All File Changes

v283_base to v284_preview (2013-05-07 to 2013-05-14) v284

• src/hg/encode3/encodeDataWarehouse/README
  • lines changed 48, context: html, text, full: html, text
    Updating docs.
  • lines changed 2, context: html, text, full: html, text
    fix some typos
• src/hg/encode3/encodeDataWarehouse/edwMetaManiToTdb/edwMetaManiToTdb.c
  • lines changed 564, context: html, text, full: html, text
    Starting to work.
• src/hg/encode3/encodeDataWarehouse/edwMetaManiToTdb/makefile
  • lines changed 4, context: html, text, full: html, text
    Starting to work.
• src/hg/encode3/encodeDataWarehouse/edwScriptSubmit/edwScriptSubmit.c
  • lines changed 30, context: html, text, full: html, text
    Making script name be randomly generated since Laurence needs it to be unique across the project, not just unique across user. Using baby-babble name since name needs to be without special characters to fit into https basic authorization. Adding five second delay after password fails to check before reporting to make password cracking harder.
• src/hg/encode3/encodeDataWarehouse/edwSubmit/edwSubmit.c
  • lines changed 30, context: html, text, full: html, text
    Switching to using parallelFetch instead of simple cpFile for data transfer.
  • lines changed 6, context: html, text, full: html, text
    Taking the number of connections to open for parallel fetch from edwHost table instead of always 10. This will let us give more to Barcelona without making everybody else just thrash the disk harder.
• src/hg/encode3/encodeDataWarehouse/edwWebRegisterScript/edwWebRegisterScript.c
  • lines changed 6, context: html, text, full: html, text
    Reducing size of access key.
  • lines changed 43, context: html, text, full: html, text
    Making script name be randomly generated since Laurence needs it to be unique across the project, not just unique across user. Using baby-babble name since name needs to be without special characters to fit into https basic authorization. Adding five second delay after password fails to check before reporting to make password cracking harder.
• src/hg/encode3/encodeDataWarehouse/edwWebSubmit/edwWebSubmit.c
  • lines changed 22, context: html, text, full: html, text
    Switching to using parallelFetch instead of simple cpFile for data transfer.
• src/hg/encode3/encodeDataWarehouse/inc/edwLib.h
  • lines changed 3, context: html, text, full: html, text
    Exporting baby-name maker and making sure it works for larger ids.
• src/hg/encode3/encodeDataWarehouse/inc/encodeDataWarehouse.h
  • lines changed 6, context: html, text, full: html, text
    Adding paraFetchStream to host so can open extra streams for Barcelona. Adding an index to edwScriptRegistry.name since need to look it up now to find associated user.
• src/hg/encode3/encodeDataWarehouse/lib/edwLib.c
  • lines changed 1, context: html, text, full: html, text
    Increasing time out for single file transfers to accommodate Barcelona speeds.
  • lines changed 5, context: html, text, full: html, text
    Exporting baby-name maker and making sure it works for larger ids.
  • lines changed 1, context: html, text, full: html, text
    fixed little typo
• src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.as
  • lines changed 1, context: html, text, full: html, text
    Explicitly putting fileIdInTransit in edwSubmit record, since it was losing track of files transferred but not yet MD5 summed.
  • lines changed 3, context: html, text, full: html, text
    Adding paraFetchStream to host so can open extra streams for Barcelona. Adding an index to edwScriptRegistry.name since need to look it up now to find associated user.
• src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.c
  • lines changed 24, context: html, text, full: html, text
    Adding paraFetchStream to host so can open extra streams for Barcelona. Adding an index to edwScriptRegistry.name since need to look it up now to find associated user.
• src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.sql
  • lines changed 6, context: html, text, full: html, text
    Adding paraFetchStream to host so can open extra streams for Barcelona. Adding an index to edwScriptRegistry.name since need to look it up now to find associated user.
• src/hg/encode3/encodeDataWarehouse/lib/resetEdw
  • lines changed 1, context: html, text, full: html, text
    Adding Laurence as an automatically added user.
