTimeout in hubCheck to be 1 second.
• src/hg/makeDb/doc/choHof1.txt
  • lines changed 4, context: html, text, full: html, text
    reloading genbank with genbank.mrna.xeno.load = yes
• src/hg/makeDb/doc/hg19.txt
  • lines changed 30, context: html, text, full: html, text
    Track #7964 (1000 Genomes Phase 1 Variant Calls): Reloaded -- thedownload files have been updated with new dbSNP and dbVar IDs.
    
• src/hg/makeDb/doc/mm10.txt
  • lines changed 180, context: html, text, full: html, text
    frames reloaded for conservation 60-way, and the patch and haplotype tracks are underway
• src/hg/makeDb/doc/petMar2.txt
  • lines changed 280, context: html, text, full: html, text
    starting new Lamprey browser, ready to complete masking
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 2, context: html, text, full: html, text
    set up mRNA defaults the way we actually want them.
• src/hg/makeDb/hgLoadSqlTab/hgLoadSqlTab.c
  • lines changed 1, context: html, text, full: html, text
    hgLoadSqlTab: check NULL to avoid crashing on SQL files that don't include "(" at the end of their "CREATE TABLE" line.
• src/hg/makeDb/trackDb/alpaca/vicPac1/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    adding quality track overrides to indicate maximum data value, redmine 7681
• src/hg/makeDb/trackDb/armadillo/dasNov1/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    adding quality track overrides to indicate maximum data value, redmine 7681
• src/hg/makeDb/trackDb/armadillo/dasNov2/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    adding quality track overrides to indicate maximum data value, redmine 7681
• src/hg/makeDb/trackDb/baboon/papHam1/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    adding quality track overrides to indicate maximum data value, redmine 7681
• src/hg/makeDb/trackDb/bushbaby/otoGar1/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    adding quality track overrides to indicate maximum data value, redmine 7681
• src/hg/makeDb/trackDb/cat/felCat3/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    adding quality track overrides to indicate maximum data value, redmine 7681
• src/hg/makeDb/trackDb/chicken/galGal2/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    adding quality track overrides to indicate maximum data value, redmine 7681
• src/hg/makeDb/trackDb/chicken/galGal3/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    adding quality track overrides to indicate maximum data value, redmine 7681
• src/hg/makeDb/trackDb/chimp/panTro1/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    adding quality track overrides to indicate maximum data value, redmine 7681
• src/hg/makeDb/trackDb/chimp/panTro2/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    adding quality track overrides to indicate maximum data value, redmine 7681
• src/hg/makeDb/trackDb/cow/bosTau1/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    adding quality track overrides to indicate maximum data value, redmine 7681
• src/hg/makeDb/trackDb/cow/bosTau2/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    adding quality track overrides to indicate maximum data value, redmine 7681
• src/hg/makeDb/trackDb/cow/bosTau3/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    adding quality track overrides to indicate maximum data value, redmine 7681
• src/hg/makeDb/trackDb/cow/bosTau4/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    adding quality track overrides to indicate maximum data value, redmine 7681
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 6, context: html, text, full: html, text
    Changing link for SK-N-SH termId term URL RM#9282
  • lines changed 18, context: html, text, full: html, text
    Moving RipInput to the Control section. This can be verified in tracks like http://hgwdev.cse.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeSunyAlbanyTiling. This is trying to standardize the confusion between Control and Antibody. We have most Controls listed under Control but accepted as an Antibody term. I know this is confusing, but this is one of the only controls that was different.
  • lines changed 2, context: html, text, full: html, text
    Changing termId and link for LHCN-M2 RM#9282
  • lines changed 18, context: html, text, full: html, text
    More random changes regarding capitilizations, order of lines, spelling errors
  • lines changed 10720, context: html, text, full: html, text
    alphabetized the cv
  • lines changed 42, context: html, text, full: html, text
    Trying to fix the Tenebaum registrations according to an email from Scott Tenebaum in ticket http://redmine.soe.ucsc.edu/issues/9159#note-16
  • lines changed 188, context: html, text, full: html, text
    Removing the alternative tissue comments, removing the commented out unused cell lines. Trying to clean up the spacing of the comments.
