All File Changes

v244_preview to v244_preview2 (2010-11-16 to 2010-11-30) v244

• src/hg/encode/DAFs/2.0/caltechRnaSeq.daf
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    Caltech changed to Caltech(Wold)
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    changed the bam mismatches to 6
• src/hg/encode/DAFs/2.0/haibChipSeq.daf
  • lines changed 8, context: html, text, full: html, text
    Added RawData view to the daf.
• src/hg/encode/DAFs/2.0/haibCnv.daf
  • lines changed 44, context: html, text, full: html, text
    new Dafs for Haib, in progress
  • lines changed 22, context: html, text, full: html, text
    working on improving DAFs for HAIB
• src/hg/encode/DAFs/2.0/haibMethyl27.daf
  • lines changed 35, context: html, text, full: html, text
    new Dafs for Haib, in progress
  • lines changed 26, context: html, text, full: html, text
    working on improving DAFs for HAIB
• src/hg/encode/DAFs/2.0/haibRnaSeq.daf
  • lines changed 30, context: html, text, full: html, text
    new Dafs for Haib, in progress
  • lines changed 3, context: html, text, full: html, text
    working on improving DAFs for HAIB
• src/hg/encode/DAFs/2.0/licrMm9Histone.daf
  • lines changed 2, context: html, text, full: html, text
    Fixed lab value in the DAF
• src/hg/encode/DAFs/2.0/licrMm9Tfbs.daf
  • lines changed 2, context: html, text, full: html, text
    Fixed lab value in the DAF
• src/hg/encode/docId/docIdMetaShow/docIdMetaShow.c
  • lines changed 43, context: html, text, full: html, text
    working on validation reports
  • lines changed 9, context: html, text, full: html, text
    interim... changed things...
  • lines changed 7, context: html, text, full: html, text
    more changes in advance of roll-out
• src/hg/encode/docId/docIdSubmitDir/docIdSubmitDir.c
  • lines changed 119, context: html, text, full: html, text
    an interim check-in...
  • lines changed 33, context: html, text, full: html, text
    working on validation reports
  • lines changed 48, context: html, text, full: html, text
    interim... changed things...
  • lines changed 18, context: html, text, full: html, text
    more changes in advance of roll-out
• src/hg/encode/docId/docIdSubmitDir/makefile
  • lines changed 1, context: html, text, full: html, text
    interim... changed things...
• src/hg/encode/docId/inc/docId.h
  • lines changed 1, context: html, text, full: html, text
    an interim check-in...
  • lines changed 2, context: html, text, full: html, text
    interim... changed things...
  • lines changed 1, context: html, text, full: html, text
    more changes in advance of roll-out
• src/hg/encode/docId/lib/docIdSub.c
  • lines changed 4, context: html, text, full: html, text
    an interim check-in...
  • lines changed 5, context: html, text, full: html, text
    interim... changed things...
  • lines changed 3, context: html, text, full: html, text
    more changes in advance of roll-out
• src/hg/encode/encodeMkChangeNotes/encodeMkChangeNotes
  • lines changed 1, context: html, text, full: html, text
    added support for fpkm, insDist, and junction files
• src/hg/encode/encodeReport/encodeReport.pl
  • lines changed 438, context: html, text, full: html, text
    Experiment spreadsheet reporter based on metaDb
• src/hg/encode/encodeValidate/doEncodeValidate.pl
  • lines changed 37, context: html, text, full: html, text
    add submissions to docId system
• src/hg/encode/validateFiles/validateFiles.c
  • lines changed 154, context: html, text, full: html, text
    add building reports
• src/hg/hgApi/hgApi.c
  • lines changed 67, context: html, text, full: html, text
    Made freeText search instead of drop downs for track search advanced when cv.ra reports 'searchable freeText'. This is useful for labVersion among others.
• src/hg/hgGateway/hgGateway.c
  • lines changed 2, context: html, text, full: html, text
    Removed a lot of ifdefs whose time had come. Renamed one function for clarity.