• src/hg/encode3/validateManifest/validateManifest.c
  • lines changed 1, context: html, text, full: html, text
    detect a common misspelling of filename as file_name
  • lines changed 15, context: html, text, full: html, text
    making output more informative and added double spacing for readability
  • lines changed 2, context: html, text, full: html, text
    oops, verbose 0 should be verbose 1
• src/hg/hgBlat/hgBlat.c
  • lines changed 2, context: html, text, full: html, text
    set the UDC cache dir before calling the cart functions.
• src/hg/hgGene/alleles.c
  • lines changed 95, context: html, text, full: html, text
    Initial check in of new hgGene section: Gene Alleles. The ra file is not being checked in yet.
  • lines changed 1, context: html, text, full: html, text
    A couple of cart vars got screwed up in the last change to no longer support timeout vars.
  • lines changed 1, context: html, text, full: html, text
    Fixed 2 objscure bugs resulting from deletions overlapping each other. Also did some name changing and comment clarification suggested by Angie.
  • lines changed 2, context: html, text, full: html, text
    Fixed Synonymous variant sorting, changed full sequence and all variant cart vars to global (instead of gene specific) and conditionally added the haplotype ID to a hover message at Kate's request.
• src/hg/hgGene/hgGene.c
  • lines changed 15, context: html, text, full: html, text
    Initial check in of new hgGene section: Gene Alleles. The ra file is not being checked in yet.
• src/hg/hgGene/hgGene.h
  • lines changed 9, context: html, text, full: html, text
    Initial check in of new hgGene section: Gene Alleles. The ra file is not being checked in yet.
• src/hg/hgGene/hgGeneData/Human/hg19/section.ra
  • lines changed 9, context: html, text, full: html, text
    Adding the Gene Alleles section with this one ra file. To prevent it from being released this cycle, merely revoke this one file.
• src/hg/hgGene/makefile
  • lines changed 1, context: html, text, full: html, text
    Initial check in of new hgGene section: Gene Alleles. The ra file is not being checked in yet.
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 11, context: html, text, full: html, text
    new pubsBlat format allows to specify mouseover text and labels as part of primary table, without join. Also allows to define classes of papers and color them via a second table
  • lines changed 15, context: html, text, full: html, text
    adding publisher filter to pubs trackui
  • lines changed 3, context: html, text, full: html, text
    filters work on main table now if table is in new format, added publisher filter
• src/hg/hgTracks/bigBedTrack.c
  • lines changed 1, context: html, text, full: html, text
    uniprot variants track also can generate annotations now
  • lines changed 63, context: html, text, full: html, text
    adding mouseOverField to trackDb for bigBed and using it for the spMut track
  • lines changed 2, context: html, text, full: html, text
    temporarily taking back a change as it proved deadly for bed3 files
  • lines changed 21, context: html, text, full: html, text
    fixing a bug where a bed3 file crashed the mouseOver mapItem method. Moved this method now into the linkedFeatures code, where it should have been from the start
• src/hg/hgTracks/hgTracks.h
  • lines changed 2, context: html, text, full: html, text
    adding mouseOverField to trackDb for bigBed and using it for the spMut track
• src/hg/hgTracks/makefile
  • lines changed 1, context: html, text, full: html, text
    moving the publication track code into its own .h/.c files
• src/hg/hgTracks/pubsTracks.c
  • lines changed 485, context: html, text, full: html, text
    moving the publication track code into its own .h/.c files
  • lines changed 42, context: html, text, full: html, text
    filters work on main table now if table is in new format, added publisher filter
  • lines changed 18, context: html, text, full: html, text
    change impact colors
  • lines changed 5, context: html, text, full: html, text
    fixed publisher filter and publisher logo bugs
  • lines changed 9, context: html, text, full: html, text
    if impact coloring is activated, show impact factor in mouse over
  • lines changed 2, context: html, text, full: html, text
    forgot to init a variable
  • lines changed 0, context: html, text, full: html, text
    fixing a bug where a bed3 file crashed the mouseOver mapItem method. Moved this method now into the linkedFeatures code, where it should have been from the start
  • lines changed 3, context: html, text, full: html, text
    stricter-compiler warning: 'true' and 'false' are not defined on all systems; use our defines 'TRUE' and 'FALSE'
• src/hg/hgTracks/pubsTracks.h
  • lines changed 7, context: html, text, full: html, text
    moving the publication track code into its own .h/.c files