  • lines changed 37, context: html, text, full: html, text
    standardizing more vendorNames, orderurls, and vendorIds
  • lines changed 84, context: html, text, full: html, text
    Standardizing the antibodyDescription to start with host and type
  • lines changed 22, context: html, text, full: html, text
    Adding a targetUrl for T7 tag, adding targetClass where it is known for other antibodies of the same target, fixing capitalization for Maf and Max
  • lines changed 53, context: html, text, full: html, text
    Reconciling the target versus the HGNC symbol by hand using the orderUrl information and HGNC synonyms. There were around 40 mismatches and this is my first round at reconciling
  • lines changed 6, context: html, text, full: html, text
    Replacing termId and termUrl for GM12878 RM#9307 RM#9282
  • lines changed 28, context: html, text, full: html, text
    Changing target P300 to the approved EP300 and merging the TFIIB with GTF2B which finds a missing validation document
  • lines changed 13, context: html, text, full: html, text
    Adding host species and antibody type (Poly/mono-clonal) for antibodies: BRF2 COREST_(ab24166) SEZH2_(39875) H3K4me3_(04-745) HDAC2_(A300-705A) HDAC6_(A301-341A) Mxi1_(AF4185) NELFe PHF8_(A301-772A) PLU1 RBBP5_(A300-109A) SAP30_(39731) RM#9342
  • lines changed 30, context: html, text, full: html, text
    Still going through one by one and comparing why we have conflicting target names. Also, changed all entries of Epstein to Bernstein
  • lines changed 9, context: html, text, full: html, text
    Fixing conflict
  • lines changed 11, context: html, text, full: html, text
    Fixing things from code review 9305
  • lines changed 1, context: html, text, full: html, text
    Space changes only
  • lines changed 28, context: html, text, full: html, text
    Still cleaning up the antibodys that did not have target matching the gene AND removed the Novagen reference from from the T7 Tag as specified by Soctt Tenenbaum
• src/hg/makeDb/trackDb/cv/beta/cv.ra
  • lines changed 11003, context: html, text, full: html, text
    Copying alpha/cv.ra to beta/cv.ra, alphabetized restructuring of stanzas so that fields appear consistent, for example such as vendorId and vendorName always coming last across cell lines and antibodies.
  • lines changed 260, context: html, text, full: html, text
    Copying alpha cv.ra to beta cv.ra changes to unify vendor name and antibody description, removal of spaces, unifying gene name to antibody target name RM#9305
• src/hg/makeDb/trackDb/cv/public/cv.ra
  • lines changed 11131, context: html, text, full: html, text
    Moving beta to public
• src/hg/makeDb/trackDb/dog/canFam1/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    adding quality track overrides to indicate maximum data value, redmine 7681
• src/hg/makeDb/trackDb/dog/canFam2/trackDb.ra
  • lines changed 5, context: html, text, full: html, text
    adding quality track overrides to indicate maximum data value, redmine 7681
• src/hg/makeDb/trackDb/dolphin/turTru1/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    adding quality track overrides to indicate maximum data value, redmine 7681
• src/hg/makeDb/trackDb/elephant/loxAfr1/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    adding quality track overrides to indicate maximum data value, redmine 7681
• src/hg/makeDb/trackDb/elephant/loxAfr2/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    adding quality track overrides to indicate maximum data value, redmine 7681
• src/hg/makeDb/trackDb/elephant/loxAfr3/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    adding quality track overrides to indicate maximum data value, redmine 7681
• src/hg/makeDb/trackDb/gorilla/gorGor1/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    adding quality track overrides to indicate maximum data value, redmine 7681
• src/hg/makeDb/trackDb/guineaPig/cavPor3/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    adding quality track overrides to indicate maximum data value, redmine 7681
• src/hg/makeDb/trackDb/hedgehog/eriEur1/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    adding quality track overrides to indicate maximum data value, redmine 7681
• src/hg/makeDb/trackDb/horse/equCab1/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    adding quality track overrides to indicate maximum data value, redmine 7681
• src/hg/makeDb/trackDb/horse/equCab2/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    adding quality track overrides to indicate maximum data value, redmine 7681
• src/hg/makeDb/trackDb/human/coriellDelDup.html
  • lines changed 34, context: html, text, full: html, text
    added some description
  • lines changed 1, context: html, text, full: html, text
    tiny tweak
  • lines changed 1, context: html, text, full: html, text
    tiny tweak
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeBroadHistone.ra
  • lines changed 11, context: html, text, full: html, text
