All File Changes

v270_preview2 to v270_base (2012-07-10 to 2012-07-17) v270

• src/hg/encode/DAFs/3.0/mm9/wgEncodeCshlLongRnaSeq.daf
  • lines changed 2, context: html, text, full: html, text
    Increaseing to 10 mismatches
• src/hg/encode/encodeQaInit/encodeQaInit
  • lines changed 2, context: html, text, full: html, text
    made it so that the qa table tests aren't run on an empty table set
• src/hg/encode/validateFiles/validateFiles.c
  • lines changed 5, context: html, text, full: html, text
    fixing validateFiles bug to support non-tab default fieldCount with chopByWhite that somehow got lost
• src/hg/hgCustom/hgCustom.c
  • lines changed 3, context: html, text, full: html, text
    fixing simple html table tag errors caught with htmlCheck
• src/hg/hgFileSearch/hgFileSearch.c
  • lines changed 2, context: html, text, full: html, text
    fixing bug in html output found by htmlCheck
• src/hg/hgGene/hgGeneData/Mouse/mm10/links.ra
  • lines changed 9, context: html, text, full: html, text
    add some data files for mm10 UCSC genes (#7045)
  • lines changed 8, context: html, text, full: html, text
    comment out ExonPrimer for the moment (#7045)
• src/hg/hgGene/hgGeneData/Mouse/mm10/otherOrgs.ra
  • lines changed 17, context: html, text, full: html, text
    add some data files for mm10 UCSC genes (#7045)
• src/hg/hgHubConnect/hgHubConnect.c
  • lines changed 17, context: html, text, full: html, text
    fixed html error found by htmlCheck; added some newlines to make show source more legible
• src/hg/hgLiftOver/hgLiftOver.c
  • lines changed 1, context: html, text, full: html, text
    fix html error in hgLiftOver found by htmlCheck
• src/hg/hgTables/bedList.c
  • lines changed 11, context: html, text, full: html, text
    Next batch of many checkins as dictated by Jim. Formatting if and limiting lines to 100 chars. Changes limited to lines last touched by tdreszer (git blame) so as not to ruin history. None of these changes should affect executables in any way.
• src/hg/hgTables/correlate.c
  • lines changed 4, context: html, text, full: html, text
    Next batch of many checkins as dictated by Jim. Formatting if and limiting lines to 100 chars. Changes limited to lines last touched by tdreszer (git blame) so as not to ruin history. None of these changes should affect executables in any way.
• src/hg/hgTables/filterFields.c
  • lines changed 6, context: html, text, full: html, text
    Next batch of many checkins as dictated by Jim. Formatting if and limiting lines to 100 chars. Changes limited to lines last touched by tdreszer (git blame) so as not to ruin history. None of these changes should affect executables in any way.
• src/hg/hgTables/hgTables.c
  • lines changed 2, context: html, text, full: html, text
    Next batch of many checkins as dictated by Jim. Formatting if and limiting lines to 100 chars. Changes limited to lines last touched by tdreszer (git blame) so as not to ruin history. None of these changes should affect executables in any way.
• src/hg/hgTables/mainPage.c
  • lines changed 40, context: html, text, full: html, text
    Next batch of many checkins as dictated by Jim. Formatting if and limiting lines to 100 chars. Changes limited to lines last touched by tdreszer (git blame) so as not to ruin history. None of these changes should affect executables in any way.
• src/hg/hgTables/schema.c
  • lines changed 6, context: html, text, full: html, text
    Next batch of many checkins as dictated by Jim. Formatting if and limiting lines to 100 chars. Changes limited to lines last touched by tdreszer (git blame) so as not to ruin history. None of these changes should affect executables in any way.
• src/hg/hgTrackUi/encodePeakUi.c
  • lines changed 0, context: html, text, full: html, text
    Next batch of many checkins as dictated by Jim. Formatting if and limiting lines to 100 chars. Changes limited to lines last touched by tdreszer (git blame) so as not to ruin history. None of these changes should affect executables in any way.
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 2, context: html, text, full: html, text
    Just removed old ifdef SUBTRACK_CFG. That feature released for 6 months. Not going back.
  • lines changed 66, context: html, text, full: html, text
    Next batch of many checkins as dictated by Jim. Formatting if and limiting lines to 100 chars. Changes limited to lines last touched by tdreszer (git blame) so as not to ruin history. None of these changes should affect executables in any way.
• src/hg/hgTracks/chromGraphTrack.c
  • lines changed 2, context: html, text, full: html, text
    Next batch of many checkins as dictated by Jim. Formatting if and limiting lines to 100 chars. Changes limited to lines last touched by tdreszer (git blame) so as not to ruin history. None of these changes should affect executables in any way.
• src/hg/hgTracks/config.c
  • lines changed 27, context: html, text, full: html, text
    Next batch of many checkins as dictated by Jim. Formatting if and limiting lines to 100 chars. Changes limited to lines last touched by tdreszer (git blame) so as not to ruin history. None of these changes should affect executables in any way.