• src/hg/hgTracks/simpleTracks.c
  • lines changed 123, context: html, text, full: html, text
    new pubsBlat format allows to specify mouseover text and labels as part of primary table, without join. Also allows to define classes of papers and color them via a second table
  • lines changed 22, context: html, text, full: html, text
    trying to come up with better color shades for impact coloring
  • lines changed 18, context: html, text, full: html, text
    use only best color if several defined
  • lines changed 1, context: html, text, full: html, text
    adding mouseOverField to trackDb for bigBed and using it for the spMut track
  • lines changed 480, context: html, text, full: html, text
    moving the publication track code into its own .h/.c files
  • lines changed 17, context: html, text, full: html, text
    fixing a bug where a bed3 file crashed the mouseOver mapItem method. Moved this method now into the linkedFeatures code, where it should have been from the start
  • lines changed 26, context: html, text, full: html, text
    last change broke hgGene links, temporarily taking it back
  • lines changed 21, context: html, text, full: html, text
    fixed linkedFeatures mouseOver text to work with hgGenes linkouts, tested on refseq, knownGenes, simple and extended bed files.
• src/hg/hgc/hgc.c
  • lines changed 34, context: html, text, full: html, text
    removed EXTRA_FIELDS_SUPPORT ifdef-blocks, as they made the code very hard to read, got OK from Tim by email
  • lines changed 119, context: html, text, full: html, text
    support for urls in bigBed+ fields via a new tdb statement "urls"
  • lines changed 1, context: html, text, full: html, text
    fixed one-off bug in disulf bind field
• src/hg/hgc/peakClusters.c
  • lines changed 221, context: html, text, full: html, text
    Remove obsolete code (support for 'inputTracksSubgroupDisplay' tsetting/feature, which poked through a tracks and trackDb in a related composite track for info -- to provide more features ??. The code was all bracketed with TO_BE_REMOVED. Alternate approach uses inputTableFieldDisplay setting
  • lines changed 87, context: html, text, full: html, text
    Create version of track clustered by target protein. refs #10097
• src/hg/hgc/pubs.c
  • lines changed 32, context: html, text, full: html, text
    changing hgc page
  • lines changed 82, context: html, text, full: html, text
    many changes after review by krauthammer lab to adapt display to yif OCR images
  • lines changed 56, context: html, text, full: html, text
    added link to image page on yif server, after email from mate
  • lines changed 17, context: html, text, full: html, text
    additional debug statements
  • lines changed 37, context: html, text, full: html, text
    handling explicitly specified publisher names, adding the missing nature logo
  • lines changed 10, context: html, text, full: html, text
    better html layout of publisher logo
  • lines changed 27, context: html, text, full: html, text
    making it possible to link to hgc without t and o parameters (europmc)
  • lines changed 2, context: html, text, full: html, text
    correcting weird case where file desc is empty
  • lines changed 4, context: html, text, full: html, text
    fixed publisher filter and publisher logo bugs
  • lines changed 2, context: html, text, full: html, text
    bugfix for europmc who want to link to hgc directly
  • lines changed 2, context: html, text, full: html, text
    stricter-compiler warning: address of a char[] will always evaluate as true, use a different test
• src/hg/htdocs/ENCODE/analysisTools.html
  • lines changed 28, context: html, text, full: html, text
    Making changes to Analysis Tools page per Portal update, refs #10760
• src/hg/htdocs/ENCODE/downloads.html
  • lines changed 5, context: html, text, full: html, text
    Adding link to new AWG Uniform TFBS track in ENCODE/downloads for Release #1 refs #10042
• src/hg/htdocs/ENCODE/index.html
  • lines changed 12, context: html, text, full: html, text
    Added link to Mouse ENCODE portal, by request of Mike Pazin and Bing Ren
  • lines changed 2, context: html, text, full: html, text
    Adding quotes on blank, and removing duplicate line, before pushing out new link added by Kate for CSHL mouse ENCODE talk
• src/hg/htdocs/ENCODE/usageResources.html
  • lines changed 2, context: html, text, full: html, text
    Adding link to the NHGRI Tutorial refs #10760
• src/hg/htdocs/goldenPath/help/haplotypes.html
  • lines changed 1, context: html, text, full: html, text
    Correcting minor typo. refs #10769
  • lines changed 197, context: html, text, full: html, text
    Major organization changes (suggested by Brooke). Also, less important notes have been moved to a table at the bottom. Decisions should be made as to which of these notes really shoud be in the body of the text.
