All File Changes
v282_base to v283_preview (2013-04-16 to 2013-04-23) v283
- src/hg/altSplice/affySplice/tests/makefile
- lines changed 12, context: html, text, full: html, text
all tests now using binaries from DESTBINDIR, refs #9104 #10630
- src/hg/altSplice/altSplice/tests/makefile
- lines changed 22, context: html, text, full: html, text
all tests now using binaries from DESTBINDIR, refs #9104 #10630
- src/hg/autoSql/autoSql.c
- lines changed 11, context: html, text, full: html, text
Finishing a place Fan missed in implementing -withNull
- lines changed 22, context: html, text, full: html, text
Adding defaultZeros flag - this seems to be needed with strictor MySQL configs when inserting partial records.
- lines changed 41, context: html, text, full: html, text
Adding index and auto keywords to autoSql columns.
- lines changed 35, context: html, text, full: html, text
Added -addBin option at Angie's request.
- src/hg/autoSql/autoSql.doc
- lines changed 34, context: html, text, full: html, text
Adding docs and test cases for index and autoincrement feature.
- lines changed 1, context: html, text, full: html, text
Correcting English a little.
- src/hg/autoSql/doc.as
- lines changed 5, context: html, text, full: html, text
Adding docs and test cases for index and autoincrement feature.
- src/hg/autoSql/tests/expected/binTest.c
- lines changed 388, context: html, text, full: html, text
Added -addBin option at Angie's request.
- src/hg/autoSql/tests/expected/binTest.h
- lines changed 173, context: html, text, full: html, text
Added -addBin option at Angie's request.
- src/hg/autoSql/tests/expected/binTest.sql
- lines changed 37, context: html, text, full: html, text
Added -addBin option at Angie's request.
- src/hg/autoSql/tests/expected/index.sql
- lines changed 30, context: html, text, full: html, text
Adding docs and test cases for index and autoincrement feature.
- src/hg/autoSql/tests/input/binTest.as
- lines changed 30, context: html, text, full: html, text
Added -addBin option at Angie's request.
- src/hg/autoSql/tests/input/index.as
- lines changed 18, context: html, text, full: html, text
Adding docs and test cases for index and autoincrement feature.
- src/hg/autoSql/tests/makefile
- lines changed 5, context: html, text, full: html, text
Adding docs and test cases for index and autoincrement feature.
- lines changed 7, context: html, text, full: html, text
Added -addBin option at Angie's request.
- lines changed 2, context: html, text, full: html, text
all tests now using binaries from DESTBINDIR, refs #9104 #10630
- src/hg/baseMask/tests/makefile
- lines changed 6, context: html, text, full: html, text
all tests now using binaries from DESTBINDIR, refs #9104 #10630
- src/hg/bedIntersect/tests/makefile
- lines changed 1, context: html, text, full: html, text
all tests now using binaries from DESTBINDIR, refs #9104 #10630
- src/hg/blastToPsl/tests/makefile
- lines changed 29, context: html, text, full: html, text
all tests now using binaries from DESTBINDIR, refs #9104 #10630
- src/hg/checkTableCoords/tests/makefile
- lines changed 13, context: html, text, full: html, text
all tests now using binaries from DESTBINDIR, refs #9104 #10630
- src/hg/chimpStuff/chimpChromContigAgp/tests/makefile
- lines changed 3, context: html, text, full: html, text
all tests now using binaries from DESTBINDIR, refs #9104 #10630
- src/hg/embossToPsl/tests/makefile
- lines changed 7, context: html, text, full: html, text
all tests now using binaries from DESTBINDIR, refs #9104 #10630
- src/hg/encode3/encodeDataWarehouse/edwAddAssembly/edwAddAssembly.c
- lines changed 5, context: html, text, full: html, text
Including non-N base count in edwAssembly.
- lines changed 2, context: html, text, full: html, text
Making assembly and enrichment target adders put their files on QA job list.
