All File Changes

v284_preview to v284_preview2 (2013-05-14 to 2013-05-21) v284

• src/hg/encode3/encodeDataWarehouse/edwChangeFormat/edwChangeFormat.c
  • lines changed 121, context: html, text, full: html, text
    Making it so can change format of a file after upload, mostly at the moment to help get rid of unknowns that really are fastqs.
• src/hg/encode3/encodeDataWarehouse/edwChangeFormat/makefile
  • lines changed 4, context: html, text, full: html, text
    Making it so can change format of a file after upload, mostly at the moment to help get rid of unknowns that really are fastqs.
• src/hg/encode3/encodeDataWarehouse/edwMakeValidFile/edwMakeValidFile.c
  • lines changed 55, context: html, text, full: html, text
    Adjusting so that can revalidate an existing record.
• src/hg/encode3/encodeDataWarehouse/edwMetaManiToTdb/edwMetaManiToTdb.c
  • lines changed 1, context: html, text, full: html, text
    Setting viewLimits.
• src/hg/encode3/encodeDataWarehouse/edwRunner/edwRunner.c
  • lines changed 232, context: html, text, full: html, text
    Removing daemons that are replaced with edwRunDaemon.
• src/hg/encode3/encodeDataWarehouse/edwRunner/makefile
  • lines changed 4, context: html, text, full: html, text
    Removing daemons that are replaced with edwRunDaemon.
• src/hg/encode3/encodeDataWarehouse/edwSubmitSpooler/edwSubmitSpooler.c
  • lines changed 99, context: html, text, full: html, text
    Removing daemons that are replaced with edwRunDaemon.
• src/hg/encode3/encodeDataWarehouse/edwSubmitSpooler/makefile
  • lines changed 3, context: html, text, full: html, text
    Removing daemons that are replaced with edwRunDaemon.
• src/hg/encode3/encodeDataWarehouse/edwWebRegisterScript/edwWebRegisterScript.c
  • lines changed 1, context: html, text, full: html, text
    Adding debugging message.
  • lines changed 25, context: html, text, full: html, text
    Adding CFLAGs to makefile and turning 33 constant to a define to address Kate's feedback during code review.
• src/hg/encode3/encodeDataWarehouse/edwWebRegisterScript/makefile
  • lines changed 1, context: html, text, full: html, text
    Adding CFLAGs to makefile and turning 33 constant to a define to address Kate's feedback during code review.
• src/hg/encode3/encodeDataWarehouse/edwWebSubmit/edwWebSubmit.c
  • lines changed 1, context: html, text, full: html, text
    Making start up delay a little longer to get daemons more of a chance to work before first report.
• src/hg/encode3/encodeDataWarehouse/lib/edwLib.c
  • lines changed 1, context: html, text, full: html, text
    Making duration estimate formatting a little better for 1 day 0 hour case.
• src/hg/encode3/encodeDataWarehouse/lib/resetEdw
  • lines changed 1, context: html, text, full: html, text
    Adding Kate to users added when test database is reset.
• src/hg/encode3/validateFiles/validateFiles.c
  • lines changed 27, context: html, text, full: html, text
    removing unneeded newlines, making some error messages more consistent in minor ways
• src/hg/encode3/validateManifest/validateManifest.c
  • lines changed 1, context: html, text, full: html, text
    updating version to 1.5
  • lines changed 1, context: html, text, full: html, text
    hiding vf exit code status back to verbose level 2
• src/hg/hgGene/hgGeneData/Human/hg19/links.ra
  • lines changed 6, context: html, text, full: html, text
    making new knownToWikipedia work only in hg19. refs #10707
• src/hg/hgGene/hgGeneData/links.ra
  • lines changed 7, context: html, text, full: html, text
    making new knownToWikipedia work only in hg19. refs #10707
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 2, context: html, text, full: html, text
    Cleanup libification of factorSource UI. refs #10097
• src/hg/hgTracks/factorSource.c
  • lines changed 1, context: html, text, full: html, text
    Cleanup libification of factorSource UI. refs #10097
• src/hg/hgTracks/pubsTracks.c
  • lines changed 48, context: html, text, full: html, text
    trying to work around some sort of bug in mysql 5.6, see rm #10688
  • lines changed 4, context: html, text, full: html, text
    changes according to code review #10813
• src/hg/hgTracks/snakeTrack.c
  • lines changed 24, context: html, text, full: html, text
    use Glenn's new API... still needs some work to display the target duplications
• src/hg/hgc/peakClusters.c
  • lines changed 1, context: html, text, full: html, text