• src/hg/hgTracks/encode.c
  • lines changed 0, context: html, text, full: html, text
    Next batch of many checkins as dictated by Jim. Formatting if and limiting lines to 100 chars. Changes limited to lines last touched by tdreszer (git blame) so as not to ruin history. None of these changes should affect executables in any way.
• src/hg/hgTracks/expRatioTracks.c
  • lines changed 10, context: html, text, full: html, text
    Next batch of many checkins as dictated by Jim. Formatting if and limiting lines to 100 chars. Changes limited to lines last touched by tdreszer (git blame) so as not to ruin history. None of these changes should affect executables in any way.
• src/hg/hgTracks/hgTracks.c
  • lines changed 188, context: html, text, full: html, text
    Maybe last batch of many checkins as dictated by Jim. Formatting if and limiting lines to 100 chars. Changes (mostly) limited to lines last touched by tdreszer (git blame) so as not to ruin history. Some things not mine were 'fixed' so that my changes were in context. None of these changes should affect executables in any way.
• src/hg/hgTracks/hgTracks.h
  • lines changed 13, context: html, text, full: html, text
    Next batch of many checkins as dictated by Jim. Formatting if and limiting lines to 100 chars. Changes limited to lines last touched by tdreszer (git blame) so as not to ruin history. None of these changes should affect executables in any way.
• src/hg/hgTracks/imageV2.c
  • lines changed 259, context: html, text, full: html, text
    Maybe last batch of many checkins as dictated by Jim. Formatting if and limiting lines to 100 chars. Changes (mostly) limited to lines last touched by tdreszer (git blame) so as not to ruin history. Some things not mine were 'fixed' so that my changes were in context. None of these changes should affect executables in any way.
• src/hg/hgTracks/imageV2.h
  • lines changed 190, context: html, text, full: html, text
    Maybe last batch of many checkins as dictated by Jim. Formatting if and limiting lines to 100 chars. Changes (mostly) limited to lines last touched by tdreszer (git blame) so as not to ruin history. Some things not mine were 'fixed' so that my changes were in context. None of these changes should affect executables in any way.
• src/hg/hgTracks/mainMain.c
  • lines changed 1, context: html, text, full: html, text
    Next batch of many checkins as dictated by Jim. Formatting if and limiting lines to 100 chars. Changes limited to lines last touched by tdreszer (git blame) so as not to ruin history. None of these changes should affect executables in any way.
• src/hg/hgTracks/oneTrack.c
  • lines changed 0, context: html, text, full: html, text
    Next batch of many checkins as dictated by Jim. Formatting if and limiting lines to 100 chars. Changes limited to lines last touched by tdreszer (git blame) so as not to ruin history. None of these changes should affect executables in any way.
• src/hg/hgTracks/rnaFoldTrack.c
  • lines changed 0, context: html, text, full: html, text
    Next batch of many checkins as dictated by Jim. Formatting if and limiting lines to 100 chars. Changes limited to lines last touched by tdreszer (git blame) so as not to ruin history. None of these changes should affect executables in any way.
• src/hg/hgTracks/searchTracks.c
  • lines changed 130, context: html, text, full: html, text
    Maybe last batch of many checkins as dictated by Jim. Formatting if and limiting lines to 100 chars. Changes (mostly) limited to lines last touched by tdreszer (git blame) so as not to ruin history. Some things not mine were 'fixed' so that my changes were in context. None of these changes should affect executables in any way.
• src/hg/hgTracks/simpleTracks.c
  • lines changed 6, context: html, text, full: html, text
    Just removed old ifdef SUBTRACK_CFG. That feature released for 6 months. Not going back.
  • lines changed 93, context: html, text, full: html, text
    Maybe last batch of many checkins as dictated by Jim. Formatting if and limiting lines to 100 chars. Changes (mostly) limited to lines last touched by tdreszer (git blame) so as not to ruin history. Some things not mine were 'fixed' so that my changes were in context. None of these changes should affect executables in any way.
• src/hg/hgTracks/variation.c
  • lines changed 4, context: html, text, full: html, text
    Next batch of many checkins as dictated by Jim. Formatting if and limiting lines to 100 chars. Changes limited to lines last touched by tdreszer (git blame) so as not to ruin history. None of these changes should affect executables in any way.
• src/hg/hgTracks/wigMafTrack.c
  • lines changed 8, context: html, text, full: html, text
    Next batch of many checkins as dictated by Jim. Formatting if and limiting lines to 100 chars. Changes limited to lines last touched by tdreszer (git blame) so as not to ruin history. None of these changes should affect executables in any way.
• src/hg/hgTracks/wigTrack.c
  • lines changed 1, context: html, text, full: html, text
    Next batch of many checkins as dictated by Jim. Formatting if and limiting lines to 100 chars. Changes limited to lines last touched by tdreszer (git blame) so as not to ruin history. None of these changes should affect executables in any way.
