All File Changes

v254_base to v255_preview (2011-07-19 to 2011-07-26) v255

• src/blat/version.doc
  • lines changed 1, context: html, text, full: html, text
    fixed segfault when -fine -minIdentity=0 -minScore=0
• src/hg/cartDump/cartDump.c
  • lines changed 5, context: html, text, full: html, text
    Adding lm parameter to cartTdbTreeCleanupOverrides. Sorry I missed this on initial checkin.
• src/hg/encode/DAFs/2.0/awgUniform.daf
  • lines changed 54, context: html, text, full: html, text
    First pass at the DAF for AWG uniform analysis track. Also added new view to cv to accomadate for data. Redmine #4522.
• src/hg/encode/DAFs/2.0/uw5c.daf
  • lines changed 2, context: html, text, full: html, text
    modified daf to match changes to emtadata for 5c
• src/hg/encode/encodeExp/tests/expected/modifyTest.out.ra
  • lines changed 1, context: html, text, full: html, text
    Support adding an expVar. Use oldVal=None to update command
• src/hg/encode/encodeExp/tests/makefile
  • lines changed 1, context: html, text, full: html, text
    Support adding an expVar. Use oldVal=None to update command
• src/hg/encode/encodeLoad/doEncodeLoad.pl
  • lines changed 2, context: html, text, full: html, text
    Eliminate the submission path from tars that we generate.
• src/hg/encode/encodeReport/gencodeStats
  • lines changed 31, context: html, text, full: html, text
    added program for generate GENCODE statistics for ENCODE report
• src/hg/encode/encodeValidate/doEncodeValidate.pl
  • lines changed 55, context: html, text, full: html, text
    added functionality to handle blank spaces, added function to reject blank spaces for required variables, reworked how 'None' is handled as a value, added function to check if there are more values in a ddf line than in the ddfheader
• src/hg/hgGateway/hgGateway.c
  • lines changed 3, context: html, text, full: html, text
    turn on fit browser image to screen (redmine #2633)
• src/hg/hgHubConnect/hgHubConnect.c
  • lines changed 3, context: html, text, full: html, text
    changes out of code review #4647
  • lines changed 3, context: html, text, full: html, text
    fix a bug that Greg found. #4627
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 22, context: html, text, full: html, text
    Remove preview links from hgc (wasnt intended to go there, and was producing broken link)
  • lines changed 10, context: html, text, full: html, text
    Changed phenotype class into phenotype mape key per OMIM request.
  • lines changed 1, context: html, text, full: html, text
    Fix for redmine 4686. Don't show navlinks when called by ajax.
• src/hg/hgTracks/hgTracks.c
  • lines changed 3, context: html, text, full: html, text
    Optimizing parentChildCartCleanup by creating a faster version of cartVarsWithPrefix that works in local memory.
  • lines changed 5, context: html, text, full: html, text
    Renaming uglyTime to measureTime since it is no longer temporary.
  • lines changed 12, context: html, text, full: html, text
    more IN_PLACE_UPDATE stuff
  • lines changed 5, context: html, text, full: html, text
    Putting in cart-fetch-time measureTiming call.
  • lines changed 8, context: html, text, full: html, text
    turn on fit browser image to screen (redmine #2633); more in place update changes (only live in larrym's tree)
• src/hg/hgTracks/hgTracks.h
  • lines changed 2, context: html, text, full: html, text
    Renaming uglyTime to measureTime since it is no longer temporary.
• src/hg/hgTracks/imageV2.c
  • lines changed 2, context: html, text, full: html, text
    change trackDbJson to syntax used by scrapeVariable
• src/hg/hgTracks/imageV2.h
  • lines changed 1, context: html, text, full: html, text
    turn on fit browser image to screen (redmine #2633); more in place update changes (only live in larrym's tree)
• src/hg/hgTracks/mainMain.c
  • lines changed 1, context: html, text, full: html, text
    Renaming uglyTime to measureTime since it is no longer temporary.
  • lines changed 1, context: html, text, full: html, text
    change trackDbJson to syntax used by scrapeVariable
• src/hg/hgTracks/searchTracks.c
  • lines changed 3, context: html, text, full: html, text
    Renaming uglyTime to measureTime since it is no longer temporary.