    Fix inaccurate comment found in code review (AH)
  • lines changed 85, context: html, text, full: html, text
    Libify condensed cell table for factorSource tracks, shown in both hgc and hgTrackUi. refs #10097
  • lines changed 2, context: html, text, full: html, text
    Cleanup libification of factorSource UI. refs #10097
• src/hg/hgc/pubs.c
  • lines changed 10, context: html, text, full: html, text
    trying to work around some sort of bug in mysql 5.6, see rm #10688
• src/hg/htdocs/ENCODE/analysis.html
  • lines changed 4, context: html, text, full: html, text
    Add link to Analysis page (request of Michael Hoffman of AWG). Clarifies location of analysis datasets
• src/hg/htdocs/ENCODE/analysisTools.html
  • lines changed 3, context: html, text, full: html, text
    Changing punctuation Code Review refs #10808 #10760
• src/hg/htdocs/ENCODE/downloads.html
  • lines changed 1, context: html, text, full: html, text
    Fix obsolete assembly ref in FAQ link
• src/hg/htdocs/ENCODE/index.html
  • lines changed 60, context: html, text, full: html, text
    Abbreviate old news
  • lines changed 42, context: html, text, full: html, text
    Add news item for Uniform TFBS release
• src/hg/htdocs/ENCODE/newsarch.html
  • lines changed 60, context: html, text, full: html, text
    Abbreviate old news
• src/hg/htdocs/ENCODE/qualityMetrics.html
  • lines changed 12, context: html, text, full: html, text
    Adding changes to quality metrics page per May update, refs #10760
• src/hg/htdocs/ENCODE/usageResources.html
  • lines changed 2, context: html, text, full: html, text
    Update pubs section to include 2013 NAR article
  • lines changed 1, context: html, text, full: html, text
    Update pubs section to include 2013 NAR article (correction)
• src/hg/htdocs/goldenPath/help/haplotypes.html
  • lines changed 2, context: html, text, full: html, text
    Quick change to remove 'antisense' as requested by B0b.
• src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
  • lines changed 2, context: html, text, full: html, text
    added a direct link to the parameter definition page from the top of help page after having much difficulty finding it in a workshop
  • lines changed 0, context: html, text, full: html, text
    added in two spaces between words
• src/hg/htdocs/style/HGStyle.css
  • lines changed 1, context: html, text, full: html, text
    Moved 'topHat' style to HGStyle.css
  • lines changed 1, context: html, text, full: html, text
    Sorry, screwed up the topHat style. This works.
• src/hg/htdocs/training.html
  • lines changed 8, context: html, text, full: html, text
    Fixing broken link to UCSC genome browser tutorial on training.html, adding link to Track Hubs User Guide, adjusted nearby lines to open blank page
• src/hg/inc/haplotypes.h
  • lines changed 1, context: html, text, full: html, text
    Significant changes to the UI as negotiated with Brooke, Pauline and B0b
• src/hg/inc/hui.h
  • lines changed 3, context: html, text, full: html, text
    Libify condensed cell table for factorSource tracks, shown in both hgc and hgTrackUi. refs #10097
  • lines changed 9, context: html, text, full: html, text
    Cleanup libification of factorSource UI. refs #10097
• src/hg/js/alleles.js
  • lines changed 46, context: html, text, full: html, text
    Significant changes to the UI as negotiated with Brooke, Pauline and B0b
  • lines changed 8, context: html, text, full: html, text
    Fixed problem where showing full sequence caused other sections to scroll horizontally off the page.
• src/hg/lib/annoStreamDb.c
  • lines changed 29, context: html, text, full: html, text
    Added 2 new args to annoStreamer:nextRow: minChrom and minEnd(which could also be called regionStart depending on point of view).
    Streamers may use those hints to skip over data that precedes
    minChrom and minEnd, to avoid the overhead of creating annoRows
    that annoGrators will then have to skip over. When primary data
    are sparse and grator data are very dense, this saves significant
    memory and user-cycles. Unfortunately mysql can still be the
    bottleneck for elapsed time. Room for improvement in annoStreamDb:
    when assembly has a reasonably small number of sequences (<1000),
    genome-wide queries could be internally broken down into per-seq
    queries; that would let us skip over chroms that precede minChrom.
    refs #6152
    