    Adding ENCODE GEO Accession numbers to hg19 BroadHistone OpenChromDnase OpenChromFaire
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeGisRnaPet.ra
  • lines changed 51, context: html, text, full: html, text
    Adding GEO numbers, updates to metaData for ENCODE GisRnaPet UwDgf HaibTfbs RM#9359
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeHaibTfbs.ra
  • lines changed 1136, context: html, text, full: html, text
    Adding GEO numbers, updates to metaData for ENCODE GisRnaPet UwDgf HaibTfbs RM#9359
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeOpenChromDnase.ra
  • lines changed 269, context: html, text, full: html, text
    Adding ENCODE GEO Accession numbers to hg19 BroadHistone OpenChromDnase OpenChromFaire
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeOpenChromFaire.ra
  • lines changed 59, context: html, text, full: html, text
    Adding ENCODE GEO Accession numbers to hg19 BroadHistone OpenChromDnase OpenChromFaire
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeUwDgf.ra
  • lines changed 176, context: html, text, full: html, text
    Adding GEO numbers, updates to metaData for ENCODE GisRnaPet UwDgf HaibTfbs RM#9359
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeUwHistone.ra
  • lines changed 17, context: html, text, full: html, text
    Adding GEO numbers, updates to metaData for ENCODE UwHistone RM#9359
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeBroadHistone.ra
  • lines changed 11, context: html, text, full: html, text
    Adding ENCODE GEO Accession numbers to hg19 BroadHistone OpenChromDnase OpenChromFaire
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeGisRnaPet.ra
  • lines changed 51, context: html, text, full: html, text
    Adding GEO numbers, updates to metaData for ENCODE GisRnaPet UwDgf HaibTfbs RM#9359
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeHaibTfbs.ra
  • lines changed 1136, context: html, text, full: html, text
    Adding GEO numbers, updates to metaData for ENCODE GisRnaPet UwDgf HaibTfbs RM#9359
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeOpenChromDnase.ra
  • lines changed 269, context: html, text, full: html, text
    Adding ENCODE GEO Accession numbers to hg19 BroadHistone OpenChromDnase OpenChromFaire
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeOpenChromFaire.ra
  • lines changed 59, context: html, text, full: html, text
    Adding ENCODE GEO Accession numbers to hg19 BroadHistone OpenChromDnase OpenChromFaire
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeUwDgf.ra
  • lines changed 176, context: html, text, full: html, text
    Adding GEO numbers, updates to metaData for ENCODE GisRnaPet UwDgf HaibTfbs RM#9359
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeUwHistone.ra
  • lines changed 17, context: html, text, full: html, text
    Adding GEO numbers, updates to metaData for ENCODE UwHistone RM#9359
• src/hg/makeDb/trackDb/human/hg19/tgpPhase1.html
  • lines changed 1, context: html, text, full: html, text
    Small update to tgpPhase1 description: paper has been accepted.
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    added 18-ball because track is lifted
• src/hg/makeDb/trackDb/kangarooRat/dipOrd1/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    adding quality track overrides to indicate maximum data value, redmine 7681
• src/hg/makeDb/trackDb/lamprey/petMar1/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    adding quality track overrides to indicate maximum data value, redmine 7681
• src/hg/makeDb/trackDb/lamprey/petMar2/description.html
  • lines changed 63, context: html, text, full: html, text
    initial files from the makeGenomeDb.pl script, should be in good shape
• src/hg/makeDb/trackDb/lamprey/petMar2/gap.html
  • lines changed 30, context: html, text, full: html, text
    initial files from the makeGenomeDb.pl script, should be in good shape
• src/hg/makeDb/trackDb/lamprey/petMar2/gold.html
  • lines changed 34, context: html, text, full: html, text
    initial files from the makeGenomeDb.pl script, should be in good shape
• src/hg/makeDb/trackDb/lamprey/petMar2/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    initial files from the makeGenomeDb.pl script, should be in good shape
• src/hg/makeDb/trackDb/marmoset/calJac1/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    adding quality track overrides to indicate maximum data value, redmine 7681
• src/hg/makeDb/trackDb/medaka/oryLat1/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    adding quality track overrides to indicate maximum data value, redmine 7681
• src/hg/makeDb/trackDb/medaka/oryLat2/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    adding quality track overrides to indicate maximum data value, redmine 7681
• src/hg/makeDb/trackDb/megabat/pteVam1/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    adding quality track overrides to indicate maximum data value, redmine 7681