- src/hg/encode3/encodeDataWarehouse/edwAddQaEnrichTarget/edwAddQaEnrichTarget.c
- lines changed 2, context: html, text, full: html, text
Making assembly and enrichment target adders put their files on QA job list.
- src/hg/encode3/encodeDataWarehouse/edwMakeEnrichments/edwMakeEnrichments.c
- lines changed 40, context: html, text, full: html, text
Starting to implement replicate analysis.
- lines changed 5, context: html, text, full: html, text
Centralizing bigBed variant format detection.
- lines changed 97, context: html, text, full: html, text
Fixed a source of rounding error, measured timing of parts because it's slow, and implemented a ~2x faster algorithm.
- lines changed 5, context: html, text, full: html, text
Checking for empty input and not crashing!
- src/hg/encode3/encodeDataWarehouse/edwMakeReplicateQa/edwMakeReplicateQa.c
- lines changed 200, context: html, text, full: html, text
Starting to implement replicate analysis.
- lines changed 5, context: html, text, full: html, text
Centralizing bigBed variant format detection.
- lines changed 151, context: html, text, full: html, text
Splitting qaPairCorrelate into two tables - one for sample overlap, one for correlation. Adding several new correlation fields.
- src/hg/encode3/encodeDataWarehouse/edwMakeValidFile/edwMakeValidFile.c
- lines changed 6, context: html, text, full: html, text
Removing some debugging statments and adding more bigBed variants.
- lines changed 5, context: html, text, full: html, text
Centralizing bigBed variant format detection.
- lines changed 105, context: html, text, full: html, text
Files that fail validation get reason why filled in in edwFile.errorMessage. Improving status output a little.
- lines changed 2, context: html, text, full: html, text
Removing some debugging code and turning some into logging code.
- src/hg/encode3/encodeDataWarehouse/edwMakeValidFile/sorted.bb
- lines changed 0, context: html, text, full: html, text
Removing some debugging code and turning some into logging code.
- src/hg/encode3/encodeDataWarehouse/edwMakeValidFile/sorted.bed
- lines changed 331449, context: html, text, full: html, text
Removing some debugging code and turning some into logging code.
- src/hg/encode3/encodeDataWarehouse/edwRunner/edwRunner.c
- lines changed 211, context: html, text, full: html, text
First cut of qa job scheduler.
- lines changed 46, context: html, text, full: html, text
Making it have a few less points where it's waiting when it could be doing something.
- lines changed 8, context: html, text, full: html, text
Making it keep track of last ID to save a little database time.
- lines changed 5, context: html, text, full: html, text
Improving comments and turning some debugging uglyfs into verbose-2's.
- lines changed 1, context: html, text, full: html, text
Removing a temp file when it's no longer needed.
- src/hg/encode3/encodeDataWarehouse/edwRunner/makefile
- lines changed 4, context: html, text, full: html, text
First cut of qa job scheduler.
- src/hg/encode3/encodeDataWarehouse/edwSubmit/edwSubmit.c
- lines changed 137, context: html, text, full: html, text
Separating edwParseSubmitFile into it's own function, and making it check each field so as to give error messages earlier before time consuming uploads.
- lines changed 6, context: html, text, full: html, text
Adding more supported enrichments. Making it actually try to load files again after parsing submission.
- lines changed 15, context: html, text, full: html, text
Improving error reporting for missing required fields in submission file.
- lines changed 35, context: html, text, full: html, text
Making command line for edwSubmit use email address rather than username + password. This is just a temporary thing while working out edwWebSubmit.
- lines changed 65, context: html, text, full: html, text
Adapting this to be run initiated from web. Using a database profile so can have read/write access to mysql encodeDataWarehouse. Making it so will attempt not to be run twice on the same URL at once.
- lines changed 85, context: html, text, full: html, text
A number of changes to put more status info on submission in progress into database so web app can report on it.
- lines changed 18, context: html, text, full: html, text
Reporting file level errors in the submission as well as file tables.