• src/hg/hgTracks/simpleTracks.c
  • lines changed 118, context: html, text, full: html, text
    Added functions for COSMIC and updated functions for OMIM.
  • lines changed 2, context: html, text, full: html, text
    Replaced tdfbExtras hash with struct for efficiency. Redmine 4674.
  • lines changed 1, context: html, text, full: html, text
    simpleTracks.c git check in problem?
• src/hg/hgc/hgc.c
  • lines changed 66, context: html, text, full: html, text
    Updated functions for COSMIC and OMIM.
• src/hg/htdocs/ENCODE/downloads.html
  • lines changed 3, context: html, text, full: html, text
    fixed links that I accidentally had reversed
• src/hg/htdocs/ENCODE/downloadsMouse.html
  • lines changed 4, context: html, text, full: html, text
    adding Stan/Yale Histone to downloads page, redmine #97
  • lines changed 6, context: html, text, full: html, text
    adding LICR TFBS, redmine# 101
• src/hg/htdocs/images/Macropus_eugenii.jpg
  • lines changed 0, context: html, text, full: html, text
    use Wallby picture from NHGRI
• src/hg/inc/cart.h
  • lines changed 10, context: html, text, full: html, text
    Optimizing parentChildCartCleanup by creating a faster version of cartVarsWithPrefix that works in local memory.
• src/hg/inc/encode/encodeExp.h
  • lines changed 1, context: html, text, full: html, text
    Support adding an expVar. Use oldVal=None to update command
• src/hg/inc/hubConnect.h
  • lines changed 4, context: html, text, full: html, text
    changes out of code review #4647
• src/hg/inc/jsHelper.h
  • lines changed 3, context: html, text, full: html, text
    add jsonErrPrintf
• src/hg/inc/trackDb.h
  • lines changed 106, context: html, text, full: html, text
    Replaced tdfbExtras hash with struct for efficiency. Redmine 4674.
• src/hg/js/ajax.js
  • lines changed 1, context: html, text, full: html, text
    Ajax call without declaring dataType 'html' can cause browser errors.
• src/hg/js/ddcl.js
  • lines changed 1, context: html, text, full: html, text
    Fix for redmine 4687. Called ddclSetup instead of ddcl.setup()
• src/hg/js/hgTracks.js
  • lines changed 105, context: html, text, full: html, text
    more work on in-place updating (redmine #4667); also some code and comments cleanup
  • lines changed 89, context: html, text, full: html, text
    add some comments; more in place update changes (only live in larrym's tree)
  • lines changed 10, context: html, text, full: html, text
    change trackDbJson to syntax used by scrapeVariable
• src/hg/js/jquery.cookie.js
  • lines changed 41, context: html, text, full: html, text
    adding a new js file to be used for storing and retrieving cookies with jquery. Ref: https://github.com/carhartl/jquery-cookie
• src/hg/js/utils.js
  • lines changed 4, context: html, text, full: html, text
    add some comments and code cleanup
• src/hg/lib/cart.c
  • lines changed 33, context: html, text, full: html, text
    Optimizing parentChildCartCleanup by creating a faster version of cartVarsWithPrefix that works in local memory.
  • lines changed 3, context: html, text, full: html, text
    Replaced tdfbExtras hash with struct for efficiency. Redmine 4674.
• src/hg/lib/customFactory.c
  • lines changed 1, context: html, text, full: html, text
    Replaced tdfbExtras hash with struct for efficiency. Redmine 4674.
• src/hg/lib/cv.c
  • lines changed 1, context: html, text, full: html, text
    Minor fixes to sizes of hash used by cv.ra
• src/hg/lib/encode/encodeExp.c
  • lines changed 24, context: html, text, full: html, text
    Support adding an expVar. Use oldVal=None to update command
• src/hg/lib/fileUi.c
  • lines changed 21, context: html, text, full: html, text
    Added 'Parent directory' link to support redirection from index.html.
