All File Changes

v305_preview to v305_preview2 (2014-08-18 to 2014-08-25) v305

• src/hg/encode3/eap/oneShot/dnaseHg38AddTreatments/dnaseHg38AddTreatments.c
  • lines changed 83, context: html, text, full: html, text
    Little wrangling program to add treatments and augment short labels with them.
• src/hg/encode3/eap/oneShot/dnaseHg38AddTreatments/makefile
  • lines changed 3, context: html, text, full: html, text
    Little wrangling program to add treatments and augment short labels with them.
• src/hg/encode3/eap/oneShot/dnaseHg38Batch/dnaseHg38Batch.c
  • lines changed 74, context: html, text, full: html, text
    A little utility to help generate batches for dnase.
  • lines changed 65, context: html, text, full: html, text
    Creating meta.tab output to associate experiment and biosample. Making jobList explicitly to deal with difference between single file and pooled file cases.
  • lines changed 1, context: html, text, full: html, text
    Suppressing a near duplicate line in meta.txt.
• src/hg/encode3/eap/oneShot/dnaseHg38Batch/makefile
  • lines changed 4, context: html, text, full: html, text
    A little utility to help generate batches for dnase.
• src/hg/hgTracks/bamTrack.c
  • lines changed 1, context: html, text, full: html, text
    Revert "Two problems noticed by Angie in code review. Redmine #13704."
    This reverts commit 936b5b5319541bf59421b258703a4f6af54790e3.
    
    refs #13833
    
  • lines changed 5, context: html, text, full: html, text
    Revert "Checking in changes to make 'spectrum' (aka 'useScore') actually work on any pair of color/altColor settings. It used to be that only shadesOfGray, shadesOfBrown and shadesOfSea worked, leaving most cases to be shadesOfGray. I have sat on these changes for months. I am also checking in ifdef'd out code to calc the shade on the fly, rather than relaying on track->colorShades set of precomputed 10 shades. The only reason this code is not used is that it would require changing many many places/uses of colorShades. Since I am bein laid off, it seems inappropriate to make this more dramatic change at this time."
    This reverts commit a4adfa326bf8bec73020ee1a8aa0cb6251ea8663.
    
    refs #13833
    
• src/hg/hgTracks/bedTrack.c
  • lines changed 2, context: html, text, full: html, text
    Revert "Checking in changes to make 'spectrum' (aka 'useScore') actually work on any pair of color/altColor settings. It used to be that only shadesOfGray, shadesOfBrown and shadesOfSea worked, leaving most cases to be shadesOfGray. I have sat on these changes for months. I am also checking in ifdef'd out code to calc the shade on the fly, rather than relaying on track->colorShades set of precomputed 10 shades. The only reason this code is not used is that it would require changing many many places/uses of colorShades. Since I am bein laid off, it seems inappropriate to make this more dramatic change at this time."
    This reverts commit a4adfa326bf8bec73020ee1a8aa0cb6251ea8663.
    
    refs #13833
    
• src/hg/hgTracks/bigBedTrack.c
  • lines changed 46, context: html, text, full: html, text
    bigGenePred support in track hubs limping along #13861
• src/hg/hgTracks/chainTrack.c
  • lines changed 1, context: html, text, full: html, text
    Revert "Checking in changes to make 'spectrum' (aka 'useScore') actually work on any pair of color/altColor settings. It used to be that only shadesOfGray, shadesOfBrown and shadesOfSea worked, leaving most cases to be shadesOfGray. I have sat on these changes for months. I am also checking in ifdef'd out code to calc the shade on the fly, rather than relaying on track->colorShades set of precomputed 10 shades. The only reason this code is not used is that it would require changing many many places/uses of colorShades. Since I am bein laid off, it seems inappropriate to make this more dramatic change at this time."
    This reverts commit a4adfa326bf8bec73020ee1a8aa0cb6251ea8663.
    