- lines changed 5, context: html, text, full: html, text
Changing file permissions to be world readable and group writable. Improving an error message.
- src/hg/encode3/encodeDataWarehouse/edwSubmitSpooler/edwSubmitSpooler.c
- lines changed 98, context: html, text, full: html, text
First cut of a web submission ap. It communicates with command line edwSubmit program via a named pipe managed by edwSubmitSpooler, which also manages multiple edwSubmit processes so as to allow more than one, but not too many.
- lines changed 1, context: html, text, full: html, text
Bumped default process count to 5.
- src/hg/encode3/encodeDataWarehouse/edwSubmitSpooler/makefile
- lines changed 3, context: html, text, full: html, text
First cut of a web submission ap. It communicates with command line edwSubmit program via a named pipe managed by edwSubmitSpooler, which also manages multiple edwSubmit processes so as to allow more than one, but not too many.
- src/hg/encode3/encodeDataWarehouse/edwWebSubmit/edwWebSubmit.c
- lines changed 217, context: html, text, full: html, text
First cut of a web submission ap. It communicates with command line edwSubmit program via a named pipe managed by edwSubmitSpooler, which also manages multiple edwSubmit processes so as to allow more than one, but not too many.
- lines changed 38, context: html, text, full: html, text
Improving error messages and removing quirky javascript (doc.write seems to be very frowned upon) in header. Improving status display during and after upload.
- lines changed 129, context: html, text, full: html, text
Polishing upload tracking part of page, and leaving validations for later.
- src/hg/encode3/encodeDataWarehouse/edwWebSubmit/makefile
- lines changed 16, context: html, text, full: html, text
First cut of a web submission ap. It communicates with command line edwSubmit program via a named pipe managed by edwSubmitSpooler, which also manages multiple edwSubmit processes so as to allow more than one, but not too many.
- src/hg/encode3/encodeDataWarehouse/inc/edwLib.h
- lines changed 13, context: html, text, full: html, text
Starting to implement replicate analysis.
- lines changed 3, context: html, text, full: html, text
Centralizing bigBed variant format detection.
- lines changed 3, context: html, text, full: html, text
Adding edwWriteErrToStderrAndTable library function.
- lines changed 12, context: html, text, full: html, text
Adding function to fetch user record given emailaddress and functions to add jobs to be run.
- lines changed 1, context: html, text, full: html, text
Exporting edwSingleFileTimeout.
- lines changed 3, context: html, text, full: html, text
Moving edwMostRecentSubmission to library.
- lines changed 3, context: html, text, full: html, text
Making edwWriteErrToTable - similar to an existing function but doesn't also write to stdout.
- src/hg/encode3/encodeDataWarehouse/inc/encodeDataWarehouse.h
- lines changed 86, context: html, text, full: html, text
Adding new edwQaPairCorrelate table, and including non-N base count in edwAssembly.
- lines changed 121, context: html, text, full: html, text
Splitting edwQaPairCorrelate into two tables.
- lines changed 240, context: html, text, full: html, text
Adding edwJob and removing edwQaAgent and edwQaRun to manage jobs.
- lines changed 5, context: html, text, full: html, text
Adding some fields to edwSubmit to make it so web app can report progress better.
- src/hg/encode3/encodeDataWarehouse/lib/edwLib.c
- lines changed 45, context: html, text, full: html, text
Starting to implement replicate analysis.
- lines changed 1, context: html, text, full: html, text
Removing some debugging statements.
- lines changed 9, context: html, text, full: html, text
Centralizing bigBed variant format detection.
- lines changed 14, context: html, text, full: html, text
Adding edwWriteErrToStderrAndTable library function.
- lines changed 3, context: html, text, full: html, text
Moving to San Diego paths.
- lines changed 38, context: html, text, full: html, text
Adding function to fetch user record given emailaddress and functions to add jobs to be run.
- lines changed 3, context: html, text, full: html, text
Exporting edwSingleFileTimeout.