  • lines changed 1, context: html, text, full: html, text
    Fixed 2 objscure bugs resulting from deletions overlapping each other. Also did some name changing and comment clarification suggested by Angie.
  • lines changed 17, context: html, text, full: html, text
    Removed reference to gene specific cart vars which are no longer accurate. Added a note about haplotype IDs which may not be included in the released version.
  • lines changed 13, context: html, text, full: html, text
    Removed the ID note as not ready for prime time and clarified some wording.
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 25, context: html, text, full: html, text
    first try at "urls" statement documentation
  • lines changed 21, context: html, text, full: html, text
    adding mouse over statement doc
  • lines changed 7, context: html, text, full: html, text
    fixed linkedFeatures mouseOver text to work with hgGenes linkouts, tested on refseq, knownGenes, simple and extended bed files.
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 1, context: html, text, full: html, text
    fixed mangled HTML
• src/hg/htdocs/images/pubs_asm.png
  • lines changed 0, context: html, text, full: html, text
    fixed publisher filter and publisher logo bugs
• src/hg/htdocs/images/pubs_elsevier.png
  • lines changed 0, context: html, text, full: html, text
    fixed publisher filter and publisher logo bugs
• src/hg/htdocs/images/pubs_nature.png
  • lines changed 0, context: html, text, full: html, text
    handling explicitly specified publisher names, adding the missing nature logo
• src/hg/htdocs/images/pubs_npg.png
  • lines changed 0, context: html, text, full: html, text
    handling explicitly specified publisher names, adding the missing nature logo
• src/hg/htdocs/images/pubs_oup.png
  • lines changed 0, context: html, text, full: html, text
    adding oup image for pubs track
• src/hg/htdocs/images/pubs_oxfordjournals.png
  • lines changed 0, context: html, text, full: html, text
    adding oup image for pubs track
• src/hg/htdocs/images/pubs_pmc.png
  • lines changed 0, context: html, text, full: html, text
    fixed publisher filter and publisher logo bugs
• src/hg/htdocs/images/pubs_pnas.png
  • lines changed 0, context: html, text, full: html, text
    fixed publisher filter and publisher logo bugs
• src/hg/htdocs/images/pubs_wiley.png
  • lines changed 0, context: html, text, full: html, text
    fixed publisher filter and publisher logo bugs
• src/hg/htdocs/images/title.jpg
  • lines changed 0, context: html, text, full: html, text
    this image was remade by Kent C. to get rid of some of the compression artifacts
• src/hg/inc/cart.h
  • lines changed 5, context: html, text, full: html, text
    Removing cartBooleanTimeout as disappearing cart variables are not really a good idea at this time.
• src/hg/inc/haplotypes.h
  • lines changed 7, context: html, text, full: html, text
    Fixed 2 objscure bugs resulting from deletions overlapping each other. Also did some name changing and comment clarification suggested by Angie.
• src/hg/inc/trackHub.h
  • lines changed 10, context: html, text, full: html, text
    first cut at track item search in track hubs that have bigBed files with a searchIndex field refs #10426
• src/hg/js/alleles.js
  • lines changed 1, context: html, text, full: html, text
    Fixed minor js warning.