• src/hg/makeDb/trackDb/microbat/myoLuc1/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    adding quality track overrides to indicate maximum data value, redmine 7681
• src/hg/makeDb/trackDb/mouse/mm10/cons60way.html
  • lines changed 1, context: html, text, full: html, text
    Added missing comma.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrTfbs.ra
  • lines changed 154, context: html, text, full: html, text
    Removing stanzas that have no files attached to them, these files are in LicrHistone. This came from a script that QA runs.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/wgEncodeUwDnase.ra
  • lines changed 493, context: html, text, full: html, text
    Adding GEO numbers, updates to metaData for ENCODE mm9 UwDnase RM#9359
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/public/wgEncodeUwDnase.ra
  • lines changed 493, context: html, text, full: html, text
    Adding GEO numbers, updates to metaData for ENCODE mm9 UwDnase RM#9359
• src/hg/makeDb/trackDb/mouseLemur/micMur1/trackDb.ra
  • lines changed 5, context: html, text, full: html, text
    adding quality track overrides to indicate maximum data value, redmine 7681
• src/hg/makeDb/trackDb/opossum/monDom1/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    adding quality track overrides to indicate maximum data value, redmine 7681
• src/hg/makeDb/trackDb/opossum/monDom4/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    adding quality track overrides to indicate maximum data value, redmine 7681
• src/hg/makeDb/trackDb/opossum/monDom5/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    adding quality track overrides to indicate maximum data value, redmine 7681
• src/hg/makeDb/trackDb/orangutan/ponAbe2/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    adding quality track overrides to indicate maximum data value, redmine 7681
• src/hg/makeDb/trackDb/pika/ochPri2/trackDb.ra
  • lines changed 5, context: html, text, full: html, text
    adding quality track overrides to indicate maximum data value, redmine 7681
• src/hg/makeDb/trackDb/platypus/ornAna1/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    adding quality track overrides to indicate maximum data value, redmine 7681
• src/hg/makeDb/trackDb/rabbit/oryCun1/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    adding quality track overrides to indicate maximum data value, redmine 7681
• src/hg/makeDb/trackDb/rabbit/oryCun2/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    adding quality track overrides to indicate maximum data value, redmine 7681
• src/hg/makeDb/trackDb/rat/rn4/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    adding quality track overrides to indicate maximum data value, redmine 7681
• src/hg/makeDb/trackDb/rhesus/rheMac1/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    adding quality track overrides to indicate maximum data value, redmine 7681
• src/hg/makeDb/trackDb/rhesus/rheMac2/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    adding quality track overrides to indicate maximum data value, redmine 7681
  • lines changed 3, context: html, text, full: html, text
    Removed duplicate quality track override.
• src/hg/makeDb/trackDb/rockHyrax/proCap1/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    adding quality track overrides to indicate maximum data value, redmine 7681
• src/hg/makeDb/trackDb/rockHyrax/proCav1/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    adding quality track overrides to indicate maximum data value, redmine 7681
• src/hg/makeDb/trackDb/seaHare/aplCal1/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    adding quality track overrides to indicate maximum data value, redmine 7681
• src/hg/makeDb/trackDb/shrew/sorAra1/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    adding quality track overrides to indicate maximum data value, redmine 7681
• src/hg/makeDb/trackDb/sloth/choHof1/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    adding quality track overrides to indicate maximum data value, redmine 7681
• src/hg/makeDb/trackDb/squirrel/speTri1/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    adding quality track overrides to indicate maximum data value, redmine 7681
• src/hg/makeDb/trackDb/stickleback/gasAcu1/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    adding quality track overrides to indicate maximum data value, redmine 7681
• src/hg/makeDb/trackDb/tarsier/tarSyr1/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    adding quality track overrides to indicate maximum data value, redmine 7681
• src/hg/makeDb/trackDb/tenrec/echTel1/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    adding quality track overrides to indicate maximum data value, redmine 7681
• src/hg/makeDb/trackDb/tenrec/trackDb.ra
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    Feature #9297 Items in Ensembl Assembly track need to be searchable.
• src/hg/makeDb/trackDb/trackDb.ra
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    Feature #9297 Items in Ensembl Assembly track need to be searchable.