- lines changed 19, context: html, text, full: html, text
Moving edwMostRecentSubmission to library.
- lines changed 10, context: html, text, full: html, text
Making edwWriteErrToTable - similar to an existing function but doesn't also write to stdout.
- src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.as
- lines changed 15, context: html, text, full: html, text
Adding new edwQaPairCorrelate table, and including non-N base count in edwAssembly.
- lines changed 13, context: html, text, full: html, text
Splitting edwQaPairCorrelate into two tables.
- lines changed 33, context: html, text, full: html, text
Adding edwJob and removing edwQaAgent and edwQaRun to manage jobs.
- lines changed 21, context: html, text, full: html, text
Adding some fields to edwSubmit to make it so web app can report progress better.
- src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.c
- lines changed 204, context: html, text, full: html, text
Adding new edwQaPairCorrelate table, and including non-N base count in edwAssembly.
- lines changed 227, context: html, text, full: html, text
Splitting edwQaPairCorrelate into two tables.
- lines changed 575, context: html, text, full: html, text
Adding edwJob and removing edwQaAgent and edwQaRun to manage jobs.
- lines changed 23, context: html, text, full: html, text
Adding some fields to edwSubmit to make it so web app can report progress better.
- src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.sql
- lines changed 17, context: html, text, full: html, text
Adding new edwQaPairCorrelate table, and including non-N base count in edwAssembly.
- lines changed 14, context: html, text, full: html, text
Splitting edwQaPairCorrelate into two tables.
- lines changed 119, context: html, text, full: html, text
Adding -defaultZeros to make it work in San Diego.
- lines changed 36, context: html, text, full: html, text
Adding edwJob and removing edwQaAgent and edwQaRun to manage jobs.
- lines changed 4, context: html, text, full: html, text
Adding some fields to edwSubmit to make it so web app can report progress better.
- src/hg/encode3/encodeDataWarehouse/lib/redoSchema
- lines changed 2, context: html, text, full: html, text
Starting to implement replicate analysis.
- lines changed 2, context: html, text, full: html, text
Adding -defaultZeros to make it work in San Diego.
- lines changed 4, context: html, text, full: html, text
Forcing remake of all edw source on schema change.
- lines changed 2, context: html, text, full: html, text
Removed a few lines not needed since improvements in autoSql.
- src/hg/encode3/encodeDataWarehouse/lib/resetEdw
- lines changed 1, context: html, text, full: html, text
Adding a view shortcut for pairCorrelate
- lines changed 10, context: html, text, full: html, text
Adding more enrichment targets.
- lines changed 1, context: html, text, full: html, text
Splitting edwQaPairCorrelate into two tables.
- lines changed 8, context: html, text, full: html, text
Adding views for correatios and crossEnrichments. Removing edwQaAgent stuff.
- lines changed 1, context: html, text, full: html, text
Removing little edwSubmit from resetEdw script.
- lines changed 7, context: html, text, full: html, text
Making resetEdw create fifo for submission spooler if it doesn't exist.
- src/hg/encode3/encodeDataWarehouse/makefile
- lines changed 3, context: html, text, full: html, text
First cut of a web submission ap. It communicates with command line edwSubmit program via a named pipe managed by edwSubmitSpooler, which also manages multiple edwSubmit processes so as to allow more than one, but not too many.