• src/hg/hgGene/hgGene.c
  • lines changed 1, context: html, text, full: html, text
    Fix a couple of places broken by the use of [] as a placeholder for empty in an old cart var
  • lines changed 1, context: html, text, full: html, text
    Sorry... fix sloppy checkin
• src/hg/hgTables/great.c
  • lines changed 62, context: html, text, full: html, text
    Changes from Bejerano lab to support great on multiple assemblies
• src/hg/hgTables/greatData/supportedAssemblies.txt
  • lines changed 4, context: html, text, full: html, text
    Changes from Bejerano lab to support great on multiple assemblies
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 1, context: html, text, full: html, text
    Removed a lot of ifdefs whose time had come. Renamed one function for clarity.
• src/hg/hgTracks/bamTrack.c
  • lines changed 6, context: html, text, full: html, text
    Removed obsolete ifdef for SUBTRACKS_HAVE_VIS. Streamlined some composite vis code. Added support for remote tracks being rendered by AJAX callback. Currently ifdefed out.
• src/hg/hgTracks/cds.c
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    change spacing per tim's code review
• src/hg/hgTracks/config.c
  • lines changed 2, context: html, text, full: html, text
    Removed a lot of ifdefs whose time had come. Renamed one function for clarity.
• src/hg/hgTracks/hgTracks.c
  • lines changed 129, context: html, text, full: html, text
    Removed obsolete ifdef for SUBTRACKS_HAVE_VIS. Streamlined some composite vis code. Added support for remote tracks being rendered by AJAX callback. Currently ifdefed out.
  • lines changed 25, context: html, text, full: html, text
    Removed side buttons and nextItem arrows from 'view image' rightClick image
  • lines changed 2, context: html, text, full: html, text
    Explicitly declare custom tracks as custom, to support drag virgins being on top
  • lines changed 3, context: html, text, full: html, text
    Assert tripped, with Larry's help. wigMaf can look like subtrack but isn't.
  • lines changed 7, context: html, text, full: html, text
    Removed a lot of ifdefs whose time had come. Renamed one function for clarity.
  • lines changed 6, context: html, text, full: html, text
    Only one meassage is needed when the image exceeds 32,000 pixels.
• src/hg/hgTracks/hgTracks.h
  • lines changed 22, context: html, text, full: html, text
    Removed obsolete ifdef for SUBTRACKS_HAVE_VIS. Streamlined some composite vis code. Added support for remote tracks being rendered by AJAX callback. Currently ifdefed out.
  • lines changed 1, context: html, text, full: html, text
    Explicitly declare custom tracks as custom, to support drag virgins being on top
• src/hg/hgTracks/imageV2.c
  • lines changed 11, context: html, text, full: html, text
    Removed obsolete ifdef for SUBTRACKS_HAVE_VIS. Streamlined some composite vis code. Added support for remote tracks being rendered by AJAX callback. Currently ifdefed out.
  • lines changed 15, context: html, text, full: html, text
    show trackDbJson even when doing only a single track; make trackDbJson valid json (i.e. quote keys)
  • lines changed 18, context: html, text, full: html, text
    Changed configureByPopup json boolean to configureBy none,popup or clickThrough.
  • lines changed 1, context: html, text, full: html, text
    Added 'inset' style so that BLAT sideButton is visibly different, as it is non-configurable.
  • lines changed 6, context: html, text, full: html, text
    Realized a little late that track->hasUi is the same as configurable.
  • lines changed 97, context: html, text, full: html, text
    Support for drag virgins being on top
  • lines changed 6, context: html, text, full: html, text
    Removed a lot of ifdefs whose time had come. Renamed one function for clarity.
• src/hg/hgTracks/imageV2.h
  • lines changed 14, context: html, text, full: html, text
    Removed obsolete ifdef for SUBTRACKS_HAVE_VIS. Streamlined some composite vis code. Added support for remote tracks being rendered by AJAX callback. Currently ifdefed out.
  • lines changed 1, context: html, text, full: html, text
    Changed configureByPopup json boolean to configureBy none,popup or clickThrough.
  • lines changed 2, context: html, text, full: html, text
    Support for drag virgins being on top
• src/hg/hgTracks/mainMain.c
  • lines changed 4, context: html, text, full: html, text
    Removed a lot of ifdefs whose time had come. Renamed one function for clarity.
• src/hg/hgTracks/searchTracks.c
  • lines changed 1, context: html, text, full: html, text
    check for NULL before stripChar'ing descSearch
  • lines changed 3, context: html, text, full: html, text
    Removed obsolete ifdef for SUBTRACKS_HAVE_VIS. Streamlined some composite vis code. Added support for remote tracks being rendered by AJAX callback. Currently ifdefed out.
