All File Changes

v316_preview to v316_preview2 (2015-04-27 to 2015-05-04) v316

• src/browserbox/root/updateBrowser.sh
  • lines changed 11, context: html, text, full: html, text
    trying to fix overwriting of hg.conf.local in gbib. refs #15254
    
• src/hg/hgIntegrator/hgIntegrator.c
  • lines changed 6, context: html, text, full: html, text
    Add descriptions to columns in Choose Fields popup.
    refs #14579
    
  • lines changed 2, context: html, text, full: html, text
    Change 'Annotation Integrator' to 'Data Integrator'. refs #14579
    
  • lines changed 301, context: html, text, full: html, text
    Added support for pasted/uploaded user regions to hgIntegrator.
    Currently it's using hgTables' cart variables, so the two CGIs share
    user regions; adding regions in hgTables makes them available in
    hgIntegrator and vice versa.
    refs #14579
    
• src/hg/hgTables/hgTables.h
  • lines changed 1, context: html, text, full: html, text
    Libifying hgTables' code that parses user's region input, so I can use
    it to add support for user regions to hgIntegrator.
    refs #14579
    
• src/hg/hgTables/userRegions.c
  • lines changed 171, context: html, text, full: html, text
    Libifying hgTables' code that parses user's region input, so I can use
    it to add support for user regions to hgIntegrator.
    refs #14579
    
• src/hg/hgTracks/bamTrack.c
  • lines changed 2, context: html, text, full: html, text
    don't pay attention to mate pos information if it's on a different chrom
    refs #15248
    
• src/hg/hgTracks/simpleTracks.c
  • lines changed 40, context: html, text, full: html, text
    collect CDS frame information for Gencode knownGene refs #14639
    
• src/hg/htdocs/FAQ/FAQformat.html
  • lines changed 16, context: html, text, full: html, text
    Adding notes about gappedPeak to FAQ formats refs #12258
    
• src/hg/htdocs/goldenPath/help/gbib.html
  • lines changed 2, context: html, text, full: html, text
    Adding some bold text on GBiB doc about hgMirror process refs #15059
    
  • lines changed 9, context: html, text, full: html, text
    Adding a note about download hgMirror error example on GBiB in problem/solution note 50 refs #15059
    
  • lines changed 6, context: html, text, full: html, text
    Updating GEO note about ftp link on gbib help page refs #15061
    
• src/hg/htdocs/goldenPath/help/hgIntegratorHelp.html
  • lines changed 4, context: html, text, full: html, text
    Change 'Annotation Integrator' to 'Data Integrator'. refs #14579
    
• src/hg/htdocs/goldenPath/pubs.html
  • lines changed 8, context: html, text, full: html, text
    added pan-genome paper
    
• src/hg/htdocs/inc/globalNavBar.inc
  • lines changed 1, context: html, text, full: html, text
    Links to genome-store must be GET, not POST, refs #15251
    
  • lines changed 1, context: html, text, full: html, text
    Add hgIntegrator to menuBar on hgwdev*, genome-test and genome-preview if it
    has been built into the current cgi-bin-*. Add hgIntegrator to top-level build.
    refs #14579
    
• src/hg/htdocs/indexNews.html
  • lines changed 7, context: html, text, full: html, text
    announcing store outage. not posting to archive page.
    
  • lines changed 7, context: html, text, full: html, text
    removing announcement
    
• src/hg/htdocs/style/HGStyle.css
  • lines changed 1, context: html, text, full: html, text
    More styling for hgIntegrator: make Modal use same title style as
    regular Sections. refs #14579
    
  • lines changed 2, context: html, text, full: html, text
    Tweak our React Modal component's width to be a bit wider in most cases, and centered horizontally.
    