  • lines changed 2, context: html, text, full: html, text
    A couple of cart vars got screwed up in the last change to no longer support timeout vars.
• src/hg/lib/annoGratorGpVar.c
  • lines changed 1, context: html, text, full: html, text
    Fixing comment typo found by Tim in code review. refs #10725
• src/hg/lib/annoStreamDb.c
  • lines changed 4, context: html, text, full: html, text
    bugfix: annoStreamDb's minFinestBin was uninitialized.
• src/hg/lib/cart.c
  • lines changed 31, context: html, text, full: html, text
    Removing cartBooleanTimeout as disappearing cart variables are not really a good idea at this time.
  • lines changed 2, context: html, text, full: html, text
    putting setUdcCacheDir() in places where cgis get launched with special params for saved sessions -- hopefully this means we will not have to actually put this call in every single cgi
• src/hg/lib/clusterInputTrackTable3.as
  • lines changed 1, context: html, text, full: html, text
    Create version of track clustered by target protein. refs #10097
• src/hg/lib/clusterInputTrackTable4.as
  • lines changed 1, context: html, text, full: html, text
    Create version of track clustered by target protein. refs #10097
• src/hg/lib/clusterInputTrackTable5.sql
  • lines changed 17, context: html, text, full: html, text
    Create version of track clustered by target protein. refs #10097
• src/hg/lib/haplotypes.c
  • lines changed 68, context: html, text, full: html, text
    Removed cart vars timing out and moved some buttons (conditionally).
  • lines changed 204, context: html, text, full: html, text
    Fixed 2 objscure bugs resulting from deletions overlapping each other. Also did some name changing and comment clarification suggested by Angie.
  • lines changed 22, context: html, text, full: html, text
    Fixed Synonymous variant sorting, changed full sequence and all variant cart vars to global (instead of gene specific) and conditionally added the haplotype ID to a hover message at Kate's request.
• src/hg/lib/hdb.c
  • lines changed 11, context: html, text, full: html, text
    first cut at track item search in track hubs that have bigBed files with a searchIndex field refs #10426
• src/hg/lib/hgFind.c
  • lines changed 4, context: html, text, full: html, text
    first cut at track item search in track hubs that have bigBed files with a searchIndex field refs #10426
• src/hg/lib/hubConnect.c
  • lines changed 15, context: html, text, full: html, text
    first cut at track item search in track hubs that have bigBed files with a searchIndex field refs #10426
• src/hg/lib/trackHub.c
  • lines changed 182, context: html, text, full: html, text
    first cut at track item search in track hubs that have bigBed files with a searchIndex field refs #10426
• src/hg/makeDb/doc/encodeRegHg19.txt
  • lines changed 40, context: html, text, full: html, text
    Create version of track clustered by target protein. refs #10097
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 1, context: html, text, full: html, text
    use ccds 104.0 on hg19
• src/hg/makeDb/trackDb/cv/public/cv.ra
  • lines changed 81, context: html, text, full: html, text
    Copying beta/cv.ra to public/cv.ra, changes included needed for the AWG TFBS Uniform Track (release 1) refs #10042
• src/hg/makeDb/trackDb/human/hg19/knownGene.html
  • lines changed 1, context: html, text, full: html, text
    For UCSC Genes long label and description page, replaced UniProt with GenBank for hg19 and removed UniProt and CCDS and added tRNAs for mm9 and mm10 (redmine #10462)
  • lines changed 1, context: html, text, full: html, text
    Capitalized the 'B' in 'GenBank' (redmine #10462)
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeAwgTfbsUniform.ra
  • lines changed 2, context: html, text, full: html, text
    HA-E2F1 now grouped with E2F1, input from Peggy Farnham (USC). refs #10042
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeAwgTfbsUniform.ra
  • lines changed 2, context: html, text, full: html, text
    Restaging AWG TFBS Uniform (Release 1) to add changes to MetaData refs #10042)
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/makefile