  • lines changed 1, context: html, text, full: html, text
    Changed configureByPopup json boolean to configureBy none,popup or clickThrough.
  • lines changed 77, context: html, text, full: html, text
    Made freeText search instead of drop downs for track search advanced when cv.ra reports 'searchable freeText'. This is useful for labVersion among others.
  • lines changed 8, context: html, text, full: html, text
    Removed a lot of ifdefs whose time had come. Renamed one function for clarity.
  • lines changed 128, context: html, text, full: html, text
    Added format type drop down to advanced search tab. Whitelist is in code and all code is wrapped with ifdefs when feature becomes more of a hassle than it is worth at this time.
  • lines changed 20, context: html, text, full: html, text
    Missing comma in whitelist of formats caused a problem
• src/hg/hgTracks/simpleTracks.c
  • lines changed 34, context: html, text, full: html, text
    Removed obsolete ifdef for SUBTRACKS_HAVE_VIS. Streamlined some composite vis code. Added support for remote tracks being rendered by AJAX callback. Currently ifdefed out.
  • lines changed 109, context: html, text, full: html, text
    Updated to implement suggestion in Issue #1571.
  • lines changed 5, context: html, text, full: html, text
    Removed temporary expansion of limitVisibility for trackImgOnly. Larry put in an in your face alert, when limitVisibility changes user requested vis via rightClick
• src/hg/htdocs/ENCODE/downloads.html
  • lines changed 6, context: html, text, full: html, text
    adding CSHL Sm RNA-seq to list
  • lines changed 11, context: html, text, full: html, text
    added GIS RNA-seq hg19 for the RR release
  • lines changed 1, context: html, text, full: html, text
    fixing longLabel of hg19 CSHL Sm RNA-seq hg19
  • lines changed 16, context: html, text, full: html, text
    fixed longLabels of CSHL Sm RNA-seq and GIS RNA-seq to the new formats; also added the # where it was missing (per general request from Vanessa)
  • lines changed 3, context: html, text, full: html, text
    Issue 144, note 14: adding link to super-track; note that link is not underlined
• src/hg/htdocs/ENCODE/index.html
  • lines changed 39, context: html, text, full: html, text
    To news: announcing RNA-seq hg19 data releases, collapsing previous releases, removing old releases; To archives: adding two items that I collapsed in news section
• src/hg/htdocs/ENCODE/newsarch.html
  • lines changed 38, context: html, text, full: html, text
    To news: announcing RNA-seq hg19 data releases, collapsing previous releases, removing old releases; To archives: adding two items that I collapsed in news section
• src/hg/htdocs/images/caution.gif
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    add caution icon for javascript disabled message
• src/hg/htdocs/images/greenChecksm.png
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    Couple new icons to support rightClick
• src/hg/htdocs/images/invisible16.png
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    Couple new icons to support rightClick
• src/hg/htdocs/style/HGStyle.css
  • lines changed 26, context: html, text, full: html, text
    add noscript rules
  • lines changed 1, context: html, text, full: html, text
    Added 'inset' style so that BLAT sideButton is visibly different, as it is non-configurable.
• src/hg/inc/cart.h
  • lines changed 1, context: html, text, full: html, text
    Added macro to tel whether cart var is really empty
  • lines changed 1, context: html, text, full: html, text
    Removed a lot of ifdefs whose time had come. Renamed one function for clarity.
• src/hg/inc/mdb.h
  • lines changed 17, context: html, text, full: html, text
    Support for searchable freeText in cv.ra
• src/hg/js/ajax.js
  • lines changed 4, context: html, text, full: html, text
    No functional consequence to check in. But it should be clear that the variable is a trackName and not a tableName. This is part of fix for redmine 1071.30.
• src/hg/js/hgTracks.js
  • lines changed 2, context: html, text, full: html, text
    deal with uppercase Antibody value in select; remove cruft from end of file
  • lines changed 47, context: html, text, full: html, text
    handle case where track cannot be changed to higher visibility; refactor code into updateVisibility
  • lines changed 10, context: html, text, full: html, text
    always pull out new visibility to update local visibility in handleUpdateTrackMap
  • lines changed 10, context: html, text, full: html, text
    Changed configureByPopup json boolean to configureBy none,popup or clickThrough.