• src/hg/hgVarAnnogrator/hgVarAnnogrator.c
  • lines changed 3, context: html, text, full: html, text
    Deal with cryptic (to say it politely) IE8 behavior (for #6152).
• src/hg/hgc/hgc.c
  • lines changed 128, context: html, text, full: html, text
    Next batch of many checkins as dictated by Jim. Formatting if and limiting lines to 100 chars. Changes limited to lines last touched by tdreszer (git blame) so as not to ruin history. None of these changes should affect executables in any way.
• src/hg/hgc/lowelab.c
  • lines changed 16, context: html, text, full: html, text
    Format changes as dictated by Jim. Formatting lines to 100 chars. Only touching lines git blames on 'tdreszer'. Because most of file has formatting differences from kent style, changes here conform to the local style. These changes should affect executable in any way.
• src/hg/hgc/mafClick.c
  • lines changed 6, context: html, text, full: html, text
    Next batch of many checkins as dictated by Jim. Formatting if and limiting lines to 100 chars. Changes limited to lines last touched by tdreszer (git blame) so as not to ruin history. None of these changes should affect executables in any way.
• src/hg/htdocs/ENCODE/dataStandards.html
  • lines changed 2, context: html, text, full: html, text
    Add News and menu highlights for Quality Metrics page on portal
• src/hg/htdocs/ENCODE/downloads.html
  • lines changed 1, context: html, text, full: html, text
    Changed '7' to '9' in title of Regulation Transcription track (redmine #7990)
• src/hg/htdocs/ENCODE/downloadsMouse.html
  • lines changed 4, context: html, text, full: html, text
    Added line for UW RNA-seq (redmine #4469)
• src/hg/htdocs/ENCODE/index.html
  • lines changed 19, context: html, text, full: html, text
    Add News and menu highlights for Quality Metrics page on portal
  • lines changed 3, context: html, text, full: html, text
    Made some corrections to Kate's additions (redmine #7780)
• src/hg/htdocs/ENCODE/qualityMetrics.html
  • lines changed 1, context: html, text, full: html, text
    Made some corrections to Kate's additions (redmine #7780)
• src/hg/htdocs/FAQ/FAQreleases.html
  • lines changed 1, context: html, text, full: html, text
    added sarHar1 release info
• src/hg/htdocs/goldenPath/credits.html
  • lines changed 58, context: html, text, full: html, text
    added tasmanina devil credits
  • lines changed 5, context: html, text, full: html, text
    Fixed a few typos
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 35, context: html, text, full: html, text
    Added new sarHar1 announcement
  • lines changed 1, context: html, text, full: html, text
    fixed a typo and added a space
  • lines changed 3, context: html, text, full: html, text
    removed sentence
  • lines changed 1, context: html, text, full: html, text
    corrected name attribute for hgText announcement
  • lines changed 1, context: html, text, full: html, text
    fixed a typo
• src/hg/htdocs/images/Trichechus_manatus_latirostris.jpg
  • lines changed 0, context: html, text, full: html, text
    Bob's photograph for Trichechus_manatus
• src/hg/htdocs/images/Vicugna_pacos.png
  • lines changed 0, context: html, text, full: html, text
    WUSTL says this photo is from USDA - can not find at USDA
• src/hg/htdocs/indexNews.html
  • lines changed 140, context: html, text, full: html, text
    Added sarHar1 announcement
  • lines changed 1, context: html, text, full: html, text
    fixed a typo
• src/hg/inc/hui.h
  • lines changed 109, context: html, text, full: html, text
    Next batch of many checkins as dictated by Jim. Formatting space after if and limiting lines to 100 chars. Changes limited to lines last touched by tdreszer (git blame) so as not to ruin history. This checkin also includes removal of SUBTRACK_CFG ifdefs, and a bug fix for downloads link.
• src/hg/inc/mafGene.h
  • lines changed 1, context: html, text, full: html, text
    Added support for option to add UTR.
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    New version number v270
• src/hg/js/hgVarAnnogrator.js
  • lines changed 2, context: html, text, full: html, text
    Deal with cryptic (to say it politely) IE8 behavior (for #6152).
• src/hg/lib/hui.c
  • lines changed 1044, context: html, text, full: html, text
    Next batch of many checkins as dictated by Jim. Formatting space after if and limiting lines to 100 chars. Changes limited to lines last touched by tdreszer (git blame) so as not to ruin history. This checkin also includes removal of SUBTRACK_CFG ifdefs, and a bug fix for downloads link.
• src/hg/lib/mafGene.c
  • lines changed 18, context: html, text, full: html, text
    Added code so that if the utr option is set, then alignments are retrieved for all exons not just the CDS region.