• src/hg/lib/hubConnect.c
  • lines changed 23, context: html, text, full: html, text
    changes out of code review #4647
• src/hg/lib/hui.c
  • lines changed 14, context: html, text, full: html, text
    Remove preview links from hgc (wasnt intended to go there, and was producing broken link)
  • lines changed 31, context: html, text, full: html, text
    Replaced tdfbExtras hash with struct for efficiency. Redmine 4674.
• src/hg/lib/jsHelper.c
  • lines changed 14, context: html, text, full: html, text
    add jsonErrPrintf
• src/hg/lib/mdb.c
  • lines changed 5, context: html, text, full: html, text
    Replaced tdfbExtras hash with struct for efficiency. Redmine 4674.
• src/hg/lib/trackDb.c
  • lines changed 1, context: html, text, full: html, text
    Replaced tdfbExtras hash with struct for efficiency. Redmine 4674.
• src/hg/lib/trackDbCustom.c
  • lines changed 1, context: html, text, full: html, text
    use smaller hash size in tdbExtrasAddOrUpdate to fix a performance issue (see redmine 4620 and 4674)
  • lines changed 31, context: html, text, full: html, text
    Replaced tdfbExtras hash with struct for efficiency. Redmine 4674.
• src/hg/lib/trackHub.c
  • lines changed 3, context: html, text, full: html, text
    fix segvio; if udcDir can't be opened. Add Hub clear from command line.
• src/hg/lib/wiggleCart.c
  • lines changed 11, context: html, text, full: html, text
    fix right click track config for bigWigs not retaining vertical viewing max (redmine #4402)
• src/hg/makeDb/doc/danRer7.txt
  • lines changed 82, context: html, text, full: html, text
    adding cpgIslandExt track
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeUwDnase.release3.notes
  • lines changed 2017, context: html, text, full: html, text
    notes files for uw tracks to be put into pushQ
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeUwHistone.release2.notes
  • lines changed 2212, context: html, text, full: html, text
    notes files for uw tracks to be put into pushQ
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeUwTfbs.release2.notes
  • lines changed 1464, context: html, text, full: html, text
    notes files for uw tracks to be put into pushQ
• src/hg/makeDb/doc/encodeDccMm9/wgEncodeSydhHistone.release1.notes
  • lines changed 2, context: html, text, full: html, text
    Loaded replacement peak file, but had to update name since tag changed in cv. Fixes Redmine #97, note 28.
• src/hg/makeDb/doc/encodeDccMm9/wgEncodeSydhTfbs.release2.notes
  • lines changed 2, context: html, text, full: html, text
    Added replacment Peak files loaded from subId 4610. Updated notes files because 1 tag was changed in cv causing name of file and table to change.
• src/hg/makeDb/doc/hg19.txt
  • lines changed 81, context: html, text, full: html, text
    reached a conclusion for fosEnds and add Ensembl gene name search
  • lines changed 50, context: html, text, full: html, text
    resolve this merge conflict
• src/hg/makeDb/doc/macEug2.txt
  • lines changed 290, context: html, text, full: html, text
    Macropus eugenii (wallaby) macEug2 initial assembly
• src/hg/makeDb/trackDb/README
  • lines changed 8, context: html, text, full: html, text
    Added pgSnp type to README for trackDb
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 3, context: html, text, full: html, text
    Fixed broken links
  • lines changed 1, context: html, text, full: html, text
    Commented out wrong BJ protocol, no correct one exists
  • lines changed 37, context: html, text, full: html, text
    Adding the typeOfTerm type, removing parentTable and fileIndex, changing the names of geoSeries and geoSample to have accession in the name. Mostly I am trying to get the CV to match what we have in the database so that the validators work.
  • lines changed 8, context: html, text, full: html, text
    Reviewed the provisinal tags
  • lines changed 10, context: html, text, full: html, text
    removed some region views
  • lines changed 30, context: html, text, full: html, text
    First pass at the DAF for AWG uniform analysis track. Also added new view to cv to accomadate for data. Redmine #4522.