• src/hg/lib/annoStreamWig.c
  • lines changed 3, context: html, text, full: html, text
    Added 2 new args to annoStreamer:nextRow: minChrom and minEnd(which could also be called regionStart depending on point of view).
    Streamers may use those hints to skip over data that precedes
    minChrom and minEnd, to avoid the overhead of creating annoRows
    that annoGrators will then have to skip over. When primary data
    are sparse and grator data are very dense, this saves significant
    memory and user-cycles. Unfortunately mysql can still be the
    bottleneck for elapsed time. Room for improvement in annoStreamDb:
    when assembly has a reasonably small number of sequences (<1000),
    genome-wide queries could be internally broken down into per-seq
    queries; that would let us skip over chroms that precede minChrom.
    refs #6152
    
• src/hg/lib/haplotypes.c
  • lines changed 304, context: html, text, full: html, text
    Significant changes to the UI as negotiated with Brooke, Pauline and B0b
  • lines changed 5, context: html, text, full: html, text
    Forgot one simple hover message.
  • lines changed 2, context: html, text, full: html, text
    Moved 'topHat' style to HGStyle.css
  • lines changed 38, context: html, text, full: html, text
    Still trying to perfect the popScore. I think Fst calc is correct now.
  • lines changed 17, context: html, text, full: html, text
    Well that was short-lived. I do need to multiply Fst*N to get a good popScore.
  • lines changed 0, context: html, text, full: html, text
    Going overboard trying to get changes in before beta build.
• src/hg/lib/hui.c
  • lines changed 76, context: html, text, full: html, text
    Libify condensed cell table for factorSource tracks, shown in both hgc and hgTrackUi. refs #10097
  • lines changed 5, context: html, text, full: html, text
    Cleanup libification of factorSource UI. refs #10097
• src/hg/lib/jksql.c
  • lines changed 6, context: html, text, full: html, text
    does not work on innodb
• src/hg/makeDb/doc/encodeDccHg19/haibMethyl450.txt
  • lines changed 57, context: html, text, full: html, text
    Fixes to HAIB Methyl 450 track. refs #10447
• src/hg/makeDb/doc/hg19.txt
  • lines changed 12, context: html, text, full: html, text
    makedoc for swiss prot mutations track
  • lines changed 9, context: html, text, full: html, text
    makedoc for lovd track
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethyl450.ra
  • lines changed 127, context: html, text, full: html, text
    Fixes to HAIB Methyl 450 track. refs #10447
• src/hg/makeDb/trackDb/human/hg19/wgEncodeAwgTfbsUniform.html
  • lines changed 6, context: html, text, full: html, text
    Adding list of origin track names, link to ENC TF super-track, for Uniform TFBS HTML page refs #10042
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethyl450.html
  • lines changed 12, context: html, text, full: html, text
    Fixes to HAIB Methyl 450 track. refs #10447
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethyl450.ra
  • lines changed 2, context: html, text, full: html, text
    Fixes to HAIB Methyl 450 track. refs #10447
• src/hg/makeDb/trackDb/human/hg19/wgEncodeReg.ra
  • lines changed 3, context: html, text, full: html, text
    Cleanup libification of factorSource UI. refs #10097
• src/hg/makeDb/trackDb/tagTypes.tab
  • lines changed 1, context: html, text, full: html, text
    Cleanup libification of factorSource UI. refs #10097
• src/hg/oneShot/freen/freen.c
  • lines changed 19, context: html, text, full: html, text
    Freen tests parallelFetch.
• src/hg/utils/automation/doHgNearBlastp.pl
  • lines changed 1, context: html, text, full: html, text
    docummented option was missing from the options list so make it available, refs #9104
• src/hg/utils/lovd/check.sh
  • lines changed 47, context: html, text, full: html, text
    change lovd ottomatization scripts to not squeak if rowcount has not changed
• src/hg/utils/lovd/checkAndLoad.sh
  • lines changed 54, context: html, text, full: html, text
    change lovd ottomatization scripts to not squeak if rowcount has not changed
• src/hg/utils/lovd/doUpdate.sh
  • lines changed 2, context: html, text, full: html, text
    change lovd ottomatization scripts to not squeak if rowcount has not changed
• src/hg/utils/lovd/load.sh
  • lines changed 21, context: html, text, full: html, text
    change lovd ottomatization scripts to not squeak if rowcount has not changed
• src/hg/utils/uniprotMutations/liftUniprotMut.py
  • lines changed 5, context: html, text, full: html, text
    changes according to code review #10813
• src/inc/annoStreamer.h
  • lines changed 5, context: html, text, full: html, text
    Added 2 new args to annoStreamer:nextRow: minChrom and minEnd(which could also be called regionStart depending on point of view).
    Streamers may use those hints to skip over data that precedes
    minChrom and minEnd, to avoid the overhead of creating annoRows
    that annoGrators will then have to skip over. When primary data
    are sparse and grator data are very dense, this saves significant
    memory and user-cycles. Unfortunately mysql can still be the
    bottleneck for elapsed time. Room for improvement in annoStreamDb:
    when assembly has a reasonably small number of sequences (<1000),
    genome-wide queries could be internally broken down into per-seq
    queries; that would let us skip over chroms that precede minChrom.
    refs #6152
    