• src/hg/lib/pal.c
  • lines changed 3, context: html, text, full: html, text
    fix simple html error in pal.c found by htmlCheck
• src/hg/lib/web.c
  • lines changed 1, context: html, text, full: html, text
    fixed typo in comment
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeUchicagoTfbs.release2.notes
  • lines changed 420, context: html, text, full: html, text
    Adding a notes files for UChicago
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeUncBsuProt.release2.notes
  • lines changed 106, context: html, text, full: html, text
    creating the notes file
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeUwAffyExonArray.release3.notes
  • lines changed 429, context: html, text, full: html, text
    Preparing for pushQ, adding expIds, notes file, fixing names in the downloads files
• src/hg/makeDb/doc/gorGor3.txt
  • lines changed 19, context: html, text, full: html, text
    Finished LASTZ rheMac3 vw hg19, gorGor3, ponAbe2.
• src/hg/makeDb/doc/hg19.txt
  • lines changed 402, context: html, text, full: html, text
    Track #8360 (snp137): after the usual slog through slightly changingformats and contents, snp137 and its auxiliary tables are here!
    
  • lines changed 65, context: html, text, full: html, text
    Finished LASTZ rheMac3 vw hg19, gorGor3, ponAbe2.
  • lines changed 62, context: html, text, full: html, text
    started patch9 build
• src/hg/makeDb/doc/ponAbe2.txt
  • lines changed 19, context: html, text, full: html, text
    Finished LASTZ rheMac3 vw hg19, gorGor3, ponAbe2.
• src/hg/makeDb/doc/rheMac3.txt
  • lines changed 125, context: html, text, full: html, text
    Finished LASTZ rheMac3 vw hg19, gorGor3, ponAbe2.
• src/hg/makeDb/doc/ucscGenes/mm10.ucscGenes13.csh
  • lines changed 11, context: html, text, full: html, text
    more work on mm10 UCSC genes
• src/hg/makeDb/genbank/etc/hgwbeta.dbs
  • lines changed 1, context: html, text, full: html, text
    Adding sacCer1 updates again. The assembly is not being archived, by popular demand.
• src/hg/makeDb/genbank/etc/rr.dbs
  • lines changed 1, context: html, text, full: html, text
    Adding sacCer1 updates again. The assembly is not being archived, by popular demand.
  • lines changed 1, context: html, text, full: html, text
    added sarHar1
• src/hg/makeDb/schema/all.joiner
  • lines changed 4, context: html, text, full: html, text
    add ce10 and dm3 to Human Protein key checks
  • lines changed 19, context: html, text, full: html, text
    Track #8360 (snp137): added to trackDb, all.joiner.
• src/hg/makeDb/trackDb/alpaca/vicPac1/description.html
  • lines changed 116, context: html, text, full: html, text
    minimal page from makeGenomeDb.pl
• src/hg/makeDb/trackDb/baboon/papHam1/description.html
  • lines changed 118, context: html, text, full: html, text
    minimal page from makeGenomeDb.pl
• src/hg/makeDb/trackDb/cat/felCat5/gap.html
  • lines changed 31, context: html, text, full: html, text
    gold and gap pages from the new template procedure in makeGenomeDb.pl
  • lines changed 4, context: html, text, full: html, text
    update size count format
  • lines changed 1, context: html, text, full: html, text
    missing a comma
  • lines changed 4, context: html, text, full: html, text
    add link to NCBI assembly specifics
  • lines changed 9, context: html, text, full: html, text
    clean up text due to review comments
  • lines changed 2, context: html, text, full: html, text
    calrify link to NCBI assembly information
• src/hg/makeDb/trackDb/cat/felCat5/gold.html
  • lines changed 33, context: html, text, full: html, text
    gold and gap pages from the new template procedure in makeGenomeDb.pl
  • lines changed 4, context: html, text, full: html, text
    add link to NCBI assembly specifics
  • lines changed 5, context: html, text, full: html, text
    clean up text due to review comments
  • lines changed 2, context: html, text, full: html, text
    calrify link to NCBI assembly information
• src/hg/makeDb/trackDb/cat/felCat5/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    gold and gap pages from the new template procedure in makeGenomeDb.pl
• src/hg/makeDb/trackDb/chimp/panTro4/gap.html
  • lines changed 61, context: html, text, full: html, text
    add link to NCBI assembly specifics
  • lines changed 11, context: html, text, full: html, text
    clean up text due to review comments
  • lines changed 2, context: html, text, full: html, text
    calrify link to NCBI assembly information
• src/hg/makeDb/trackDb/chimp/panTro4/gold.html
  • lines changed 21, context: html, text, full: html, text
    add link to NCBI assembly specifics
  • lines changed 4, context: html, text, full: html, text
    clean up text due to review comments
  • lines changed 2, context: html, text, full: html, text
    calrify link to NCBI assembly information
• src/hg/makeDb/trackDb/chimp/trackDb.chainNet.ra
  • lines changed 5, context: html, text, full: html, text
    Finish build chaniNet track for rheMac3.
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 17, context: html, text, full: html, text
    Adding endometrium cell type to CV
  • lines changed 48, context: html, text, full: html, text
    Adding bone marrow cell types to CV
  • lines changed 1, context: html, text, full: html, text
    change FASP label
  • lines changed 6, context: html, text, full: html, text
    added MudPIT
  • lines changed 2, context: html, text, full: html, text
    Fixed description of C57BL/6J and spelling of donor, found by Kate.