  • lines changed 14, context: html, text, full: html, text
    Moved rightClick slected vis check icon to front to have text of all options line up
  • lines changed 45, context: html, text, full: html, text
    Made freeText search instead of drop downs for track search advanced when cv.ra reports 'searchable freeText'. This is useful for labVersion among others.
  • lines changed 5, context: html, text, full: html, text
    remove popUpTrackDescriptionOnly test for code that fixes up links in handleTrackUi
  • lines changed 1, context: html, text, full: html, text
    New format type search drop-down needs to be cleared.
  • lines changed 17, context: html, text, full: html, text
    Small corrections to when 'view in browser' is seen and vis that composites get set to. Also removed unused and unworking function
• src/hg/js/hui.js
  • lines changed 80, context: html, text, full: html, text
    Made filterComposite work with matrix.
• src/hg/js/utils.js
  • lines changed 4, context: html, text, full: html, text
    No functional consequence to check in. But it should be clear that the variable is a trackName and not a tableName. This is part of fix for redmine 1071.30.
• src/hg/lib/cart.c
  • lines changed 174, context: html, text, full: html, text
    Removed a bunch of composite reshaping ifdefs, now that track search is out the door.
  • lines changed 1, context: html, text, full: html, text
    Removed a lot of ifdefs whose time had come. Renamed one function for clarity.
• src/hg/lib/customFactory.c
  • lines changed 5, context: html, text, full: html, text
    fixing bug #1471 for translated PSL custom tracks
• src/hg/lib/encode/shortFrags.as
  • lines changed 1, context: html, text, full: html, text
    add bin column
• src/hg/lib/hui.c
  • lines changed 4, context: html, text, full: html, text
    Removed a lot of ifdefs whose time had come. Renamed one function for clarity.
  • lines changed 3, context: html, text, full: html, text
    Fixed redmine 1071.30. Two tracks in findtracks results with same table were tripping each others '...' metadata links. Link should be based on track name, not table name.
  • lines changed 13, context: html, text, full: html, text
    Fix for redmine 1883. NHGRI BIPs are found in 7 different genomes but only hg18 has downloads.
  • lines changed 18, context: html, text, full: html, text
    Made filterComposite work with matrix.
• src/hg/lib/jsHelper.c
  • lines changed 2, context: html, text, full: html, text
    make noscript message more assertive (see redmine #1776)
• src/hg/lib/mdb.c
  • lines changed 34, context: html, text, full: html, text
    Support for searchable freeText in cv.ra
  • lines changed 6, context: html, text, full: html, text
    Standardize 'Antibody' to 'antibody' in cv hash, since this is the mdb term of record
• src/hg/lib/metaTbl.as
  • lines changed 9, context: html, text, full: html, text
    Removed three obsolete files that were replaced by metaDb(mdb) long ago.
• src/hg/lib/metaTbl.c
  • lines changed 1852, context: html, text, full: html, text
    Removed three obsolete files that were replaced by metaDb(mdb) long ago.
• src/hg/lib/metaTbl.sql
  • lines changed 22, context: html, text, full: html, text
    Removed three obsolete files that were replaced by metaDb(mdb) long ago.
• src/hg/lib/searchTracks.c
  • lines changed 4, context: html, text, full: html, text
    Removed a lot of ifdefs whose time had come. Renamed one function for clarity.
• src/hg/lib/web.c
  • lines changed 3, context: html, text, full: html, text
    Fix a couple of places broken by the use of [] as a placeholder for empty in an old cart var
  • lines changed 5, context: html, text, full: html, text
    Removed a lot of ifdefs whose time had come. Renamed one function for clarity.
• src/hg/makeDb/doc/encodeDccHg19/broadHistoneBernstein.hg19.txt
  • lines changed 828, context: html, text, full: html, text
    Updated Illumina platform into labVersion metadata nd added 17 more submissions
  • lines changed 86, context: html, text, full: html, text
    Seven more submissions
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeHaibMethylRrbs.release1.notes
  • lines changed 280, context: html, text, full: html, text
    Added release Notes for Methyl RRBS Track
• src/hg/makeDb/doc/hg18.txt
  • lines changed 49, context: html, text, full: html, text
    Track #1229 (Denisova ancient genome data): Downloaded data fromEd / Max Planck Institut and loaded tables in hg18 and panTro2.