  • lines changed 1, context: html, text, full: html, text
    Staging metaData to public for AWG TFBS Uniform (Release #1) refs #10042
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeAwgTfbsUniform.ra
  • lines changed 13532, context: html, text, full: html, text
    Staging metaData to public for AWG TFBS Uniform (Release #1) refs #10042
• src/hg/makeDb/trackDb/human/hg19/numtSeqHg19.html
  • lines changed 27, context: html, text, full: html, text
    Updating refs as per code review. Also adding PMIDs. refs #10767
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    For UCSC Genes long label and description page, replaced UniProt with GenBank for hg19 and removed UniProt and CCDS and added tRNAs for mm9 and mm10 (redmine #10462)
• src/hg/makeDb/trackDb/human/hg19/wgEncodeAwgTfbsUniform.html
  • lines changed 6, context: html, text, full: html, text
    Making corrections to AWG Uniform TFBS html from Code Review refs #10766
  • lines changed 0, context: html, text, full: html, text
    HA-E2F1 now grouped with E2F1, input from Peggy Farnham (USC). refs #10042
• src/hg/makeDb/trackDb/human/hg19/wgEncodeAwgTfbsUniform.ra
  • lines changed 1, context: html, text, full: html, text
    Fix problem with downloads page column. QA issue 11. refs 10042
  • lines changed 4, context: html, text, full: html, text
    Fix short label inconsistencies. QA #14. refs #10042
  • lines changed 6, context: html, text, full: html, text
    Clarify protocol in long labels. QA #13. refs #10042
  • lines changed 5, context: html, text, full: html, text
    HA-E2F1 now grouped with E2F1, input from Peggy Farnham (USC). refs #10042
  • lines changed 13, context: html, text, full: html, text
    Uniqify short labels. refs #10042
  • lines changed 6, context: html, text, full: html, text
    Correct misassignment of IMR90 to tier2 (it's in tier 2.5). refs #10042
  • lines changed 75, context: html, text, full: html, text
    1. Set track defaults (1 'interesting' TF, CTCF, and POL2 for tier1 and tier2, plus a few tier 2.5. refs #10042. Also track setting for factorSource. refs #10097
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.release3.ra
  • lines changed 1, context: html, text, full: html, text
    Adjust TFBS track visibilities. The uniform track shows all labs, so lab-specific tracks can now be hidden by default. refs #10042
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromChip.release2.ra
  • lines changed 1, context: html, text, full: html, text
    Adjust TFBS track visibilities. The uniform track shows all labs, so lab-specific tracks can now be hidden by default. refs #10042
• src/hg/makeDb/trackDb/human/hg19/wgEncodeReg.ra
  • lines changed 35, context: html, text, full: html, text
    Create version of track clustered by target protein. refs #10097
  • lines changed 46, context: html, text, full: html, text
    ENCODE TFBS clusters track update. refs #10097
  • lines changed 4, context: html, text, full: html, text
    Adjust TFBS track visibilities. The uniform track shows all labs, so lab-specific tracks can now be hidden by default. refs #10042
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.ra
  • lines changed 1, context: html, text, full: html, text
    Adjust TFBS track visibilities. The uniform track shows all labs, so lab-specific tracks can now be hidden by default. refs #10042
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.release3.ra
  • lines changed 1, context: html, text, full: html, text
    Adjust TFBS track visibilities. The uniform track shows all labs, so lab-specific tracks can now be hidden by default. refs #10042
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUchicagoTfbs.ra
  • lines changed 1, context: html, text, full: html, text
    Tweak visibility -- can be hidden now that Uniform TFBS is public. refs #10042
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUchicagoTfbs.release2.ra
  • lines changed 1, context: html, text, full: html, text
    Adjust TFBS track visibilities. The uniform track shows all labs, so lab-specific tracks can now be hidden by default. refs #10042