  • lines changed 30, context: html, text, full: html, text
    Adding open chromatin cell type termId and termUrl to CV
• src/hg/makeDb/trackDb/cv/beta/cv.ra
  • lines changed 809, context: html, text, full: html, text
    Copying alpha CV to beta
• src/hg/makeDb/trackDb/dog/trackDb.chainNet.ra
  • lines changed 1, context: html, text, full: html, text
    Cow bosTau7 vs canFam2, hg19, mm10, mo,Dom5 and ornAna1 chain/Net.
• src/hg/makeDb/trackDb/dolphin/turTru2/description.html
  • lines changed 117, context: html, text, full: html, text
    minimal page from makeGenomeDb.pl
• src/hg/makeDb/trackDb/drosophila/dm3/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    Changed Human Proteins tracks default visbility to hide for dm3 and ce10.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUchicagoTfbs.ra
  • lines changed 221, context: html, text, full: html, text
    adding accessions
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUncBsuProt.ra
  • lines changed 57, context: html, text, full: html, text
    remove datasets using the new database search scheme, they have been unloaded and loaded for displaying in a new track
  • lines changed 5, context: html, text, full: html, text
    update after mdbPrint
  • lines changed 5, context: html, text, full: html, text
    mdbUpdate
  • lines changed 15, context: html, text, full: html, text
    change SDS-Page to In-gel
  • lines changed 6, context: html, text, full: html, text
    Fixing the expIds
  • lines changed 3, context: html, text, full: html, text
    update after expId change, see note 93, 97, 98
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwAffyExonArray.ra
  • lines changed 321, context: html, text, full: html, text
    Adding new data in, changing the matrix around a little bit
  • lines changed 53, context: html, text, full: html, text
    Preparing for pushQ, adding expIds, notes file, fixing names in the downloads files
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDnase.ra
  • lines changed 1735, context: html, text, full: html, text
    added in enw data tracks
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/makefile
  • lines changed 3, context: html, text, full: html, text
    Cricket reorganized the structure of wgEncodeReg.ra by breaking it up into three separate files as it should be. Also updated the makefiles. (redmine #7990)
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeReg.ra
  • lines changed 295, context: html, text, full: html, text
    Cricket reorganized the structure of wgEncodeReg.ra by breaking it up into three separate files as it should be. Also updated the makefiles. (redmine #7990)
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeRegDnaseClustered.ra
  • lines changed 37, context: html, text, full: html, text
    Cricket reorganized the structure of wgEncodeReg.ra by breaking it up into three separate files as it should be. Also updated the makefiles. (redmine #7990)
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeRegTfbsClustered.ra
  • lines changed 53, context: html, text, full: html, text
    Cricket reorganized the structure of wgEncodeReg.ra by breaking it up into three separate files as it should be. Also updated the makefiles. (redmine #7990)
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeRegTxn.ra
  • lines changed 211, context: html, text, full: html, text
    Cricket reorganized the structure of wgEncodeReg.ra by breaking it up into three separate files as it should be. Also updated the makefiles. (redmine #7990)
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeUchicagoTfbs.ra
  • lines changed 2856, context: html, text, full: html, text
    Staging UChicago TFBS (Release 2) on beta (redmine #5697)
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeUwAffyExonArray.ra
  • lines changed 369, context: html, text, full: html, text
    Staging on beta Univ Wash Affymetrix Exon Array (Release 3) RM#6777
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/makefile
  • lines changed 3, context: html, text, full: html, text
    Cricket reorganized the structure of wgEncodeReg.ra by breaking it up into three separate files as it should be. Also updated the makefiles. (redmine #7990)
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeReg.ra
  • lines changed 295, context: html, text, full: html, text
    Cricket reorganized the structure of wgEncodeReg.ra by breaking it up into three separate files as it should be. Also updated the makefiles. (redmine #7990)
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeRegDnaseClustered.ra
  • lines changed 37, context: html, text, full: html, text
    Cricket reorganized the structure of wgEncodeReg.ra by breaking it up into three separate files as it should be. Also updated the makefiles. (redmine #7990)
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeRegTfbsClustered.ra
  • lines changed 53, context: html, text, full: html, text
    Cricket reorganized the structure of wgEncodeReg.ra by breaking it up into three separate files as it should be. Also updated the makefiles. (redmine #7990)
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeRegTxn.ra
  • lines changed 211, context: html, text, full: html, text
    Cricket reorganized the structure of wgEncodeReg.ra by breaking it up into three separate files as it should be. Also updated the makefiles. (redmine #7990)
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeUwAffyExonArray.ra
  • lines changed 369, context: html, text, full: html, text
    Staging on public Univ Wash Affy Exon Array (Release 3) RM# 6777
• src/hg/makeDb/trackDb/human/hg19/snp137.html
  • lines changed 36, context: html, text, full: html, text
    Track #8360 (snp137): added to trackDb, all.joiner.