  • lines changed 25, context: html, text, full: html, text
    Built rdmr track.
• src/hg/makeDb/doc/hg19.txt
  • lines changed 11, context: html, text, full: html, text
    added to makedoc on behalf of Chin using his notes in RM #1727
  • lines changed 360, context: html, text, full: html, text
    Track #1684 (SNPs 132 (dbSNP)): dbSNP re-dumped their rs_fasta/* files,restoring almost 3,000 SNPs that we screened out because their sequences were missing or in the wrong file. I rebuilt snp132 parts that depend on rs_fasta. Also added auxiliary tables for orthologous SNPs in chimp/orang/macaque (snp132OrthoPanTro2PonAbe2RheMac2) and NCBI's annotations of coding changes (snp132CodingDbSnp). Made copy of hg19 sequence with single-nt substitutions converted to the IUPAC ambiguous character for the observed bases.
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    removing unneeded chip-name prefixes from affyU95 and affyU133Plus2 and re-loading psl into database and sequence into ext/seq
• src/hg/makeDb/doc/panTro2.txt
  • lines changed 26, context: html, text, full: html, text
    Track #1229 (Denisova ancient genome data): Downloaded data fromEd / Max Planck Institut and loaded tables in hg18 and panTro2.
• src/hg/makeDb/genbank/doc/to-do.txt
  • lines changed 4, context: html, text, full: html, text
    added problem case to notes
• src/hg/makeDb/schema/all.joiner
  • lines changed 7, context: html, text, full: html, text
    microsat is used by human mouse and a few others, but this simple table should be just ignored
  • lines changed 20, context: html, text, full: html, text
    Track #1684 (SNPs 132 (dbSNP)): dbSNP re-dumped their rs_fasta/* files,restoring almost 3,000 SNPs that we screened out because their sequences were missing or in the wrong file. I rebuilt snp132 parts that depend on rs_fasta. Also added auxiliary tables for orthologous SNPs in chimp/orang/macaque (snp132OrthoPanTro2PonAbe2RheMac2) and NCBI's annotations of coding changes (snp132CodingDbSnp). Made copy of hg19 sequence with single-nt substitutions converted to the IUPAC ambiguous character for the observed bases.
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 29, context: html, text, full: html, text
    Removed growth protocol variables that was in protocol variables in meta-data and cv.ra
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    Changed one entry from provisional to non-provisional after discussion with Tim
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    1. At request of Tim, changed labVersion and softwareVersion from searchable select to searchable freeText.2. Removed the provisional designation from "term cellType" and added a comment describing why this is an exception, in that term cellType describes the term cell line entries. 3. Changed all instances of Dot_plot to Dot_blot. Dot blots are lab procedures for antibody validation. Dot plots are sequence comparison visualizations. 4. Removed some extraneous nonprinting characters from the BTO entries.
  • lines changed 10, context: html, text, full: html, text
    resolved merge conflict
  • lines changed 21, context: html, text, full: html, text
    Added the first of the HudsonAlpha BioChain cell types
  • lines changed 8, context: html, text, full: html, text
    Filled in special stories from Cricket
  • lines changed 228, context: html, text, full: html, text
    In the antibody stanzas, replaced all GeneCards accessions with the proper GeneCards locus names. The locus names do not change over time, but the accessions occasionally do.
  • lines changed 6, context: html, text, full: html, text
    Fixed a couple broken links that became broken when cleaning up the GeneCards accession numbers
  • lines changed 86, context: html, text, full: html, text
    Removed some nonprinting characters from BTO hyperlinks
  • lines changed 4, context: html, text, full: html, text
    Changed the search settings in some mdb entries, per request of Tim
  • lines changed 2, context: html, text, full: html, text
    A few corrections
  • lines changed 562, context: html, text, full: html, text
    Added the BioChain cell type stanzas
  • lines changed 112, context: html, text, full: html, text
    Added several new antibodies for the Myers lab
  • lines changed 1, context: html, text, full: html, text
    take out spurious "Va"
• src/hg/makeDb/trackDb/dog/canFam2/description.html
  • lines changed 108, context: html, text, full: html, text
    Fixed link to Agencourt, now goes to Beckman Coulter, and also cleaned up html
• src/hg/makeDb/trackDb/human/hg18/hg18ContigDiff.html
  • lines changed 1, context: html, text, full: html, text
    changing wording. requested by code review: http://redmine.soe.ucsc.edu/issues/1816
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeBroadChipSeq.ra
  • lines changed 369, context: html, text, full: html, text
    Added Illumina info into lab version of fastqs and tagAligns
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaCnv.html
  • lines changed 5, context: html, text, full: html, text
    Updated track descriptions to have Flo Pauli has primary contact for the given data.