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwTfbs.release4.ra
  • lines changed 1, context: html, text, full: html, text
    Adjust TFBS track visibilities. The uniform track shows all labs, so lab-specific tracks can now be hidden by default. refs #10042
• src/hg/makeDb/trackDb/human/lovd.html
  • lines changed 66, context: html, text, full: html, text
    uniprot variants track also can generate annotations now
• src/hg/makeDb/trackDb/human/numtSeq.html
  • lines changed 11, context: html, text, full: html, text
    Updating refs as per code review. Also adding PMIDs. refs #10767
• src/hg/makeDb/trackDb/human/spMut.html
  • lines changed 56, context: html, text, full: html, text
    uniprot variants track also can generate annotations now
  • lines changed 6, context: html, text, full: html, text
    adding mouseOverField to trackDb for bigBed and using it for the spMut track
  • lines changed 3, context: html, text, full: html, text
    changes to html for spMut
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 20, context: html, text, full: html, text
    support for urls in bigBed+ fields via a new tdb statement "urls"
  • lines changed 11, context: html, text, full: html, text
    uniprot variants track also can generate annotations now
  • lines changed 2, context: html, text, full: html, text
    adding mouseOverField to trackDb for bigBed and using it for the spMut track
• src/hg/makeDb/trackDb/mouse/mm10/knownGene.html
  • lines changed 2, context: html, text, full: html, text
    For UCSC Genes long label and description page, replaced UniProt with GenBank for hg19 and removed UniProt and CCDS and added tRNAs for mm9 and mm10 (redmine #10462)
  • lines changed 1, context: html, text, full: html, text
    Capitalized the 'B' in 'GenBank' (redmine #10462)
• src/hg/makeDb/trackDb/mouse/mm9/knownGene.html
  • lines changed 2, context: html, text, full: html, text
    For UCSC Genes long label and description page, replaced UniProt with GenBank for hg19 and removed UniProt and CCDS and added tRNAs for mm9 and mm10 (redmine #10462)
• src/hg/makeDb/trackDb/mouse/mm9/numtSeqMm9.html
  • lines changed 15, context: html, text, full: html, text
    Updating refs as per code review. Also adding PMIDs. refs #10767
• src/hg/makeDb/trackDb/tagTypes.tab
  • lines changed 1, context: html, text, full: html, text
    support for urls in bigBed+ fields via a new tdb statement "urls"
  • lines changed 1, context: html, text, full: html, text
    adding mouseOverField to trackDb for bigBed and using it for the spMut track
  • lines changed 1, context: html, text, full: html, text
    1. Set track defaults (1 'interesting' TF, CTCF, and POL2 for tier1 and tier2, plus a few tier 2.5. refs #10042. Also track setting for factorSource. refs #10097
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    For UCSC Genes long label and description page, replaced UniProt with GenBank for hg19 and removed UniProt and CCDS and added tRNAs for mm9 and mm10 (redmine #10462)
  • lines changed 1, context: html, text, full: html, text
    Changed formatting of the UCSC Genes long label to match the formatting of the hg19 long label (redmine #10462)
• src/hg/regulate/regClusterBedExpCfg/regClusterBedExpCfg.c
  • lines changed 1, context: html, text, full: html, text
    Suggestion from JK during code review. Simpler is better
  • lines changed 1, context: html, text, full: html, text
    Oops, simplification changed functionality -- rolling back
• src/hg/utils/lovd/bedDetail4.sql
  • lines changed 16, context: html, text, full: html, text
    lovd and uniprot mutation tracks scripts
• src/hg/utils/lovd/check.sh
  • lines changed 47, context: html, text, full: html, text
    lovd and uniprot mutation tracks scripts
• src/hg/utils/lovd/download.sh
  • lines changed 24, context: html, text, full: html, text
    lovd and uniprot mutation tracks scripts
• src/hg/utils/lovd/load.sh
  • lines changed 21, context: html, text, full: html, text
    lovd and uniprot mutation tracks scripts
• src/hg/utils/uniprotMutations/README.txt
  • lines changed 30, context: html, text, full: html, text
    lovd and uniprot mutation tracks scripts