  • lines changed 11, context: html, text, full: html, text
    Added support for pasted/uploaded user regions to hgIntegrator.
    Currently it's using hgTables' cart variables, so the two CGIs share
    user regions; adding regions in hgTables makes them available in
    hgIntegrator and vice versa.
    refs #14579
    
• src/hg/inc/annoStreamDbFactorSource.h
  • lines changed 4, context: html, text, full: html, text
    Use the right autoSql for annoStreamDbFactorSource (with cellType and
    treatment columns) so those extra columns can be selected/deselected from output.
    refs #14579
    
• src/hg/inc/userRegions.h
  • lines changed 21, context: html, text, full: html, text
    Libifying hgTables' code that parses user's region input, so I can use
    it to add support for user regions to hgIntegrator.
    refs #14579
    
• src/hg/js/external/jquery.bifrost.1.0.1.min.js
  • lines changed 0, context: html, text, full: html, text
    Adding JQuery plugin Bifröst (https://github.com/matiasgagliano/bifrost) for ajax file uploading.
    Older browsers (IE 8 & 9) don't support FileReader; the trick is to submit the form with a hidden
    iframe as target, and get the response contents from that hidden iframe. No progress bar, but
    if we have to support IE 8 & 9, this appears to be the best way.
    
• src/hg/js/external/makefile
  • lines changed 1, context: html, text, full: html, text
    Adding JQuery plugin Bifröst (https://github.com/matiasgagliano/bifrost) for ajax file uploading.
    Older browsers (IE 8 & 9) don't support FileReader; the trick is to submit the form with a hidden
    iframe as target, and get the response contents from that hidden iframe. No progress bar, but
    if we have to support IE 8 & 9, this appears to be the best way.
    
• src/hg/js/hgTracks.js
  • lines changed 1, context: html, text, full: html, text
    Links to genome-store must be GET, not POST, refs #15251
    
• src/hg/js/model/hgIntegrator/hgIntegratorModel.js
  • lines changed 11, context: html, text, full: html, text
    Add descriptions to columns in Choose Fields popup.
    refs #14579
    
  • lines changed 55, context: html, text, full: html, text
    Added support for pasted/uploaded user regions to hgIntegrator.
    Currently it's using hgTables' cart variables, so the two CGIs share
    user regions; adding regions in hgTables makes them available in
    hgIntegrator and vice versa.
    refs #14579
    
• src/hg/js/model/lib/ImModel.js
  • lines changed 10, context: html, text, full: html, text
    Before pushing to undoStack, make sure that the state actually changed;
    otherwise 'undo' would have no effect, kinda confusing.
    
  • lines changed 5, context: html, text, full: html, text
    Added support for pasted/uploaded user regions to hgIntegrator.
    Currently it's using hgTables' cart variables, so the two CGIs share
    user regions; adding regions in hgTables makes them available in
    hgIntegrator and vice versa.
    refs #14579
    
• src/hg/js/model/lib/UserRegionsMixin.js
  • lines changed 102, context: html, text, full: html, text
    Added support for pasted/uploaded user regions to hgIntegrator.
    Currently it's using hgTables' cart variables, so the two CGIs share
    user regions; adding regions in hgTables makes them available in
    hgIntegrator and vice versa.
    refs #14579
    
• src/hg/js/model/lib/cart.js
  • lines changed 4, context: html, text, full: html, text
    Added support for pasted/uploaded user regions to hgIntegrator.
    Currently it's using hgTables' cart variables, so the two CGIs share
    user regions; adding regions in hgTables makes them available in
    hgIntegrator and vice versa.
    refs #14579
    
• src/hg/js/model/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    Added support for pasted/uploaded user regions to hgIntegrator.
    Currently it's using hgTables' cart variables, so the two CGIs share
    user regions; adding regions in hgTables makes them available in
    hgIntegrator and vice versa.
    refs #14579
    
• src/hg/js/react/hgIntegrator/hgIntegrator.jsx
  • lines changed 3, context: html, text, full: html, text
    More styling for hgIntegrator: make Modal use same title style as
    regular Sections. refs #14579
    