- src/hg/encode3/validateManifest/validateManifest.c
- lines changed 54, context: html, text, full: html, text
checking for allowed values in experiment and replicate fields
- lines changed 3, context: html, text, full: html, text
incremented version, removed a bambai check that Eurie seemed to not like
- lines changed 15, context: html, text, full: html, text
fixed bug to flip logic correctly on 2bit file-existence - and incremented version number to 1.4
- src/hg/estOrient/tests/makefile
- lines changed 1, context: html, text, full: html, text
all tests now using binaries from DESTBINDIR, refs #9104 #10630
- src/hg/gbGetEntries/tests/makefile
- lines changed 11, context: html, text, full: html, text
all tests now using binaries from DESTBINDIR, refs #9104 #10630
- src/hg/geneBounds/clusterGenes/tests/makefile
- lines changed 10, context: html, text, full: html, text
all tests now using binaries from DESTBINDIR, refs #9104 #10630
- src/hg/genePredHisto/tests/makefile
- lines changed 1, context: html, text, full: html, text
all tests now using binaries from DESTBINDIR, refs #9104 #10630
- src/hg/genePredSingleCover/tests/makefile
- lines changed 3, context: html, text, full: html, text
all tests now using binaries from DESTBINDIR, refs #9104 #10630
- src/hg/genePredToGtf/tests/makefile
- lines changed 6, context: html, text, full: html, text
all tests now using binaries from DESTBINDIR, refs #9104 #10630
- src/hg/hgGene/domains.c
- lines changed 4, context: html, text, full: html, text
fix linkout to Interpro in hgGene
- src/hg/hgGenome/hgGenome.c
- lines changed 1, context: html, text, full: html, text
add calls to setUdcCacheDir to genome graphs and hub connect #8072
- lines changed 1, context: html, text, full: html, text
Brian put setUdcCacheDir() earlier, but he should have cleaned the later ones out.
- src/hg/hgGetAnn/tests/makefile
- lines changed 13, context: html, text, full: html, text
all tests now using binaries from DESTBINDIR, refs #9104 #10630
- src/hg/hgHubConnect/hgHubConnect.c
- lines changed 1, context: html, text, full: html, text
add calls to setUdcCacheDir to genome graphs and hub connect #8072
- lines changed 1, context: html, text, full: html, text
Brian put setUdcCacheDir() earlier, but he should have cleaned the later ones out.
- src/hg/hgSession/hgSession.c
- lines changed 15, context: html, text, full: html, text
adding support for HTTPS by not hardwiring the protocol and port in the URL but detecting when https is in use
- src/hg/hgTables/mainPage.c
- lines changed 1, context: html, text, full: html, text
Made link to public mysql server relative.
- src/hg/hgTracks/bigBedTrack.c
- lines changed 4, context: html, text, full: html, text
fix some problems with assembly data hubs that Hiram found. refs #8072
- src/hg/hgTracks/hgTracks.c
- lines changed 6, context: html, text, full: html, text
polishing some of the snake track code, added support for HAL snakes in assembly hubs. refs #10637
- src/hg/hgTracks/hgTracks.h
- lines changed 7, context: html, text, full: html, text
polishing some of the snake track code, added support for HAL snakes in assembly hubs. refs #10637
- src/hg/hgTracks/simpleTracks.c
- lines changed 8, context: html, text, full: html, text
polishing some of the snake track code, added support for HAL snakes in assembly hubs. refs #10637
- src/hg/hgTracks/snakeTrack.c
- lines changed 588, context: html, text, full: html, text
polishing some of the snake track code, added support for HAL snakes in assembly hubs. refs #10637
- lines changed 1, context: html, text, full: html, text
a tweak to common.mk to look for stdc++ library, and to snakeTrack to keep track of mapName
- src/hg/hgVarAnnogrator/hgVarAnnogrator.c
- lines changed 22, context: html, text, full: html, text
Refactoring to remove dependencies on annoGratorQuery from streamers,grators and formatters. Instead, provide basic assembly info and
explicitly pass streamers(/grators) along with the rows that they
produced into formatters. ref #6152
- lines changed 44, context: html, text, full: html, text
