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
- 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.
- 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
- src/tagStorm/tagStormFromTab/in.tab
- src/tagStorm/tagStormFromTab/makefile
- 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