  • lines changed 5, context: html, text, full: html, text
    Add descriptions to columns in Choose Fields popup.
    refs #14579
    
  • lines changed 30, context: html, text, full: html, text
    Use table formatting for column descriptions in Choose fields popup.
    refs #14579
    
  • lines changed 2, context: html, text, full: html, text
    Change 'Annotation Integrator' to 'Data Integrator'. refs #14579
    
  • lines changed 53, context: html, text, full: html, text
    Added support for pasted/uploaded user regions to hgIntegrator.
    Currently it's using hgTables' cart variables, so the two CGIs share
    user regions; adding regions in hgTables makes them available in
    hgIntegrator and vice versa.
    refs #14579
    
• src/hg/js/react/lib/Modal.jsx
  • lines changed 9, context: html, text, full: html, text
    More styling for hgIntegrator: make Modal use same title style as
    regular Sections. refs #14579
    
• src/hg/js/react/lib/Section.jsx
  • lines changed 4, context: html, text, full: html, text
    More styling for hgIntegrator: make Modal use same title style as
    regular Sections. refs #14579
    
• src/hg/js/react/lib/TextArea.jsx
  • lines changed 60, context: html, text, full: html, text
    Added support for pasted/uploaded user regions to hgIntegrator.
    Currently it's using hgTables' cart variables, so the two CGIs share
    user regions; adding regions in hgTables makes them available in
    hgIntegrator and vice versa.
    refs #14579
    
• src/hg/js/react/lib/UserRegions.jsx
  • lines changed 169, context: html, text, full: html, text
    Added support for pasted/uploaded user regions to hgIntegrator.
    Currently it's using hgTables' cart variables, so the two CGIs share
    user regions; adding regions in hgTables makes them available in
    hgIntegrator and vice versa.
    refs #14579
    
• src/hg/js/react/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    Added support for pasted/uploaded user regions to hgIntegrator.
    Currently it's using hgTables' cart variables, so the two CGIs share
    user regions; adding regions in hgTables makes them available in
    hgIntegrator and vice versa.
    refs #14579
    
• src/hg/js/react/react.mk
  • lines changed 2, context: html, text, full: html, text
    Remove all compiled/* files before running jsx because it may be fooled
    by timestamps when you're switching between branches.
    
  • lines changed 2, context: html, text, full: html, text
    Fixing overzealous clean target that broke the js/react install.
    
• src/hg/lib/annoStreamDbFactorSource.c
  • lines changed 4, context: html, text, full: html, text
    Bugfix: in absence of filters, data values were not copied over as intended.
    refs #11461, #14579
    
• src/hg/lib/hAnno.c
  • lines changed 7, context: html, text, full: html, text
    Fixing bug introduced in 45990976 that broke custom tracks in hgIntegrator.
    refs #14579
    
  • lines changed 4, context: html, text, full: html, text
    Use the right autoSql for annoStreamDbFactorSource (with cellType and
    treatment columns) so those extra columns can be selected/deselected from output.
    refs #14579
    
• src/hg/lib/jsHelper.c
  • lines changed 2, context: html, text, full: html, text
    Added support for pasted/uploaded user regions to hgIntegrator.
    Currently it's using hgTables' cart variables, so the two CGIs share
    user regions; adding regions in hgTables makes them available in
    hgIntegrator and vice versa.
    refs #14579
    
• src/hg/lib/knownCds.as
  • lines changed 10, context: html, text, full: html, text
    collect CDS frame information for Gencode knownGene refs #14639
    
• src/hg/lib/knownCds.sql
  • lines changed 15, context: html, text, full: html, text
    collect CDS frame information for Gencode knownGene refs #14639
    
• src/hg/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    Libifying hgTables' code that parses user's region input, so I can use
    it to add support for user regions to hgIntegrator.
    refs #14579
    