  • lines changed 1, context: html, text, full: html, text
    Fixed broken email address for Flo in HudsonAlpha track descriptions
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaMethyl27.html
  • lines changed 3, context: html, text, full: html, text
    Updated track descriptions to have Flo Pauli has primary contact for the given data.
  • lines changed 1, context: html, text, full: html, text
    Fixed broken email address for Flo in HudsonAlpha track descriptions
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaMethylSeq.html
  • lines changed 3, context: html, text, full: html, text
    Updated track descriptions to have Flo Pauli has primary contact for the given data.
  • lines changed 1, context: html, text, full: html, text
    Fixed broken email address for Flo in HudsonAlpha track descriptions
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaRnaSeq.html
  • lines changed 6, context: html, text, full: html, text
    removed Rami Rauch from contact
• src/hg/makeDb/trackDb/human/hg19/ctgPos.html
  • lines changed 7, context: html, text, full: html, text
    fixes to html for Map Contigs and GRC Map Contigs. Indicating that the contigs in the two tracks are identical, except for different names
• src/hg/makeDb/trackDb/human/hg19/ctgPos2.html
  • lines changed 13, context: html, text, full: html, text
    fixes to html for Map Contigs and GRC Map Contigs. Indicating that the contigs in the two tracks are identical, except for different names
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeBroadHistone.ra
  • lines changed 544, context: html, text, full: html, text
    Update labVersions with Illumina info
  • lines changed 1893, context: html, text, full: html, text
    Brand new submissions
  • lines changed 130, context: html, text, full: html, text
    Missed one submission
  • lines changed 904, context: html, text, full: html, text
    Added 8 more submisions
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCaltechRnaSeq.ra
  • lines changed 2219, context: html, text, full: html, text
    adding the new files and metadata for replacement submissions
  • lines changed 373, context: html, text, full: html, text
    changed Caltech to Caltech(Wold)
  • lines changed 399, context: html, text, full: html, text
    added rnaExtract to metaData
  • lines changed 819, context: html, text, full: html, text
    fixed dates for resubmission
  • lines changed 285, context: html, text, full: html, text
    Added MCF-7 missing rep1
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylRrbs.ra
  • lines changed 229, context: html, text, full: html, text
    Added 2395, stalled submission in the Release Q
  • lines changed 269, context: html, text, full: html, text
    Removed growth protocol variables that was in protocol variables in meta-data and cv.ra
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra
  • lines changed 4532, context: html, text, full: html, text
    Revoked bigWigs as they were not generated in correctly by Lab
  • lines changed 3337, context: html, text, full: html, text
    added hg18 fastqs
  • lines changed 4371, context: html, text, full: html, text
    added 5 new submissions with Raw Signal
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromChip.ra
  • lines changed 1194, context: html, text, full: html, text
    added hg18 fastqs
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSunyGeneST.ra
  • lines changed 22, context: html, text, full: html, text
    added origAssembly hg18
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhHistone.ra
  • lines changed 133, context: html, text, full: html, text
    Added 1 submission to SYDH Histone Track
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra
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    added 30 submissions to SYDH TFBS track
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    in the fastq names, changed Musigg to Iggmus
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDgf.ra
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    added hg18 fastqs
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDnase.ra
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    added hg18 fastqs
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwHistone.ra
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    added hg18 fastqs
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwTfbs.ra
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    added hg18 fastqs
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/makefile
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    staging hg19 ENCODE UW DNase DGF metadata on beta
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeCshlShortRnaSeq.ra
  • lines changed 224, context: html, text, full: html, text
    updating metaDb on beta and preparing metaDb for release of hg19 CSHL Sm RNA-seq
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeUwDgf.ra
  • lines changed 1199, context: html, text, full: html, text
    staging hg19 ENCODE UW DNase DGF metadata on beta
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/makefile
  • lines changed 1, context: html, text, full: html, text
    updating metaDb on beta and preparing metaDb for release of hg19 CSHL Sm RNA-seq
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    preparing to release GIS RNA seq, redmine issue #40
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeCshlShortRnaSeq.ra
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    updating metaDb on beta and preparing metaDb for release of hg19 CSHL Sm RNA-seq
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeGisRnaSeq.ra
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    preparing to release GIS RNA seq, redmine issue #40
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 14, context: html, text, full: html, text