• src/lib/annoGrator.c
  • lines changed 5, context: html, text, full: html, text
    Added 2 new args to annoStreamer:nextRow: minChrom and minEnd(which could also be called regionStart depending on point of view).
    Streamers may use those hints to skip over data that precedes
    minChrom and minEnd, to avoid the overhead of creating annoRows
    that annoGrators will then have to skip over. When primary data
    are sparse and grator data are very dense, this saves significant
    memory and user-cycles. Unfortunately mysql can still be the
    bottleneck for elapsed time. Room for improvement in annoStreamDb:
    when assembly has a reasonably small number of sequences (<1000),
    genome-wide queries could be internally broken down into per-seq
    queries; that would let us skip over chroms that precede minChrom.
    refs #6152
    
• src/lib/annoGratorQuery.c
  • lines changed 1, context: html, text, full: html, text
    Added 2 new args to annoStreamer:nextRow: minChrom and minEnd(which could also be called regionStart depending on point of view).
    Streamers may use those hints to skip over data that precedes
    minChrom and minEnd, to avoid the overhead of creating annoRows
    that annoGrators will then have to skip over. When primary data
    are sparse and grator data are very dense, this saves significant
    memory and user-cycles. Unfortunately mysql can still be the
    bottleneck for elapsed time. Room for improvement in annoStreamDb:
    when assembly has a reasonably small number of sequences (<1000),
    genome-wide queries could be internally broken down into per-seq
    queries; that would let us skip over chroms that precede minChrom.
    refs #6152
    