• src/hg/makeDb/trackDb/human/hg19/snp137.shared.html
  • lines changed 366, context: html, text, full: html, text
    Track #8360 (snp137): added to trackDb, all.joiner.
• src/hg/makeDb/trackDb/human/hg19/snp137Common.html
  • lines changed 28, context: html, text, full: html, text
    Track #8360 (snp137): added to trackDb, all.joiner.
• src/hg/makeDb/trackDb/human/hg19/snp137Flagged.html
  • lines changed 29, context: html, text, full: html, text
    Track #8360 (snp137): added to trackDb, all.joiner.
• src/hg/makeDb/trackDb/human/hg19/snp137Mult.html
  • lines changed 25, context: html, text, full: html, text
    Track #8360 (snp137): added to trackDb, all.joiner.
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 90, context: html, text, full: html, text
    Track #8360 (snp137): added to trackDb, all.joiner.
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
  • lines changed 2, context: html, text, full: html, text
    Releasing UCSC Regulation Transcription Track (Release 3) to the RR (redmine #7990)
  • lines changed 2, context: html, text, full: html, text
    Adding release 2 of FSU RepliChip
  • lines changed 2, context: html, text, full: html, text
    Removing patch file, not sure what the goal was with this pathch
  • lines changed 2, context: html, text, full: html, text
    Staging on beta Univ Wash Affymetrix Exon Array (Release 3) RM#6777
  • lines changed 2, context: html, text, full: html, text
    Staging on public Univ Wash Affy Exon Array (Release 3) RM# 6777
  • lines changed 2, context: html, text, full: html, text
    Staging UChicago TFBS (Release 2) on beta (redmine #5697)
  • lines changed 2, context: html, text, full: html, text
    fixed some subgroups
• src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHistone.release3.ra
  • lines changed 473, context: html, text, full: html, text
    Changing the cell tags to promot tiers and to fix numeric tags
• src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHmm.ra
  • lines changed 10, context: html, text, full: html, text
    Tag changes only, no visible changes
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.release3.ra
  • lines changed 1, context: html, text, full: html, text
    removing from the super track
• src/hg/makeDb/trackDb/human/hg19/wgEncodeFsuRepliChip.release2.html
  • lines changed 150, context: html, text, full: html, text
    Adding release 2 of FSU RepliChip
• src/hg/makeDb/trackDb/human/hg19/wgEncodeFsuRepliChip.release2.ra
  • lines changed 105, context: html, text, full: html, text
    Adding release 2 of FSU RepliChip
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGisChiaPet.ra
  • lines changed 31, context: html, text, full: html, text
    Promoting Tier 2 and cell line tag changes
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGisDnaPet.ra
  • lines changed 8, context: html, text, full: html, text
    Fixing the numeric tags and adding Tier 1 label
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGisRnaSeq.ra
  • lines changed 17, context: html, text, full: html, text
    Changing cell labels and view labels, should be no visible change
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibRnaSeq.patch.ra
  • lines changed 870, context: html, text, full: html, text
    Removing patch file, not sure what the goal was with this pathch
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyAlbanyGeneSt.ra
  • lines changed 25, context: html, text, full: html, text
    Tag change, no visible change
  • lines changed 3, context: html, text, full: html, text
    Adding the hyphens for H1-hesc
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyAlbanyTiling.ra
  • lines changed 9, context: html, text, full: html, text
    Fixing the numeric tags and adding Tier 1 label
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyRipSeq.ra
  • lines changed 39, context: html, text, full: html, text
    Fixing the numeric tags and adding Tier 1 label
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUchicagoTfbs.release2.html
  • lines changed 155, context: html, text, full: html, text
    Made various corrections to the description page. Added links for Bowtie, SPP and MACS. Added the reference paper for SPP to the References section. (redmine #5697)
  • lines changed 5, context: html, text, full: html, text
    Made some additional changes (redmine #5697)
  • lines changed 4, context: html, text, full: html, text
    Made yet more corrections (redmine #5697)
  • lines changed 5, context: html, text, full: html, text
    Added release notes
  • lines changed 4, context: html, text, full: html, text
    Changing the long and short labels, the defaults and adding the release notes
  • lines changed 6, context: html, text, full: html, text
    Edited the Release Notes section (redmine #5697)
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUchicagoTfbs.release2.ra
  • lines changed 141, context: html, text, full: html, text
    Answering ticket #5697Specifially, the long and short labels and
    
    1. In the track controls, Peaks are set to dense, but they should be set to pack.
    
    2. There is a cell line listed as "NCOR1", but the Input for it lists "COR1" in the matrix and in the Factor column below the matrix.
    
    3. In hgTrackUi, when sorting by the Replicated column, "Pooled" shows up before 1 and 2. It seems like "Pooled" should show up after 1 and 2.