Added determination of data type by asObject comparison instead ofkludges like special annoRowType or checking a few column names. refs #6152
- src/hg/hgc/bigBedClick.c
- lines changed 1, context: html, text, full: html, text
fix a bug in the dealing with bigBeds where it was assuming that the fields are white space delimited when they are really tab delimited
- src/hg/hgc/hgc.c
- lines changed 3, context: html, text, full: html, text
fix some problems with assembly data hubs that Hiram found. refs #8072
- lines changed 29, context: html, text, full: html, text
polishing some of the snake track code, added support for HAL snakes in assembly hubs. refs #10637
- lines changed 1, context: html, text, full: html, text
fix a couple of problems that Max found in bigBed handling. One is spaces were causing problem in custom track bigBed support (not cloning memory which was being chopped by spaces), and the second problem was that bigBedIntervalQuery was adding one character at a time to a dyString that ended up growing to megabyte, which was very slow and timed out in hgc
- src/hg/htdocs/ENCODE/FAQ/index.html
- lines changed 26, context: html, text, full: html, text
Adding a FAQ question about .bb files from MLQ refs #10650
- src/hg/htdocs/ENCODE/downloads.html
- lines changed 1, context: html, text, full: html, text
Making small edit to line in downloads.html, noticed when sending MLQ refs #10654
- src/hg/htdocs/ENCODE/index.html
- lines changed 10, context: html, text, full: html, text
Add more links to news section. refs #9712
- lines changed 7, context: html, text, full: html, text
Add quotes around _blank, and adding some tags like </a>,= to improve links ref #9712
- lines changed 1, context: html, text, full: html, text
Update content header to reflect this is generic ENCODE page (not UCSC)
- src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
- lines changed 4, context: html, text, full: html, text
reworded first sentence. refs #10625
- src/hg/htdocs/goldenPath/newsarch.html
- lines changed 3, context: html, text, full: html, text
Fixed 2 errors caught during code review -- thanks, Brian!
- src/hg/htdocs/goldenPath/pubs.html
- lines changed 12, context: html, text, full: html, text
added link to 2013 pub by Kuhn et al. refs #6734
- src/hg/inc/annoGrateWigDb.h
- lines changed 2, context: html, text, full: html, text
Refactoring to remove dependencies on annoGratorQuery from streamers,grators and formatters. Instead, provide basic assembly info and
explicitly pass streamers(/grators) along with the rows that they
produced into formatters. ref #6152
- src/hg/inc/annoGratorGpVar.h
- lines changed 2, context: html, text, full: html, text
Patching up one more mem leak for #6152.
- src/hg/inc/annoStreamDb.h
- lines changed 2, context: html, text, full: html, text
Refactoring to remove dependencies on annoGratorQuery from streamers,grators and formatters. Instead, provide basic assembly info and
explicitly pass streamers(/grators) along with the rows that they
produced into formatters. ref #6152
- src/hg/inc/annoStreamWig.h
- lines changed 2, context: html, text, full: html, text
Refactoring to remove dependencies on annoGratorQuery from streamers,grators and formatters. Instead, provide basic assembly info and
explicitly pass streamers(/grators) along with the rows that they
produced into formatters. ref #6152
- src/hg/inc/genePred.h
- lines changed 2, context: html, text, full: html, text
Added determination of data type by asObject comparison instead ofkludges like special annoRowType or checking a few column names. refs #6152
- src/hg/inc/ucscRetroInfo.h
- lines changed 2, context: html, text, full: html, text
Removed column no longer used that was commented out. Modified description for alignGapCount field.
- src/hg/lib/annoFormatVep.c
- lines changed 50, context: html, text, full: html, text
Refactoring to remove dependencies on annoGratorQuery from streamers,grators and formatters. Instead, provide basic assembly info and
explicitly pass streamers(/grators) along with the rows that they
produced into formatters. ref #6152
- lines changed 27, context: html, text, full: html, text
Patching up one more mem leak for #6152.