  • lines changed 1, context: html, text, full: html, text
    Changed None to none
• src/hg/makeDb/trackDb/cv/beta/cv.ra
  • lines changed 156, context: html, text, full: html, text
    Summary of changes: Commented out all of the variations of BJ tert until we figure it out (ticket 4536). Added views for all of the GencodeV7 data that will be coming in, changed an old view to specify GencodeV3c. Cleaned up typeOfTerms by removing parentTable and fileIndex which have been retired, changing geoSeries and geoSample to be geo*Accession to comply wiht validator, added type as a typeOfTerm. There were many changes to protocol links to try to fix those in ticket 4408. Added a new control RevXLink.
• src/hg/makeDb/trackDb/human/hg18/decode.rmap.ra
  • lines changed 93, context: html, text, full: html, text
    adding Decode Recombination map tracks
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeCaltechRnaSeq.ra
  • lines changed 555, context: html, text, full: html, text
    Changed geoSeries and geoSample to have Accession and swapped Paired for Alignments
  • lines changed 1, context: html, text, full: html, text
    Changing geoSample to geoSampleAccession and swapping Paired for Alignments
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeHudsonalphaMethylSeq.ra
  • lines changed 16, context: html, text, full: html, text
    Changed dccNotes to dccInternalNotes
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeYaleChIPseq.ra
  • lines changed 12, context: html, text, full: html, text
    correct hek293b > hek293 in hg18 sydh tfbs
• src/hg/makeDb/trackDb/human/hg18/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    adding Decode Recombination map tracks
• src/hg/makeDb/trackDb/human/hg19/evoCpg.html
  • lines changed 28, context: html, text, full: html, text
    Added evoCpg.html for hg19.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCaltechRnaSeq.ra
  • lines changed 149, context: html, text, full: html, text
    Changed var names that failed in the validation process. Riken: dateResubmitted, GisChiaPet: docId submitPath, UncBsu: dccInternalNotes, Caltech:dateSubmitted
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra
  • lines changed 400, context: html, text, full: html, text
    added accession numbers for the first part of CshlLong
  • lines changed 5116, context: html, text, full: html, text
    Long and short labels, removed V3c and added V7, fixed the cv line
  • lines changed 19, context: html, text, full: html, text
    added new sample accession #s from GEO for expIds 163-182
  • lines changed 408, context: html, text, full: html, text
    added more sample #s, first commit was only partial
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlShortRnaSeq.ra
  • lines changed 109, context: html, text, full: html, text
    accession and experimentified cshl short missing ones
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisChiaPet.ra
  • lines changed 193, context: html, text, full: html, text
    Changed var names that failed in the validation process. Riken: dateResubmitted, GisChiaPet: docId submitPath, UncBsu: dccInternalNotes, Caltech:dateSubmitted
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisRnaPet.ra
  • lines changed 15, context: html, text, full: html, text
    Changed var names that failed in the validation process. Riken: dateResubmitted, GisChiaPet: docId submitPath, UncBsu: dccInternalNotes, Caltech:dateSubmitted
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra
  • lines changed 17, context: html, text, full: html, text
    correct metadata errors in 5c, haib and sydh tfbs
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeRikenCage.ra
  • lines changed 50, context: html, text, full: html, text
    Changed var names that failed in the validation process. Riken: dateResubmitted, GisChiaPet: docId submitPath, UncBsu: dccInternalNotes, Caltech:dateSubmitted
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra
  • lines changed 121, context: html, text, full: html, text
    correct metadata errors in 5c, haib and sydh tfbs
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUncBsuProt.ra
  • lines changed 3, context: html, text, full: html, text
    Changed var names that failed in the validation process. Riken: dateResubmitted, GisChiaPet: docId submitPath, UncBsu: dccInternalNotes, Caltech:dateSubmitted
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUw5C.ra
  • lines changed 54, context: html, text, full: html, text
    correct metadata errors in 5c, haib and sydh tfbs
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwAffyExonArray.ra
  • lines changed 271, context: html, text, full: html, text
    changed accession to geoSampleAccession to fix the Uw microarray data
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwTfbs.ra
  • lines changed 485, context: html, text, full: html, text
    added Uw TFBS geo id's to metaDb
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    Switched line so that the new patch would show on beta
  • lines changed 13, context: html, text, full: html, text
    Added eveCpg for hg19.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.ra
  • lines changed 1, context: html, text, full: html, text