• src/hg/lib/userRegions.c
  • lines changed 202, context: html, text, full: html, text
    Libifying hgTables' code that parses user's region input, so I can use
    it to add support for user regions to hgIntegrator.
    refs #14579
    
• src/hg/lib/web.c
  • lines changed 9, context: html, text, full: html, text
    Add hgIntegrator to menuBar on hgwdev*, genome-test and genome-preview if it
    has been built into the current cgi-bin-*. Add hgIntegrator to top-level build.
    refs #14579
    
• src/hg/makeDb/doc/hg38/lastzRuns.txt
  • lines changed 91, context: html, text, full: html, text
    rerunning some lastz pairs refs #14560
    
  • lines changed 624, context: html, text, full: html, text
    rerunning some lastz pairs refs #14560
    
  • lines changed 193, context: html, text, full: html, text
    rerunning some lastz pairs refs #14560
    
• src/hg/makeDb/doc/rheMac2.txt
  • lines changed 78, context: html, text, full: html, text
    lastz rheMac2 to papAnu2 refs #14433
    
• src/hg/makeDb/doc/tarSyr1.txt
  • lines changed 1, context: html, text, full: html, text
    correct comment liftOver to tarSyr2 computed in 8 days refs #14410
    
• src/hg/makeDb/doc/ucscGenes/hg38.ucscGenes16.sh
  • lines changed 269, context: html, text, full: html, text
    build instructions for Gencode UCSC genes #14639
    
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 2, context: html, text, full: html, text
    fixing ornAna2 entries refs #15098
    
  • lines changed 1, context: html, text, full: html, text
    fixing ornAna2 entries refs #15098
    
• src/hg/makeDb/hgLoadBed/hgLoadBed.c
  • lines changed 6, context: html, text, full: html, text
    Allow for hgloadBed to load zero-length BEDs at the beginning of a chromosome.
    
• src/hg/makeDb/trackDb/human/hg38/trackDb.wgEncode.ra
  • lines changed 1, context: html, text, full: html, text
    Removed V22 release tag; refs #15115
    
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.euarchontoglireChainNet.ra
  • lines changed 20, context: html, text, full: html, text
    Adding entries for new tarSyr2 chain and net tracks, refs #15112
    
• src/hg/makeDb/trackDb/tarsier/tarSyr2/trackDb.17way.ra
  • lines changed 1, context: html, text, full: html, text
    specific name for this obsolete track refs #15112
    
  • lines changed 2, context: html, text, full: html, text
    move obsolete track to experimental track groups refs #15112
    
• src/hg/makeDb/trackDb/tarsier/tarSyr2/trackDb.20way.ra
  • lines changed 4, context: html, text, full: html, text
    Undoing previous changes to species numbers, refs #15112
    
• src/hg/makeDb/trackDb/trackDb.chainNet.ra
  • lines changed 2, context: html, text, full: html, text
    incorrect MicMur1 database specification should be micMur1 refs #15112
    
• src/hg/makefile
  • lines changed 1, context: html, text, full: html, text
    Add hgIntegrator to menuBar on hgwdev*, genome-test and genome-preview if it
    has been built into the current cgi-bin-*. Add hgIntegrator to top-level build.
    refs #14579
    
• src/oneShot/jsonToTagStorm/jsonToTagStorm.c
  • lines changed 93, context: html, text, full: html, text
    COmmitting latest before Jim starts editing.
    
  • lines changed 54, context: html, text, full: html, text
    C code to convert a .json file to a .tagStorm file, seems to be working.
    