- lines changed 6, context: html, text, full: html, text
Added indentifying name to annoStreamer for output header info and better error messages. refs #6152
- lines changed 17, context: html, text, full: html, text
Added determination of data type by asObject comparison instead ofkludges like special annoRowType or checking a few column names. refs #6152
- src/hg/lib/annoGrateWigDb.c
- lines changed 2, context: html, text, full: html, text
Refactoring to remove dependencies on annoGratorQuery from streamers,grators and formatters. Instead, provide basic assembly info and
explicitly pass streamers(/grators) along with the rows that they
produced into formatters. ref #6152
- src/hg/lib/annoGratorGpVar.c
- lines changed 2, context: html, text, full: html, text
Refactoring to remove dependencies on annoGratorQuery from streamers,grators and formatters. Instead, provide basic assembly info and
explicitly pass streamers(/grators) along with the rows that they
produced into formatters. ref #6152
- lines changed 17, context: html, text, full: html, text
Patching up one more mem leak for #6152.
- lines changed 3, context: html, text, full: html, text
Added indentifying name to annoStreamer for output header info and better error messages. refs #6152
- lines changed 5, context: html, text, full: html, text
Added determination of data type by asObject comparison instead ofkludges like special annoRowType or checking a few column names. refs #6152
- src/hg/lib/annoStreamDb.c
- lines changed 4, context: html, text, full: html, text
Refactoring to remove dependencies on annoGratorQuery from streamers,grators and formatters. Instead, provide basic assembly info and
explicitly pass streamers(/grators) along with the rows that they
produced into formatters. ref #6152
- lines changed 6, context: html, text, full: html, text
Added indentifying name to annoStreamer for output header info and better error messages. refs #6152
- src/hg/lib/annoStreamWig.c
- lines changed 13, context: html, text, full: html, text
Refactoring to remove dependencies on annoGratorQuery from streamers,grators and formatters. Instead, provide basic assembly info and
explicitly pass streamers(/grators) along with the rows that they
produced into formatters. ref #6152
- lines changed 7, context: html, text, full: html, text
Added indentifying name to annoStreamer for output header info and better error messages. refs #6152
- src/hg/lib/cart.c
- lines changed 1, context: html, text, full: html, text
add browser.cgiTime option to allow turning off timing information from CGIs, refs #10611
- src/hg/lib/ensemblLift.sql
- lines changed 7, context: html, text, full: html, text
redmone #10496 Adding ensemblLift.sql for descrition purpose.
- src/hg/lib/genePred.c
- lines changed 22, context: html, text, full: html, text
Added determination of data type by asObject comparison instead ofkludges like special annoRowType or checking a few column names. refs #6152
- src/hg/lib/tests/annoGratorTester.c
- lines changed 79, context: html, text, full: html, text
Refactoring to remove dependencies on annoGratorQuery from streamers,grators and formatters. Instead, provide basic assembly info and
explicitly pass streamers(/grators) along with the rows that they
produced into formatters. ref #6152
- lines changed 7, context: html, text, full: html, text
Added determination of data type by asObject comparison instead ofkludges like special annoRowType or checking a few column names. refs #6152
- src/hg/lib/tests/expected/annoGrator/vepOut.txt
- lines changed 1, context: html, text, full: html, text
Added indentifying name to annoStreamer for output header info and better error messages. refs #6152
- src/hg/lib/trackHub.c
- lines changed 3, context: html, text, full: html, text
order assemblies by orderKey in gateway drop-down.
- lines changed 3, context: html, text, full: html, text
polishing some of the snake track code, added support for HAL snakes in assembly hubs. refs #10637
- src/hg/lib/ucscRetroInfo.as
- lines changed 20, context: html, text, full: html, text
Removed oldScore column as no longer used. Renamed oldIntronCount as alignGapCount and modified description.
- src/hg/lib/ucscRetroInfo.sql
- lines changed 1, context: html, text, full: html, text
Modified comment for alignGapCount field.