    bad search and replace move replaced somwhere else
  • lines changed 826, context: html, text, full: html, text
    Long and short labels, removed V3c and added V7, fixed the cv line
  • lines changed 2, context: html, text, full: html, text
    Changed defualts for order and visibility of views
  • lines changed 163, context: html, text, full: html, text
    short labels on Cshl Long
  • lines changed 4, context: html, text, full: html, text
    adding mean+whiskers for signals and filter at 200 for Junctions
  • lines changed 48, context: html, text, full: html, text
    set defaults for cshl long
  • lines changed 1, context: html, text, full: html, text
    correct some tag errors
  • lines changed 24, context: html, text, full: html, text
    finalized defaults
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.new.r3.ra
  • lines changed 70, context: html, text, full: html, text
    changed defautls on csdhl short to be K562 only
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.new.ra
  • lines changed 27, context: html, text, full: html, text
    Changed Contigs and Junctions to be bed 6 for display purposes
  • lines changed 57, context: html, text, full: html, text
    changed defautls on csdhl short to be K562 only
  • lines changed 72, context: html, text, full: html, text
    short labels on cshl short
  • lines changed 0, context: html, text, full: html, text
    fixed spacing issues
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibGenotype.html
  • lines changed 1, context: html, text, full: html, text
    moved period out of link
• src/hg/makeDb/trackDb/human/hg19/wgEncodeRegNorm.ra
  • lines changed 774, context: html, text, full: html, text
    Adding experimental .ra file just to back it up - may be used for real at some point.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.ra
  • lines changed 470, context: html, text, full: html, text
    addeed numbers to cell lines for sorting purposes
  • lines changed 0, context: html, text, full: html, text
    correct space error
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUw5C.html
  • lines changed 8, context: html, text, full: html, text
    updated uw's html files
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUw5C.ra
  • lines changed 1, context: html, text, full: html, text
    changed short label
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.new.html
  • lines changed 6, context: html, text, full: html, text
    updated uw's html files
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.new.ra
  • lines changed 44, context: html, text, full: html, text
    corrected some long label stuff UW
  • lines changed 71, context: html, text, full: html, text
    fixed short labels
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.new.html
  • lines changed 103, context: html, text, full: html, text
    updated uw's html files
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.new.ra
  • lines changed 518, context: html, text, full: html, text
    long and short labels uw histone
  • lines changed 1, context: html, text, full: html, text
    changed file sort order fields
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwTfbs.new.html
  • lines changed 89, context: html, text, full: html, text
    updated uw's html files
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwTfbs.new.ra
  • lines changed 117, context: html, text, full: html, text
    short labels redone on uwtfbs
  • lines changed 57, context: html, text, full: html, text
    long labels uw tfbs
  • lines changed 1, context: html, text, full: html, text
    changed file sort order fields
• src/hg/makeDb/trackDb/human/omimDescriptionText.html
  • lines changed 1, context: html, text, full: html, text
    Changed phenotype class into phenotype mape key per OMIM request.
• src/hg/makeDb/trackDb/human/omimGene2.html
  • lines changed 7, context: html, text, full: html, text
    Changed phenotype class into phenotype mape key per OMIM request.
• src/hg/makeDb/trackDb/human/omimLocation.html
  • lines changed 7, context: html, text, full: html, text
    Changed phenotype class into phenotype mape key per OMIM request.
• src/hg/makeDb/trackDb/human/trackDb.pgSnp.ra
  • lines changed 166, context: html, text, full: html, text
    Adding a new subgroup to pgSnp track, dividing SNPs and indels
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrHistone.ra
  • lines changed 21, context: html, text, full: html, text
    Removed reference to parentTable in metaDb for files. Term is not used in cv anymore.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrTfbs.ra
  • lines changed 27, context: html, text, full: html, text
    Removed reference to parentTable in metaDb for files. Term is not used in cv anymore.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhHistone.ra
  • lines changed 8, context: html, text, full: html, text
    Loaded replacement peak file, but had to update name since tag changed in cv. Fixes Redmine #97, note 28.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhTfbs.ra
  • lines changed 67, context: html, text, full: html, text
    Added replacment Peak files loaded from subId 4610. Updated notes files because 1 tag was changed in cv causing name of file and table to change.