• src/lib/annoStreamBigBed.c
  • lines changed 23, context: html, text, full: html, text
    Added 2 new args to annoStreamer:nextRow: minChrom and minEnd(which could also be called regionStart depending on point of view).
    Streamers may use those hints to skip over data that precedes
    minChrom and minEnd, to avoid the overhead of creating annoRows
    that annoGrators will then have to skip over. When primary data
    are sparse and grator data are very dense, this saves significant
    memory and user-cycles. Unfortunately mysql can still be the
    bottleneck for elapsed time. Room for improvement in annoStreamDb:
    when assembly has a reasonably small number of sequences (<1000),
    genome-wide queries could be internally broken down into per-seq
    queries; that would let us skip over chroms that precede minChrom.
    refs #6152
    
• src/lib/annoStreamBigWig.c
  • lines changed 25, context: html, text, full: html, text
    Added 2 new args to annoStreamer:nextRow: minChrom and minEnd(which could also be called regionStart depending on point of view).
    Streamers may use those hints to skip over data that precedes
    minChrom and minEnd, to avoid the overhead of creating annoRows
    that annoGrators will then have to skip over. When primary data
    are sparse and grator data are very dense, this saves significant
    memory and user-cycles. Unfortunately mysql can still be the
    bottleneck for elapsed time. Room for improvement in annoStreamDb:
    when assembly has a reasonably small number of sequences (<1000),
    genome-wide queries could be internally broken down into per-seq
    queries; that would let us skip over chroms that precede minChrom.
    refs #6152
    
• src/lib/annoStreamTab.c
  • lines changed 31, context: html, text, full: html, text
    Added 2 new args to annoStreamer:nextRow: minChrom and minEnd(which could also be called regionStart depending on point of view).
    Streamers may use those hints to skip over data that precedes
    minChrom and minEnd, to avoid the overhead of creating annoRows
    that annoGrators will then have to skip over. When primary data
    are sparse and grator data are very dense, this saves significant
    memory and user-cycles. Unfortunately mysql can still be the
    bottleneck for elapsed time. Room for improvement in annoStreamDb:
    when assembly has a reasonably small number of sequences (<1000),
    genome-wide queries could be internally broken down into per-seq
    queries; that would let us skip over chroms that precede minChrom.
    refs #6152
    
• src/lib/annoStreamVcf.c
  • lines changed 49, context: html, text, full: html, text
    Added 2 new args to annoStreamer:nextRow: minChrom and minEnd(which could also be called regionStart depending on point of view).
    Streamers may use those hints to skip over data that precedes
    minChrom and minEnd, to avoid the overhead of creating annoRows
    that annoGrators will then have to skip over. When primary data
    are sparse and grator data are very dense, this saves significant
    memory and user-cycles. Unfortunately mysql can still be the
    bottleneck for elapsed time. Room for improvement in annoStreamDb:
    when assembly has a reasonably small number of sequences (<1000),
    genome-wide queries could be internally broken down into per-seq
    queries; that would let us skip over chroms that precede minChrom.
    refs #6152
    
• src/lib/obscure.c
  • lines changed 14, context: html, text, full: html, text
    Making sprintLongWithCommas work up to the trillions.
  • lines changed 2, context: html, text, full: html, text
    problem for 32bit fixed
• src/lib/vcfBits.c
  • lines changed 5, context: html, text, full: html, text
    Fixed accounting bug where chrX reference haplotypes could have >100 percent frequency.
• src/makefile
  • lines changed 11, context: html, text, full: html, text
    begin to segregate the utilities into categories all, userApps, cellar refs #9104
  • lines changed 1, context: html, text, full: html, text
    get stringify built before everything else refs #9104
• src/parasol/lib/makefile
  • lines changed 4, context: html, text, full: html, text
    construct destination directory before archiving library refs #9104
• src/utils/makefile
  • lines changed 74, context: html, text, full: html, text
    begin to segregate the utilities into categories all, userApps, cellar refs #9104
  • lines changed 2, context: html, text, full: html, text
    get stringify built before everything else refs #9104
• src/utils/qa/makefile
  • lines changed 1, context: html, text, full: html, text
    Adding blatPing.csh to makefile. refs #10796
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    v284 preview2

• lines changed: 2152
• files changed: 92