    update labels on Alt Sequence track
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    http://redmine.soe.ucsc.edu/issues/1892 plus making capitalization more consistent in longLabels
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
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    Updated Methyl RRBS file name to the track name of Methyl RRBS from HaibRrbs to HaibMethylRrbs.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeAffyRnaChip.ra
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    Removed the configuration options
  • lines changed 105, context: html, text, full: html, text
    changed labels to be the Encode standard
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    changed labels according to spreadsheet
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    changed labels according to spreadsheet
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    RT changed to rw
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    Put the filters back for configuration
• src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHistone.ra
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    New submissions
  • lines changed 141, context: html, text, full: html, text
    Added 7 (not 8) new submissions
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCaltechRnaSeq.ra
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    adding the new files and metadata for replacement submissions
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    Added MCF-7 missing rep1
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    changing long labels to match ENCODE style guide
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.html
  • lines changed 1, context: html, text, full: html, text
    fixing hgdownload links
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.ra
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    changed long label for composite
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    Changed long label of composite #44
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    changed visibility to Kate's request #44 and #40
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGisRnaSeq.ra
  • lines changed 12, context: html, text, full: html, text
    preparing GIS RNA-seq for release
  • lines changed 11, context: html, text, full: html, text
    changed visibility to Kate's request #44 and #40
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylRrbs.html
  • lines changed 4, context: html, text, full: html, text
    Fixed some typo of semi-colon(;) instead of colon(:) in the credits section
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    Updated track description to include obtainedBy description
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    Removed Release 1 notes as Release notes are not necessary for the first release of a track.
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    Updated Contacts links and header labels in track description.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylRrbs.ra
  • lines changed 1112, context: html, text, full: html, text
    Updated Methyl RRBS file name to the track name of Methyl RRBS from HaibRrbs to HaibMethylRrbs.
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    Updated composite long label format to specs of track settings style guide/
  • lines changed 118, context: html, text, full: html, text
    Changed the long labels to Encode Standard
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibRrbs.ra
  • lines changed 111, context: html, text, full: html, text
    Added 2395, stalled submission in the Release Q
  • lines changed 130, context: html, text, full: html, text
    Updated track configuration for RRBS data to include obtained from
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    Removed growth protocol variables that was in protocol variables in meta-data and cv.ra
  • lines changed 3, context: html, text, full: html, text
    Updated the default score value to be 10 and greater
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    Updated Methyl RRBS file name to the track name of Methyl RRBS from HaibRrbs to HaibMethylRrbs.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.html
  • lines changed 13, context: html, text, full: html, text
    Corrected Track Description errors
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.ra
  • lines changed 1921, context: html, text, full: html, text
    Revoked bigWigs as they were not generated in correctly by Lab
  • lines changed 2, context: html, text, full: html, text
    Update the default tracks that were one, since all protocols should be turned on by default for the selected cell, antibody combination
  • lines changed 1846, context: html, text, full: html, text
    added 5 new submissions with Raw Signal
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    Set composite up for matrix/filterComposite and changed some tags for sorting purposes
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhHistone.ra
  • lines changed 18, context: html, text, full: html, text
    Added 1 submission to SYDH Histone Track
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.ra
  • lines changed 592, context: html, text, full: html, text
    added 30 submissions to SYDH TFBS track
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDgf.html
  • lines changed 5, context: html, text, full: html, text
    Removed Release Notes section to be conistent with process of first release of data
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    Updated the the Configuration and Display convention section for Signals
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    Updated track description to include that Bowtie aligner was used.