  • lines changed 17, context: html, text, full: html, text
    Removed reference to parentTable in metaDb for files. Term is not used in cv anymore.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/makefile
  • lines changed 1, context: html, text, full: html, text
    staging Stan/Yale Histone on beta, redmine #97
  • lines changed 1, context: html, text, full: html, text
    staging LICR RNA-Seq on beta, redmine# 3629
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/wgEncodeLicrRnaSeq.ra
  • lines changed 1666, context: html, text, full: html, text
    staging LICR RNA-Seq on beta, redmine# 3629
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/wgEncodeSydhHistone.ra
  • lines changed 724, context: html, text, full: html, text
    staging Stan/Yale Histone on beta, redmine #97
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/public/makefile
  • lines changed 1, context: html, text, full: html, text
    releasing LICR TFBS, redmine# 101
  • lines changed 1, context: html, text, full: html, text
    preparing metadata for Stan/Yale Histone for release to public, redmine #97
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/public/wgEncodeLicrTfbs.ra
  • lines changed 5445, context: html, text, full: html, text
    releasing LICR TFBS, redmine# 101
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/public/wgEncodeSydhHistone.ra
  • lines changed 724, context: html, text, full: html, text
    preparing metadata for Stan/Yale Histone for release to public, redmine #97
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.wgEncode.ra
  • lines changed 1, context: html, text, full: html, text
    staging Stan/Yale Histone on beta, redmine #97
  • lines changed 1, context: html, text, full: html, text
    staging LICR RNA-Seq on beta, redmine# 3629
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrHistone.html
  • lines changed 1, context: html, text, full: html, text
    Updated line that states views present in track from 'ENCODE tracks typically contain one or more of the following views:' to 'This track contains the following views:'. Also standardized all Description about view's present paragraph to be the same in all tracks. Redmine #97, note 42.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrRnaSeq.html
  • lines changed 3, context: html, text, full: html, text
    Updated line that states views present in track from 'ENCODE tracks typically contain one or more of the following views:' to 'This track contains the following views:'. Also standardized all Description about view's present paragraph to be the same in all tracks. Redmine #97, note 42.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrTfbs.html
  • lines changed 4, context: html, text, full: html, text
    fixed a few typos, redmine# 101
  • lines changed 1, context: html, text, full: html, text
    Updated line that states views present in track from 'ENCODE tracks typically contain one or more of the following views:' to 'This track contains the following views:'. Also standardized all Description about view's present paragraph to be the same in all tracks. Redmine #97, note 42.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuHistone.html
  • lines changed 1, context: html, text, full: html, text
    Updated line that states views present in track from 'ENCODE tracks typically contain one or more of the following views:' to 'This track contains the following views:'. Also standardized all Description about view's present paragraph to be the same in all tracks. Redmine #97, note 42.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuTfbs.html
  • lines changed 1, context: html, text, full: html, text
    Updated line that states views present in track from 'ENCODE tracks typically contain one or more of the following views:' to 'This track contains the following views:'. Also standardized all Description about view's present paragraph to be the same in all tracks. Redmine #97, note 42.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhHist.html
  • lines changed 1, context: html, text, full: html, text
    Fixed working of descirption of Peaks and removed word usually to be correctly describing the Peaks for this composite track. Fixes Redmine #97, note 36.
  • lines changed 48, context: html, text, full: html, text
    Updated ordering of references to be alphabetical. Also moved period out of hyperlink at the end of a title. Redmine #97, note 38. Updated the 'Contacts' link for Sherman Weisman to a new page. Redmine #97, note 39.
  • lines changed 2, context: html, text, full: html, text
    Reworded first sentence of second paragraph of methods section, with recomendations from Katrina. Redmine #97, note 40.
  • lines changed 1, context: html, text, full: html, text
    Updated line that states views present in track from 'ENCODE tracks typically contain one or more of the following views:' to 'This track contains the following views:'. Also standardized all Description about view's present paragraph to be the same in all tracks. Redmine #97, note 42.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhHistone.ra
  • lines changed 3, context: html, text, full: html, text
    Loaded replacement peak file, but had to update name since tag changed in cv. Fixes Redmine #97, note 28.