  • lines changed 33, context: html, text, full: html, text
    Added a bit of documentation and increased robustness. Program now accepts multi-lined .json files
    
  • lines changed 12, context: html, text, full: html, text
    Fixing a couple bugs I found, improved robustness a bit as well
    
  • lines changed 3, context: html, text, full: html, text
    replaced stripString with stripChar call as recommended by Jim
    
  • lines changed 5, context: html, text, full: html, text
    Meeting with Jim, expecting some changes to the code
    
  • lines changed 121, context: html, text, full: html, text
    Completely refactored yet again, this time the code uses a tokenizer. Seems to be working and quite robust
    
  • lines changed 14, context: html, text, full: html, text
    Added the makefile. Code now accepts escaped quotes
    
  • lines changed 137, context: html, text, full: html, text
    Added tagStormToJson code, which converts a tagStorm to a .json file. Used with jsonToTagStorm
    
• src/oneShot/jsonToTagStorm/jsonToTagStorm.py
  • lines changed 82, context: html, text, full: html, text
    A python program that takes in a single line .json file and converts it to a tagStorm file.
    
  • lines changed 82, context: html, text, full: html, text
    Added tagStormToJson code, which converts a tagStorm to a .json file. Used with jsonToTagStorm
    
• src/oneShot/jsonToTagStorm/makefile
  • lines changed 3, context: html, text, full: html, text
    Added the makefile. Code now accepts escaped quotes
    
  • lines changed 3, context: html, text, full: html, text
    Added tagStormToJson code, which converts a tagStorm to a .json file. Used with jsonToTagStorm
    
• src/oneShot/jsonToTagStorm/thisCcodeStartedCrashingForNoReason.c
  • lines changed 220, context: html, text, full: html, text
    COmmitting latest before Jim starts editing.
    
  • lines changed 220, context: html, text, full: html, text
    Oops, did not mean to include that.
    
• src/oneShot/tagStormToJson/makefile
  • lines changed 3, context: html, text, full: html, text
    makefile and tagStormToJson, converts tagStorm files to json files. Made more robust
    
  • lines changed 3, context: html, text, full: html, text
    Added tagStormToJson code, which converts a tagStorm to a .json file. Used with jsonToTagStorm
    
• src/oneShot/tagStormToJson/tagStormToJson.c
  • lines changed 70, context: html, text, full: html, text
    makefile and tagStormToJson, converts tagStorm files to json files. Made more robust
    
  • lines changed 70, context: html, text, full: html, text
    Added tagStormToJson code, which converts a tagStorm to a .json file. Used with jsonToTagStorm
    
• src/tagStorm/jsonToTagStorm/jsonToTagStorm.c
  • lines changed 137, context: html, text, full: html, text
    Added tagStormToJson code, which converts a tagStorm to a .json file. Used with jsonToTagStorm
    
• src/tagStorm/jsonToTagStorm/jsonToTagStorm.py
  • lines changed 82, context: html, text, full: html, text
    Added tagStormToJson code, which converts a tagStorm to a .json file. Used with jsonToTagStorm
    
• src/tagStorm/jsonToTagStorm/makefile
  • lines changed 3, context: html, text, full: html, text
    Added tagStormToJson code, which converts a tagStorm to a .json file. Used with jsonToTagStorm
    
• src/tagStorm/tagStormFromTab/expected.tags
  • lines changed 8, context: html, text, full: html, text
    Some test case files
    
• src/tagStorm/tagStormFromTab/in.tab
  • lines changed 3, context: html, text, full: html, text
    Some test case files
    
• src/tagStorm/tagStormFromTab/makefile
  • lines changed 4, context: html, text, full: html, text
    Some test case files
    
• src/tagStorm/tagStormToJson/makefile
  • lines changed 3, context: html, text, full: html, text
    Added tagStormToJson code, which converts a tagStorm to a .json file. Used with jsonToTagStorm
    
• src/tagStorm/tagStormToJson/tagStormToJson.c
  • lines changed 71, context: html, text, full: html, text
    Added tagStormToJson code, which converts a tagStorm to a .json file. Used with jsonToTagStorm
    
• src/utils/bigWigCluster/colorRadialDend.html
  • lines changed 124, context: html, text, full: html, text
    A html file that creates a color coded radial dendrogram from an input .json file
    

• lines changed: 4377
• files changed: 98