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    Updated track description to include information about hg18 aligner.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDgf.ra
  • lines changed 48, context: html, text, full: html, text
    staging UwDnaseDgf on hgwbeta; removed release lines instead of changing to release alpha,beta because this is a first release (no release lines necessary)
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    Updated default super track configuration from full to dense
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    Updated composite long label with new conventions
  • lines changed 48, context: html, text, full: html, text
    resolved merge conflict
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    Removed line for origAssembly which produced an inncorrect message on hgc details page
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    fix bug in narrowPeak when too many bases are to displayed
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    Updated maxDisplayWindow to be used with broadPeaks and upgrade UW DGF track conform to max display window
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.html
  • lines changed 3, context: html, text, full: html, text
    fixed typos
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.ra
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    changed long labels to match Encode style guide
• src/hg/makeDb/trackDb/human/numtSeq.html
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    corrected grammar and html formatting in description
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 55, context: html, text, full: html, text
    Updated for Yale Brain.
• src/hg/makeDb/trackDb/loadTracks
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    can ignore error messages on the rm description.html
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/makefile
  • lines changed 2, context: html, text, full: html, text
    Added First two submissions for Penn State TFBS data set
  • lines changed 2, context: html, text, full: html, text
    Added 13 submission (download only) for LICR (Ren) lab
  • lines changed 1, context: html, text, full: html, text
    Accidently misstyped PSU lab data as Histone instead of TFBS
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrHistone.ra
  • lines changed 547, context: html, text, full: html, text
    Added 13 submission (download only) for LICR (Ren) lab
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrTfbs.ra
  • lines changed 811, context: html, text, full: html, text
    Added 13 submission (download only) for LICR (Ren) lab
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodePsuTfbs.ra
  • lines changed 401, context: html, text, full: html, text
    Added First two submissions for Penn State TFBS data set
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhTfbs.ra
  • lines changed 529, context: html, text, full: html, text
    Added 4 new submissions for TFBS track
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.ra
  • lines changed 81, context: html, text, full: html, text
    Changing from multiz30way (with separate conservation and most conserved tracks) to cons30way (with everything in a single Conservation track), because of addition of phyloP subtrack.
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    workaround a problem with the visibility code that is causing a crash on the RR.
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.wgEncode.ra
  • lines changed 1, context: html, text, full: html, text
    Added First two submissions for Penn State TFBS data set
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuTfbs.ra
  • lines changed 88, context: html, text, full: html, text
    Added First two submissions for Penn State TFBS data set
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    Fixed noInherit line in trackDb
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhHist.html
  • lines changed 150, context: html, text, full: html, text
    Removed and renamed the track description pages that existed for SYDh Histone
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhHistone.html
  • lines changed 131, context: html, text, full: html, text
    Removed and renamed the track description pages that existed for SYDh Histone
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhHistone.ra
  • lines changed 1, context: html, text, full: html, text
    Updated Track Long Label according to track conventions
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    Updated track configuration matrix to add third dimension for Treatment.
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    changed the long labels to the new order
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhTfbs.ra
  • lines changed 81, context: html, text, full: html, text
    Added 4 new submissions for TFBS track
• src/hg/makeDb/trackDb/recombRate.html
  • lines changed 7, context: html, text, full: html, text
    fixed a now-dead link in Refs and added a link for a Ref
• src/hg/makeDb/trackDb/tagTypes.tab
  • lines changed 1, context: html, text, full: html, text
    fix bug in narrowPeak when too many bases are to displayed
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    Updated maxDisplayWindow to be used with broadPeaks and upgrade UW DGF track conform to max display window
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    Track #1684 (SNPs 132 (dbSNP)): Adding search spec for snp132.
• src/hg/utils/automation/Encode.pm
  • lines changed 7, context: html, text, full: html, text
    Allow tag-less cv terms
• src/hg/utils/automation/EnsGeneAutomate.pm
  • lines changed 179, context: html, text, full: html, text
    first pass at version 60 specifications
  • lines changed 2, context: html, text, full: html, text
    their oryCun2 is actually the same as our oryCun2
• src/hg/utils/automation/findEnsFtpNames.sh
  • lines changed 8, context: html, text, full: html, text
    fixup output formats of each list
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    clean up ftp.rsp file
• src/hg/utils/mutationClassifier/mutationClassifier.c
  • lines changed 62, context: html, text, full: html, text
    refactor code into addHit
• src/inc/common.h
  • lines changed 15, context: html, text, full: html, text
    Added 3 state boolean to distinguish between unknown and set
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    Fixed SETTING_IS_OFF macro
• src/inc/common.mk
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    do not need the -Wno-long-double for darwin compile

• lines changed: 54187
• files changed: 266