  • lines changed 9, context: html, text, full: html, text
    uniprot variants track also can generate annotations now
• src/hg/utils/uniprotMutations/bed12UniProtAnnot.as
  • lines changed 21, context: html, text, full: html, text
    uniprot variants track also can generate annotations now
  • lines changed 1, context: html, text, full: html, text
    fixed same table name in different .as files
• src/hg/utils/uniprotMutations/bed12UniProtMut.as
  • lines changed 23, context: html, text, full: html, text
    lovd and uniprot mutation tracks scripts
  • lines changed 2, context: html, text, full: html, text
    uniprot variants track also can generate annotations now
• src/hg/utils/uniprotMutations/liftUniprotMut.py
  • lines changed 128, context: html, text, full: html, text
    lovd and uniprot mutation tracks scripts
  • lines changed 2, context: html, text, full: html, text
    remove empty strings from output in two fields
  • lines changed 120, context: html, text, full: html, text
    uniprot variants track also can generate annotations now
  • lines changed 3, context: html, text, full: html, text
    keep mutations with disease but no other comment
  • lines changed 33, context: html, text, full: html, text
    changed format to take into account new uniprot parser output, using disease codes now in bed3 field
• src/hg/utils/uniprotMutations/load.sh
  • lines changed 3, context: html, text, full: html, text
    lovd and uniprot mutation tracks scripts
  • lines changed 5, context: html, text, full: html, text
    uniprot variants track also can generate annotations now
• src/hg/utils/uniprotMutations/makeUniProtToHg.sh
  • lines changed 48, context: html, text, full: html, text
    lovd and uniprot mutation tracks scripts
• src/hg/utils/uniprotMutations/mapUniprot_doBlast
  • lines changed 18, context: html, text, full: html, text
    lovd and uniprot mutation tracks scripts
• src/inc/net.h
  • lines changed 4, context: html, text, full: html, text
    Moving parallelFetch to a new module.
• src/inc/paraFetch.h
  • lines changed 26, context: html, text, full: html, text
    Moving parallelFetch to a new module.
• src/inc/twoBit.h
  • lines changed 2, context: html, text, full: html, text
    first cut at track item search in track hubs that have bigBed files with a searchIndex field refs #10426
• src/lib/annoStreamBigBed.c
  • lines changed 38, context: html, text, full: html, text
    Bugfix: for genome-wide queries, annoStreamBig{Bed,Wig} need to do a series of per-chrom bbi queries.
• src/lib/annoStreamBigWig.c
  • lines changed 36, context: html, text, full: html, text
    Bugfix: for genome-wide queries, annoStreamBig{Bed,Wig} need to do a series of per-chrom bbi queries.
• src/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    Moving parallelFetch to a new module.
• src/lib/net.c
  • lines changed 647, context: html, text, full: html, text
    Moving parallelFetch to a new module.
• src/lib/paraFetch.c
  • lines changed 659, context: html, text, full: html, text
    Moving parallelFetch to a new module.
  • lines changed 30, context: html, text, full: html, text
    Improving commenting and making pointer return values optional.
  • lines changed 2, context: html, text, full: html, text
    Moving parallelFetch to a new module.
• src/lib/twoBit.c
  • lines changed 13, context: html, text, full: html, text
    first cut at track item search in track hubs that have bigBed files with a searchIndex field refs #10426
• src/parasol/.gitignore
  • lines changed 1, context: html, text, full: html, text
    Tell git to ignore parasol/bin .
• src/utils/paraFetch/paraFetch.c
  • lines changed 1, context: html, text, full: html, text
    Moving parallelFetch to a new module.
• src/utils/paraSync/paraSync.c
  • lines changed 1, context: html, text, full: html, text
    Moving parallelFetch to a new module.
• src/utils/qa/blatPing.csh
  • lines changed 12, context: html, text, full: html, text
    tweaks to handle long list of blatservers
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    v284 preview1

• lines changed: 20138
• files changed: 201