    
  • lines changed 147, context: html, text, full: html, text
    Changing the long and short labels, the defaults and adding the release notes
  • lines changed 1, context: html, text, full: html, text
    Changing defaut views
  • lines changed 13, context: html, text, full: html, text
    Changed the way Inputs appeared in the matrix
  • lines changed 54, context: html, text, full: html, text
    Changed the short labels to add Sg and Pk
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProt.html
  • lines changed 18, context: html, text, full: html, text
    added release note, reformatted the references, updated data release policy
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProt.release2.ra
  • lines changed 33, context: html, text, full: html, text
    remove datasets using the new database search scheme, they have been unloaded and loaded for displaying in a new track
  • lines changed 9, context: html, text, full: html, text
    add Hg19 to title and long labels
  • lines changed 1, context: html, text, full: html, text
    fixe In-gel label
  • lines changed 2, context: html, text, full: html, text
    remove protocol column from sorting list
  • lines changed 1, context: html, text, full: html, text
    add protocol back to file sortlist
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProtGenc.release1.ra
  • lines changed 1, context: html, text, full: html, text
    specify database search of hg19 and GENCODE V11 in the title
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwAffyExonArray.release3.html
  • lines changed 98, context: html, text, full: html, text
    Trying to work on the html changes for Brian in ticket #6777
  • lines changed 3, context: html, text, full: html, text
    Changing Methods line for Univ Wash Affy Exon Array (Release 3) RM# 6777
  • lines changed 2, context: html, text, full: html, text
    Add protocol information under Description and Methods for Univ Wash Affy Exon Array (Release 3) RM#6777
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwAffyExonArray.release3.ra
  • lines changed 267, context: html, text, full: html, text
    Adding new data in, changing the matrix around a little bit
  • lines changed 1, context: html, text, full: html, text
    Trying to work on the html changes for Brian in ticket #6777
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.release6.ra
  • lines changed 461, context: html, text, full: html, text
    added in enw data tracks
  • lines changed 6, context: html, text, full: html, text
    fixed some subgroups
• src/hg/makeDb/trackDb/human/trackDb.chainNet.ra
  • lines changed 6, context: html, text, full: html, text
    Finish build chaniNet track for rheMac3.
  • lines changed 5, context: html, text, full: html, text
    Cow bosTau7 vs canFam2, hg19, mm10, mo,Dom5 and ornAna1 chain/Net.
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 95, context: html, text, full: html, text
    Cleanup: remove trackDb def's for long-gone experiment.
• src/hg/makeDb/trackDb/manatee/triMan1/description.html
  • lines changed 118, context: html, text, full: html, text
    minimal page from makeGenomeDb.pl
• src/hg/makeDb/trackDb/moleRat/hetGla1/description.html
  • lines changed 127, context: html, text, full: html, text
    minimal page from makeGenomeDb.pl
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/public/makefile
  • lines changed 1, context: html, text, full: html, text
    Releasing UW RNA-Seq (Release 1) to the RR (redmine #4469)
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/public/wgEncodeUwRnaSeq.ra
  • lines changed 6123, context: html, text, full: html, text
    Releasing UW RNA-Seq (Release 1) to the RR (redmine #4469)
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.wgEncode.ra
  • lines changed 1, context: html, text, full: html, text
    Releasing UW RNA-Seq (Release 1) to the RR (redmine #4469)
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwRnaSeq.ra
  • lines changed 9, context: html, text, full: html, text
    remove 1 from ACel416B in subGroups and all the stanzas
  • lines changed 8, context: html, text, full: html, text
    correcting a typo
• src/hg/makeDb/trackDb/mouse/trackDb.chainNet.ra
  • lines changed 6, context: html, text, full: html, text
    Cow bosTau7 vs canFam2, hg19, mm10, mo,Dom5 and ornAna1 chain/Net.
• src/hg/makeDb/trackDb/mouseLemur/micMur1/gap.html
  • lines changed 60, context: html, text, full: html, text
    new style automatic generated page from makeGenomeDb.pl
  • lines changed 1, context: html, text, full: html, text
    update size count format
  • lines changed 4, context: html, text, full: html, text
    add link to NCBI assembly specifics
  • lines changed 6, context: html, text, full: html, text
    clean up text due to review comments
  • lines changed 2, context: html, text, full: html, text
    calrify link to NCBI assembly information
• src/hg/makeDb/trackDb/mouseLemur/micMur1/gold.html
  • lines changed 19, context: html, text, full: html, text
    new style automatic generated page from makeGenomeDb.pl
  • lines changed 4, context: html, text, full: html, text
    add link to NCBI assembly specifics
  • lines changed 5, context: html, text, full: html, text
    clean up text due to review comments
  • lines changed 2, context: html, text, full: html, text
    calrify link to NCBI assembly information
• src/hg/makeDb/trackDb/opossum/monDom5/trackDb.chainNet.ra
  • lines changed 1, context: html, text, full: html, text
    Cow bosTau7 vs canFam2, hg19, mm10, mo,Dom5 and ornAna1 chain/Net.
• src/hg/makeDb/trackDb/orangutan/trackDb.chainNet.ra
  • lines changed 3, context: html, text, full: html, text
    Finish build chaniNet track for rheMac3.