    refs #13833
    
• src/hg/hgTracks/hgTracks.c
  • lines changed 3, context: html, text, full: html, text
    bigGenePred support in track hubs limping along #13861
• src/hg/hgTracks/hgTracks.h
  • lines changed 6, context: html, text, full: html, text
    Revert "Checking in changes to make 'spectrum' (aka 'useScore') actually work on any pair of color/altColor settings. It used to be that only shadesOfGray, shadesOfBrown and shadesOfSea worked, leaving most cases to be shadesOfGray. I have sat on these changes for months. I am also checking in ifdef'd out code to calc the shade on the fly, rather than relaying on track->colorShades set of precomputed 10 shades. The only reason this code is not used is that it would require changing many many places/uses of colorShades. Since I am bein laid off, it seems inappropriate to make this more dramatic change at this time."
    This reverts commit a4adfa326bf8bec73020ee1a8aa0cb6251ea8663.
    
    refs #13833
    
• src/hg/hgTracks/rnaFoldTrack.c
  • lines changed 4, context: html, text, full: html, text
    Revert "Checking in changes to make 'spectrum' (aka 'useScore') actually work on any pair of color/altColor settings. It used to be that only shadesOfGray, shadesOfBrown and shadesOfSea worked, leaving most cases to be shadesOfGray. I have sat on these changes for months. I am also checking in ifdef'd out code to calc the shade on the fly, rather than relaying on track->colorShades set of precomputed 10 shades. The only reason this code is not used is that it would require changing many many places/uses of colorShades. Since I am bein laid off, it seems inappropriate to make this more dramatic change at this time."
    This reverts commit a4adfa326bf8bec73020ee1a8aa0cb6251ea8663.
    
    refs #13833
    
• src/hg/hgTracks/simpleTracks.c
  • lines changed 2, context: html, text, full: html, text
    Revert "Restoring the default values for lfColors after the changes in a4adfa326b and 936b5b531."
    This reverts commit 706b20f0ff54a3bf502e9697c35f46a267c1aec9.
    
    refs #13833
    
  • lines changed 6, context: html, text, full: html, text
    Revert "Two problems noticed by Angie in code review. Redmine #13704."
    This reverts commit 936b5b5319541bf59421b258703a4f6af54790e3.
    
    refs #13833
    
  • lines changed 146, context: html, text, full: html, text
    Revert "Checking in changes to make 'spectrum' (aka 'useScore') actually work on any pair of color/altColor settings. It used to be that only shadesOfGray, shadesOfBrown and shadesOfSea worked, leaving most cases to be shadesOfGray. I have sat on these changes for months. I am also checking in ifdef'd out code to calc the shade on the fly, rather than relaying on track->colorShades set of precomputed 10 shades. The only reason this code is not used is that it would require changing many many places/uses of colorShades. Since I am bein laid off, it seems inappropriate to make this more dramatic change at this time."
    This reverts commit a4adfa326bf8bec73020ee1a8aa0cb6251ea8663.
    
