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 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.
- 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.
- 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
- src/utils/orderMiddle/test.lst
- src/utils/orderMiddle/test.pair
- 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