• src/hg/makeDb/trackDb/pig/susScr3/description.html
  • lines changed 119, context: html, text, full: html, text
    minimal page from makeGenomeDb.pl
• src/hg/makeDb/trackDb/platypus/trackDb.chainNet.ra
  • lines changed 1, context: html, text, full: html, text
    Cow bosTau7 vs canFam2, hg19, mm10, mo,Dom5 and ornAna1 chain/Net.
• src/hg/makeDb/trackDb/squirrel/speTri2/description.html
  • lines changed 120, context: html, text, full: html, text
    minimal page from makeGenomeDb.pl
• src/hg/makeDb/trackDb/trackDb.chainNet.ra
  • lines changed 51, context: html, text, full: html, text
    Add rheMac3 to trackDb.chainNet.ra.
• src/hg/makeDb/trackDb/worm/ce10/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    Changed Human Proteins tracks default visbility to hide for dm3 and ce10.
• src/hg/ratStuff/mafGene/mafGene.c
  • lines changed 21, context: html, text, full: html, text
    Added option and support for using a genePred file as input instead of a genePred table.
  • lines changed 2, context: html, text, full: html, text
    Added comments to code.
  • lines changed 9, context: html, text, full: html, text
    Added -utr option so that alignments can be retrieved for all exons not just the CDS region. Abort if the noTrans option is not used with the utr option.
• src/hg/snp/snpLoad/snpNcbiToUcsc.c
  • lines changed 67, context: html, text, full: html, text
    Track #8360 (snp137): after the usual slog through slightly changingformats and contents, snp137 and its auxiliary tables are here!
    
• src/hg/utils/automation/EnsGeneAutomate.pm
  • lines changed 188, context: html, text, full: html, text
    Set parameters for ensGene 67 update.
• src/hg/utils/automation/HgAutomate.pm
  • lines changed 2, context: html, text, full: html, text
    restore memk to potential cluster list
• src/hg/utils/automation/configFiles/hetGla2.config.ra
  • lines changed 24, context: html, text, full: html, text
    up to date with required parameters
• src/hg/utils/automation/configFiles/speTri2.config.ra
  • lines changed 22, context: html, text, full: html, text
    up to date with required parameters
• src/hg/utils/automation/configFiles/susScr3.config.ra
  • lines changed 29, context: html, text, full: html, text
    up to date with required parameters
• src/hg/utils/automation/configFiles/triMan1.config.ra
  • lines changed 23, context: html, text, full: html, text
    up to date with required parameters
• src/hg/utils/automation/configFiles/turTru2.config.ra
  • lines changed 24, context: html, text, full: html, text
    up to date with required parameters
• src/hg/utils/automation/configFiles/vicPac1.config.ra
  • lines changed 23, context: html, text, full: html, text
    up to date with required parameters
• src/hg/utils/automation/doDbSnp.pl
  • lines changed 12, context: html, text, full: html, text
    Track #8360 (snp137): after the usual slog through slightly changingformats and contents, snp137 and its auxiliary tables are here!
    
• src/hg/utils/automation/makeGenomeDb.pl
  • lines changed 57, context: html, text, full: html, text
    update the gold.html to a generic page with external references
  • lines changed 103, context: html, text, full: html, text
    now constructing the gap description page
  • lines changed 3, context: html, text, full: html, text
    update gap page count size format
  • lines changed 6, context: html, text, full: html, text
    add link to NCBI assembly information
  • lines changed 14, context: html, text, full: html, text
    cleaning up the text for gold and gap pages
  • lines changed 4, context: html, text, full: html, text
    clarify link to NCBI assembly information for gold and gap pages
• src/hg/utils/automation/snpAddTGPAlleleFreq.pl
  • lines changed 14, context: html, text, full: html, text
    Track #8360 (snp137): after the usual slog through slightly changingformats and contents, snp137 and its auxiliary tables are here!
    
• src/hg/utils/automation/synBlastp.csh
  • lines changed 12, context: html, text, full: html, text
    allow synBlastp.csh to use something other than knownGene for gene table (part of UCSC gene pipeline)
• src/hg/visiGene/hgVisiGene/hgVisiGene.c
  • lines changed 1, context: html, text, full: html, text
    removing simple html error in hgVisiGene found by htmlCheck
• src/lib/common.c
  • lines changed 7, context: html, text, full: html, text
    fixing subtle problem with tabs and empty strings in b2bb input parsing
• src/lib/htmlPage.c
  • lines changed 3, context: html, text, full: html, text
    adding an exception for hidden db value outside form - argument has been made that such use is legal, and we cannot use htmlPage very well without it
  • lines changed 7, context: html, text, full: html, text
    adding some more chars to the list of those legal in urls
• src/utils/bedToBigBed/bedToBigBed.c
  • lines changed 2, context: html, text, full: html, text
    fixing subtle problem with tabs and empty strings in b2bb input parsing
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 3, context: html, text, full: html, text
    v270 final build

• lines changed: 24466
• files changed: 239