    refs #13833
    
  • lines changed 10, context: html, text, full: html, text
    bigGenePred support in track hubs limping along #13861
• src/hg/hgc/hgc.c
  • lines changed 6, context: html, text, full: html, text
    bigGenePred support in track hubs limping along #13861
• src/hg/htdocs/ENCODE/FAQ/index.html
  • lines changed 1, context: html, text, full: html, text
    Updating a link to Ensembl's ENCODE page, refs #13616
• src/hg/htdocs/ENCODE/analysis.html
  • lines changed 1, context: html, text, full: html, text
    Another round on ENCODE portal pages. Add notes about new portal. Aesthetics. refs #13616
• src/hg/htdocs/ENCODE/analysisTools.html
  • lines changed 1, context: html, text, full: html, text
    Another round on ENCODE portal pages. Add notes about new portal. Aesthetics. refs #13616
• src/hg/htdocs/ENCODE/antibodies.html
  • lines changed 53, context: html, text, full: html, text
    Update vocab pages. refs #13616
  • lines changed 1, context: html, text, full: html, text
    Clean up extra date. refs #13616
• src/hg/htdocs/ENCODE/cellTypes.html
  • lines changed 128, context: html, text, full: html, text
    Another round on ENCODE portal pages. Add notes about new portal. Aesthetics. refs #13616
• src/hg/htdocs/ENCODE/cellTypesMouse.html
  • lines changed 82, context: html, text, full: html, text
    Update vocab pages. refs #13616
• src/hg/htdocs/ENCODE/contacts.html
  • lines changed 1, context: html, text, full: html, text
    Change logo to UCSC. refs #13616
• src/hg/htdocs/ENCODE/contributors.html
  • lines changed 3, context: html, text, full: html, text
    Another round on ENCODE portal pages. Add notes about new portal. Aesthetics. refs #13616
• src/hg/htdocs/ENCODE/dataMatrix/encodeDataMatrixInclude.html
  • lines changed 3, context: html, text, full: html, text
    Another round on ENCODE portal pages. Add notes about new portal. Aesthetics. refs #13616
• src/hg/htdocs/ENCODE/dataSummary.html
  • lines changed 2, context: html, text, full: html, text
    Another round on ENCODE portal pages. Add notes about new portal. Aesthetics. refs #13616
• src/hg/htdocs/ENCODE/dataSummaryMouse.html
  • lines changed 2, context: html, text, full: html, text
    Another round on ENCODE portal pages. Add notes about new portal. Aesthetics. refs #13616
• src/hg/htdocs/ENCODE/downloads.html
  • lines changed 1, context: html, text, full: html, text
    Another round on ENCODE portal pages. Add notes about new portal. Aesthetics. refs #13616
• src/hg/htdocs/ENCODE/downloadsMouse.html
  • lines changed 1, context: html, text, full: html, text
    Another round on ENCODE portal pages. Add notes about new portal. Aesthetics. refs #13616
• src/hg/htdocs/ENCODE/experiment_guidelines.html
  • lines changed 1, context: html, text, full: html, text
    Another round on ENCODE portal pages. Add notes about new portal. Aesthetics. refs #13616
• src/hg/htdocs/ENCODE/index.html
  • lines changed 13, context: html, text, full: html, text
    Fix typo. refs #13616
  • lines changed 208, context: html, text, full: html, text
    Fixup layout and styling. Still needs a round of CSS simplification. refs #13616
  • lines changed 48, context: html, text, full: html, text
    Fixes to left bar layout. Embed menu layout in home page since it's only used there.
  • lines changed 19, context: html, text, full: html, text
    Cleanup CSS. refs #13616
  • lines changed 3, context: html, text, full: html, text
    Add emphasis to new portal section, per Brian L suggestion. refs #13616
  • lines changed 7, context: html, text, full: html, text
    Tweak wording of home page text after input from Eurie H and Brian L. refs #13616
  • lines changed 1, context: html, text, full: html, text
    Fix format errs. refs #13616
  • lines changed 2, context: html, text, full: html, text
    Use standard UC gold color
  • lines changed 3, context: html, text, full: html, text
    Another round on ENCODE portal pages. Add notes about new portal. Aesthetics. refs #13616
• src/hg/htdocs/ENCODE/newsarch.html
  • lines changed 1, context: html, text, full: html, text
    Fixes for some of Galt's changes to static page relatice links, refs #13663
• src/hg/htdocs/ENCODE/platform_characterization.html
  • lines changed 1, context: html, text, full: html, text
    Another round on ENCODE portal pages. Add notes about new portal. Aesthetics. refs #13616
• src/hg/htdocs/ENCODE/pubs.html
  • lines changed 1, context: html, text, full: html, text
    Another round on ENCODE portal pages. Add notes about new portal. Aesthetics. refs #13616
• src/hg/htdocs/ENCODE/pubsEncode.html
  • lines changed 7, context: html, text, full: html, text