  • lines changed 1, context: html, text, full: html, text
    Fixed parent/subTrack link from composite settings to view specific settings. Fixes: Redmine #4668 and #97, note 32.
  • lines changed 0, context: html, text, full: html, text
    Fixed rest of formatting and changed subTrack to parent to be consistent naming.
  • lines changed 18, context: html, text, full: html, text
    Fixed formating of trackDb to correct composite track format spacing. Changed naming of subTrack to parent so that track is consistent. Moved subIds that were listed above track as comment to match current formatting, these track came in over a year ago and had the old metadata formating line in the subTrack and that line was removed by Cricket. Fixes Redmine #97, note 34.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhRnaSeq.html
  • lines changed 4, context: html, text, full: html, text
    Updated line that states views present in track from 'ENCODE tracks typically contain one or more of the following views:' to 'This track contains the following views:'. Also standardized all Description about view's present paragraph to be the same in all tracks. Redmine #97, note 42.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhTfbs.new.html
  • lines changed 1, context: html, text, full: html, text
    Fixed working of descirption of Peaks and removed word usually to be correctly describing the Peaks for this composite track. Fixes Redmine #97, note 36.
  • lines changed 7, context: html, text, full: html, text
    Moved period out of hyperlink at the end of a title. Updated the 'Contacts' link for Sherman Weisman to a new page.
  • lines changed 2, context: html, text, full: html, text
    Reworded first sentence of second paragraph of methods section, with recomendations from QA.
  • lines changed 1, context: html, text, full: html, text
    Updated line that states views present in track from 'ENCODE tracks typically contain one or more of the following views:' to 'This track contains the following views:'. Also standardized all Description about view's present paragraph to be the same in all tracks. Redmine #97, note 42.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhTfbs.newR2.ra
  • lines changed 13, context: html, text, full: html, text
    Added replacment Peak files loaded from subId 4610. Updated notes files because 1 tag was changed in cv causing name of file and table to change.
  • lines changed 11, context: html, text, full: html, text
    Fixed subTrack association to View configuration rather than composite configuration. Also fixed formatting into normal trackDb composite format.
  • lines changed 31, context: html, text, full: html, text
    Fixed rest of formatting and changed subTrack to parent to be consistent naming.
  • lines changed 52, context: html, text, full: html, text
    Moved subIds that were listed above track as comment to match current formatting, these track came in over a year ago and had the old metadata formating line in the subTrack and that line was removed by Cricket.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwDnase.html
  • lines changed 2, context: html, text, full: html, text
    Updated line that states views present in track from 'ENCODE tracks typically contain one or more of the following views:' to 'This track contains the following views:'. Also standardized all Description about view's present paragraph to be the same in all tracks. Redmine #97, note 42.
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    adding ensGeneName search
• src/hg/makeDb/trackDb/wallaby/macEug2/description.html
  • lines changed 7, context: html, text, full: html, text
    Initial detail page for Wallaby macEug2
• src/hg/utils/hubCheck/hubCheck.c
  • lines changed 56, context: html, text, full: html, text
    fix segvio; if udcDir can't be opened. Add Hub clear from command line.
• src/inc/genoFind.h
  • lines changed 1, context: html, text, full: html, text
    fixed segfault when -fine -minIdentity=0 -minScore=0
• src/jkOwnLib/gfOut.c
  • lines changed 3, context: html, text, full: html, text
    fixed segfault when -fine -minIdentity=0 -minScore=0
• src/lib/ra.c
  • lines changed 1, context: html, text, full: html, text
    Minor fixes to sizes of hash used by cv.ra
• src/lib/udc.c
  • lines changed 57, context: html, text, full: html, text
    speeding up udc by not re-opening bitmap and sparseData files unnecessarilly; also combined udcCacheContains with fetchMissing so that the bitmap would not be getting read twice upon cahe-misses; tested with udcTest both interleave and fork.
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    v255 preview1

• lines changed: 28400
• files changed: 184