• src/hg/makeDb/trackDb/treeShrew/tupBel1/trackDb.ra
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    adding quality track overrides to indicate maximum data value, redmine 7681
• src/hg/makeDb/trackDb/urchin/strPur1/trackDb.ra
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    adding quality track overrides to indicate maximum data value, redmine 7681
• src/hg/makeDb/trackDb/urchin/strPur2/trackDb.ra
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    adding quality track overrides to indicate maximum data value, redmine 7681
• src/hg/makeDb/trackDb/urchin/strPur3/trackDb.ra
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    adding quality track overrides to indicate maximum data value, redmine 7681
• src/hg/makeDb/trackDb/windowmaskerSdust.html
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    Added link to first mention of WindowMasker to make getting to more detailed description of what it is easier. Corrected the code used to display an umlauted 'a'.
• src/hg/makeDb/trackDb/worm/caeJap1/trackDb.ra
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    adding quality track overrides to indicate maximum data value, redmine 7681
• src/hg/makeDb/trackDb/worm/caeJap2/trackDb.ra
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    adding quality track overrides to indicate maximum data value, redmine 7681
• src/hg/makeDb/trackDb/worm/caePb1/trackDb.ra
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    adding quality track overrides to indicate maximum data value, redmine 7681
• src/hg/makeDb/trackDb/worm/caeRem3/trackDb.ra
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    adding quality track overrides to indicate maximum data value, redmine 7681
• src/hg/makeDb/trackDb/worm/priPac1/trackDb.ra
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    adding quality track overrides to indicate maximum data value, redmine 7681
• src/hg/makeDb/trackDb/zebraFinch/taeGut1/trackDb.ra
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    adding quality track overrides to indicate maximum data value, redmine 7681
• src/hg/pslToBed/pslToBed.c
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    tweak how pslToBed generates non-coding beds so the browser displays them properly, twich bedExact to compare non-coding beds just by checking if both of them have thickStart==thickEnd. (#7045)
• src/hg/utils/hubCheck/hubCheck.c
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    this resolves the '+' in track names problem (#9254) by modifying all hub track names by changing all characters that aren't alphanumeric or dash or underbar into underbars. I also added code to check for track name overlaps, and confirmed that none of the hubs in hgcentral.hubStatus would end up with duplicated track names because of this munging. I also changed the udcTimeout in hubCheck to be 1 second.
• src/hg/utils/isca/buildISCA.csh
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    first pass at ISCA otto load (#5172)
• src/hg/utils/isca/checkISCA.sh
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    first pass at ISCA otto load (#5172)
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    some tweaks to ISCA load and validate. Only check bed fields on validate. #6553
• src/hg/utils/isca/isca.tables
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    first pass at ISCA otto load (#5172)
• src/hg/utils/isca/iscaWrapper.sh
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    first pass at ISCA otto load (#5172)
• src/hg/utils/isca/makefile
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    first pass at ISCA otto load (#5172)
• src/hg/utils/isca/validateISCA.sh
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    first pass at ISCA otto load (#5172)
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    some tweaks to ISCA load and validate. Only check bed fields on validate. #6553
• src/lib/basicBed.c
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    look at thickStart and thickEnd when checking to see if a bed is exactly the same. (#7045)
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    tweak how pslToBed generates non-coding beds so the browser displays them properly, twich bedExact to compare non-coding beds just by checking if both of them have thickStart==thickEnd. (#7045)
• src/parasol/inc/paraVersion.h
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    Fix parasol to correctly enforce memory limits.
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    v12.15 - bugfixes and better support of rlimit for parasol
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    v12.16 - fixed bug in planner which had r and c reversed so that -ramUnit option now works
• src/parasol/para/para.c
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    v12.15 - bugfixes and better support of rlimit for parasol
• src/parasol/paraHub/paraHub.c
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    v12.15 - bugfixes and better support of rlimit for parasol
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    v12.16 - fixed bug in planner which had r and c reversed so that -ramUnit option now works
• src/parasol/paraNode/paraNode.c
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    Fix parasol to correctly enforce memory limits.
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    v12.15 - bugfixes and better support of rlimit for parasol
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    v12.16 - fixed bug in planner which had r and c reversed so that -ramUnit option now works
• src/parasol/version.doc
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    Fix parasol to correctly enforce memory limits.
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    v12.15 - bugfixes and better support of rlimit for parasol
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    v12.16 - fixed bug in planner which had r and c reversed so that -ramUnit option now works
• src/utils/qa/weeklybld/buildEnv.csh
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    v275 preview1
• src/utils/qa/weeklybld/summaryEmail.sh
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    Change back 'due to Ann by 5 PM tomorrow'.

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• files changed: 168