    Fixes for some of Galt's changes to static page relatice links, refs #13663
  • lines changed 1, context: html, text, full: html, text
    Another round on ENCODE portal pages. Add notes about new portal. Aesthetics. refs #13616
• src/hg/htdocs/ENCODE/pubsOther.html
  • lines changed 1, context: html, text, full: html, text
    Fixes for some of Galt's changes to static page relatice links, refs #13663
  • lines changed 1, context: html, text, full: html, text
    Another round on ENCODE portal pages. Add notes about new portal. Aesthetics. refs #13616
• src/hg/htdocs/ENCODE/regions.html
  • lines changed 1, context: html, text, full: html, text
    Fixes for some of Galt's changes to static page relatice links, refs #13663
• src/hg/htdocs/ENCODE/search.html
  • lines changed 1, context: html, text, full: html, text
    Change logo to UCSC. refs #13616
  • lines changed 2, context: html, text, full: html, text
    Another round on ENCODE portal pages. Add notes about new portal. Aesthetics. refs #13616
• src/hg/htdocs/ENCODE/softwareTools.html
  • lines changed 1, context: html, text, full: html, text
    Another round on ENCODE portal pages. Add notes about new portal. Aesthetics. refs #13616
• src/hg/htdocs/FAQ/FAQcustom.html
  • lines changed 1, context: html, text, full: html, text
    Fixes for some of Galt's changes to static page relatice links, refs #13663
• src/hg/htdocs/FAQ/FAQdownloads.html
  • lines changed 1, context: html, text, full: html, text
    Fixes for some of Galt's changes to static page relatice links, refs #13663
• src/hg/htdocs/Neandertal/index.html
  • lines changed 1, context: html, text, full: html, text
    Fixes for some of Galt's changes to static page relatice links, refs #13663
• src/hg/htdocs/goldenPath/credits.html
  • lines changed 1, context: html, text, full: html, text
    Fixes for some of Galt's changes to static page relatice links, refs #13663
• src/hg/htdocs/goldenPath/help/customTrackText.html
  • lines changed 1, context: html, text, full: html, text
    Fixes for some of Galt's changes to static page relatice links, refs #13663
• src/hg/htdocs/goldenPath/help/gbib.html
  • lines changed 12, context: html, text, full: html, text
    documenting offline mode for gbib, after referee comment. refs #12843
  • lines changed 2, context: html, text, full: html, text
    adding a warning about OSX "unzip" tool being broken, refs #12843 and refs #11957
• src/hg/htdocs/goldenPath/help/hgTracksHelp.html
  • lines changed 1, context: html, text, full: html, text
    Fixes for some of Galt's changes to static page relatice links, refs #13663
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 3, context: html, text, full: html, text
    Fixes for some of Galt's changes to static page relatice links, refs #13663
• src/hg/htdocs/goldenPath/pubs.html
  • lines changed 1, context: html, text, full: html, text
    Fixes for some of Galt's changes to static page relatice links, refs #13663
• src/hg/htdocs/images/encode/dataMatrix.png
  • lines changed 0, context: html, text, full: html, text
    Trim screenshot. refs #131616
• src/hg/htdocs/images/encode/search.png
  • lines changed 0, context: html, text, full: html, text
    Trim screenshots. refs #13616
• src/hg/htdocs/images/encode/stanfordSearch.png
  • lines changed 0, context: html, text, full: html, text
    Trim screenshots. refs #13616
• src/hg/htdocs/inc/encode.home.topbar.html
  • lines changed 5, context: html, text, full: html, text
    Removing comments and actual link to false location, hgdownload.cse.ucsc.edu/goldenPath/wgEncode/index.html in Top Bar on older ENCODE pages. refs #13616
• src/hg/htdocs/inc/encode.terms.topbar.html
  • lines changed 4, context: html, text, full: html, text
    Removing comments and actual link to false location, hgdownload.cse.ucsc.edu/goldenPath/wgEncode/index.html in Top Bar on older ENCODE pages. refs #13616
• src/hg/htdocs/inc/encode.topbar.html
  • lines changed 1, context: html, text, full: html, text
    Add date to topbar as per Brian L input. refs #13616
  • lines changed 2, context: html, text, full: html, text
    Another round on ENCODE portal pages. Add notes about new portal. Aesthetics. refs #13616
  • lines changed 1, context: html, text, full: html, text
    Removing comments and actual link to false location, hgdownload.cse.ucsc.edu/goldenPath/wgEncode/index.html in Top Bar on older ENCODE pages. refs #13616
• src/hg/htdocs/inc/encodeProject.topbar.html
  • lines changed 1, context: html, text, full: html, text
    Add dates to top bar as per Brian L request. refs #13616
• src/hg/htdocs/inc/encodeProjectSoftware.topbar.html
  • lines changed 1, context: html, text, full: html, text
    Add date to topbar as per Brian L input. refs #13616
• src/hg/htdocs/index.html
  • lines changed 1, context: html, text, full: html, text
    Fixes for some of Galt's changes to static page relatice links, refs #13663
  • lines changed 1, context: html, text, full: html, text
    Fixing incorrect link for custom track page
• src/hg/htdocs/indexIntro.html
  • lines changed 5, context: html, text, full: html, text
    Added link to Genomics Institute (per Branwyn) and link to suggestion box (per Bob).
  • lines changed 4, context: html, text, full: html, text
    moved suggestion box comment closer to the Donate button
• src/hg/htdocs/style/encodeProject.css
  • lines changed 27, context: html, text, full: html, text
    Changes ENCODE pages to UCSC color scheme. refs #13616
  • lines changed 23, context: html, text, full: html, text
    Fixes to left bar layout. Embed menu layout in home page since it's only used there.
  • lines changed 8, context: html, text, full: html, text
    Add missing topbar rule. refs #13616
  • lines changed 1, context: html, text, full: html, text
    Use standard UC gold color
  • lines changed 37, context: html, text, full: html, text
    Another round on ENCODE portal pages. Add notes about new portal. Aesthetics. refs #13616
  • lines changed 5, context: html, text, full: html, text
    Update vocab pages. refs #13616
• src/hg/inc/bigGenePred.h
  • lines changed 80, context: html, text, full: html, text
    first cut at genePredToBigGenePred refs #13681
• src/hg/inc/genePred.h
  • lines changed 3, context: html, text, full: html, text
    first cut at genePredToBigGenePred refs #13681
• src/hg/js/encodeMatrix.js
  • lines changed 1, context: html, text, full: html, text
    Allow styling of page headers from HTML include files. Will use this to add styled dates to titles. refs #13616
• src/hg/lib/bigGenePred.as
  • lines changed 25, context: html, text, full: html, text
    add bigGenePred.as for genePred support in track hubs
  • lines changed 1, context: html, text, full: html, text
    first cut at genePredToBigGenePred refs #13681
  • lines changed 1, context: html, text, full: html, text
    bigGenePred support in track hubs limping along #13861
• src/hg/lib/bigGenePred.c
  • lines changed 284, context: html, text, full: html, text
    first cut at genePredToBigGenePred refs #13681
• src/hg/lib/genePred.c
  • lines changed 1, context: html, text, full: html, text
    first cut at genePredToBigGenePred refs #13681
• src/hg/lib/makefile
  • lines changed 2, context: html, text, full: html, text
    first cut at genePredToBigGenePred refs #13681
• src/hg/lib/trackDbCustom.c
  • lines changed 2, context: html, text, full: html, text
    bigGenePred support in track hubs limping along #13861
• src/hg/lib/trackHub.c
  • lines changed 1, context: html, text, full: html, text
    bigGenePred support in track hubs limping along #13861
• src/hg/makeDb/doc/hg38.txt
  • lines changed 343, context: html, text, full: html, text
    clone end procedure for hg38 refs #13713
• src/hg/makeDb/doc/papAnu2.txt
  • lines changed 21, context: html, text, full: html, text
    ensGenes v76 update refs 13744
• src/hg/makeDb/trackDb/human/chainNetPlacental.ra
  • lines changed 1, context: html, text, full: html, text
    added rn5 to placental group for hg38
• src/hg/makeDb/trackDb/human/hg16/description.html
  • lines changed 1, context: html, text, full: html, text
    reverting flying man logo to the original version per Jim and Bob
• src/hg/makeDb/trackDb/human/hg17/description.html
  • lines changed 1, context: html, text, full: html, text
    reverting flying man logo to the original version per Jim and Bob
• src/hg/makeDb/trackDb/human/hg18/description.html
  • lines changed 1, context: html, text, full: html, text
    reverting flying man logo to the original version per Jim and Bob
• src/hg/makeDb/trackDb/human/hg19/description.html
  • lines changed 1, context: html, text, full: html, text
    reverting flying man logo to the original version per Jim and Bob
• src/hg/makeDb/trackDb/human/hg38/description.html
  • lines changed 1, context: html, text, full: html, text
    reverting flying man logo to the original version per Jim and Bob
• src/hg/makeDb/trackDb/mouse/cloneEnd.trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    Added some additional priority values; rearranged search stanzas; refs #10083
• src/hg/makeDb/trackDb/mouse/cloneEndSuper.html
  • lines changed 43, context: html, text, full: html, text
    Added table of statistics to description page; refs #10083
• src/hg/oneShot/freen/freen.c
  • lines changed 76, context: html, text, full: html, text
    Setting up hac tree test.
  • lines changed 103, context: html, text, full: html, text
    Freen does a new type of hacTree generation.
  • lines changed 111, context: html, text, full: html, text
    Moving an alternative hacTree implementation that minimizes the merge steps to the library.
  • lines changed 1, context: html, text, full: html, text
    Adding childDistance
• src/hg/utils/genePredToBigGenePred/genePredToBigGenePred.c
  • lines changed 88, context: html, text, full: html, text
    first cut at genePredToBigGenePred refs #13681
  • lines changed 6, context: html, text, full: html, text
    bigGenePred support in track hubs limping along #13861
• src/hg/utils/genePredToBigGenePred/makefile
  • lines changed 3, context: html, text, full: html, text
    first cut at genePredToBigGenePred refs #13681
• src/hg/utils/phyloTrees/placentals.txt
  • lines changed 1, context: html, text, full: html, text
    remove useless db reference for galVar refs #13842
• src/inc/hacTree.h
  • lines changed 7, context: html, text, full: html, text
    Moving an alternative hacTree implementation that minimizes the merge steps to the library.
• src/inc/pairDistance.h
  • lines changed 31, context: html, text, full: html, text
    Oops forgot to add this.
• src/lib/bigBed.c
  • lines changed 1, context: html, text, full: html, text
    bigGenePred support in track hubs limping along #13861
• src/lib/hacTree.c
  • lines changed 103, context: html, text, full: html, text
    Moving an alternative hacTree implementation that minimizes the merge steps to the library.
  • lines changed 4, context: html, text, full: html, text
    Adding childDistance
• src/lib/makefile
  • lines changed 5, context: html, text, full: html, text
    Moving pairDistance stuff to library.
• src/lib/pairDistance.c
  • lines changed 80, context: html, text, full: html, text
    Moving pairDistance stuff to library.
• src/parasol/gensub2/gensub2.c
  • lines changed 15, context: html, text, full: html, text
    Adding selfPair as a special case second list like single.
• src/product/README.install
  • lines changed 33, context: html, text, full: html, text
    add extra database discussion and clean up examples refs #13848
• src/product/README.mysql.setup
  • lines changed 20, context: html, text, full: html, text
    add extra database discussion and clean up examples refs #13848
• src/product/ex.hg.conf
  • lines changed 3, context: html, text, full: html, text
    Adding a comment note in the mirror example file ex.hg.conf about Table Browser output to Genome Space #12559
• src/utils/distributeRgbRainbow/distributeRgbRainbow.c
  • lines changed 107, context: html, text, full: html, text
    Program to assign colors to a list based on distances seems to work.
• src/utils/distributeRgbRainbow/makefile
  • lines changed 7, context: html, text, full: html, text
    Program to assign colors to a list based on distances seems to work.
• src/utils/distributeRgbRainbow/test.expected
  • lines changed 6, context: html, text, full: html, text
    Program to assign colors to a list based on distances seems to work.
• src/utils/distributeRgbRainbow/test.lst
  • lines changed 6, context: html, text, full: html, text
    Program to assign colors to a list based on distances seems to work.
• src/utils/distributeRgbRainbow/test.pair
  • lines changed 15, context: html, text, full: html, text
    Program to assign colors to a list based on distances seems to work.
• src/utils/orderMiddle/makefile
  • lines changed 3, context: html, text, full: html, text
    Making utility that uses pair distance information to order the middle of a list while preserving ends.
• src/utils/orderMiddle/orderMiddle.c
  • lines changed 225, context: html, text, full: html, text
    Making utility that uses pair distance information to order the middle of a list while preserving ends.
  • lines changed 84, context: html, text, full: html, text
    Moving pairDistance stuff to library.
  • lines changed 4, context: html, text, full: html, text
    Removing some debugging and decreasing verbosity.
• src/utils/orderMiddle/test.expected
  • lines changed 6, context: html, text, full: html, text
    Adding test set
• src/utils/orderMiddle/test.lst
  • lines changed 6, context: html, text, full: html, text
    Adding test set
• src/utils/orderMiddle/test.pair
  • lines changed 15, context: html, text, full: html, text
    Adding test set
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    v305 preview2 refs #13703

• lines changed: 3221
• files changed: 137