- src/hg/liftAcross/tests/makefile
- lines changed 4, context: html, text, full: html, text
all tests now using binaries from DESTBINDIR, refs #9104 #10630
- src/hg/liftOver/tests/makefile
- lines changed 19, context: html, text, full: html, text
all tests now using binaries from DESTBINDIR, refs #9104 #10630
- src/hg/liftUp/test/makefile
- lines changed 19, context: html, text, full: html, text
all tests now using binaries from DESTBINDIR, refs #9104 #10630
- src/hg/makeDb/doc/hg19.txt
- lines changed 63, context: html, text, full: html, text
added option to ignore GTF groups that have no exons
- lines changed 28, context: html, text, full: html, text
COSMIC v64 installed hg19 refs #10158
- src/hg/makeDb/hgLoadMaf/tests/makefile
- lines changed 3, context: html, text, full: html, text
all tests now using binaries from DESTBINDIR, refs #9104 #10630
- src/hg/makeDb/hgPar/tests/makefile
- lines changed 3, context: html, text, full: html, text
all tests now using binaries from DESTBINDIR, refs #9104 #10630
- src/hg/makeDb/mdbUpdate/tests/makefile
- lines changed 2, context: html, text, full: html, text
all tests now using binaries from DESTBINDIR, refs #9104 #10630
- src/hg/makeDb/trackDb/cv/alpha/cv.ra
- lines changed 12, context: html, text, full: html, text
Removing two terms that were experimental confirmed by Venkat discovered by Kate and CR refs# 10627
- lines changed 13, context: html, text, full: html, text
Removing two terms not used anywhere, and an extra empty line, Code Review refs #10627
- src/hg/makeDb/trackDb/cv/beta/cv.ra
- lines changed 12, context: html, text, full: html, text
Copying alpha/cv.ra to beta/cv.ra for Removing two terms that were experimental confirmed by Venkat discovered by Kate and CR refs# 10627
- lines changed 13, context: html, text, full: html, text
Copying alpha/cv.ra to beta/cv.ra, Removing two terms not used anywhere, and an extra empty line, Code Review refs #10627
- src/hg/makeDb/trackDb/human/hg19/trackDb.ra
- lines changed 2, context: html, text, full: html, text
Changed long label for Retroposed Genes 5.0 to include version number and data. Added dataVersion for same track.
- src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
- lines changed 1, context: html, text, full: html, text
added option to ignore GTF groups that have no exons
- lines changed 1, context: html, text, full: html, text
fixed mistake commit [markd very bad]
- src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV13.ra
- src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV15.html
- lines changed 342, context: html, text, full: html, text
added option to ignore GTF groups that have no exons
- src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV15.ra
- lines changed 263, context: html, text, full: html, text
added option to ignore GTF groups that have no exons
- src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV9.ra
- src/hg/mouseStuff/axtToMaf/tests/makefile
- lines changed 4, context: html, text, full: html, text
all tests now using binaries from DESTBINDIR, refs #9104 #10630
- src/hg/mouseStuff/axtToPsl/tests/makefile
- lines changed 3, context: html, text, full: html, text
all tests now using binaries from DESTBINDIR, refs #9104 #10630
- src/hg/mouseStuff/mafRanges/tests/makefile
- lines changed 1, context: html, text, full: html, text
all tests now using binaries from DESTBINDIR, refs #9104 #10630
- src/hg/mouseStuff/netToAxt/tests/makefile
- lines changed 5, context: html, text, full: html, text
all tests now using binaries from DESTBINDIR, refs #9104 #10630
- src/hg/mrnaToGene/tests/makefile
- lines changed 23, context: html, text, full: html, text
all tests now using binaries from DESTBINDIR, refs #9104 #10630
- src/hg/oneShot/freen/blatUp.out
- lines changed 37, context: html, text, full: html, text
Cleaning out old cruft from freen dir. Making freen test named pipes.
- src/hg/oneShot/freen/freen.c
- lines changed 33, context: html, text, full: html, text
Cleaning out old cruft from freen dir. Making freen test named pipes.
- src/hg/oneShot/freen/freen.doc
- lines changed 40, context: html, text, full: html, text
Cleaning out old cruft from freen dir. Making freen test named pipes.
- src/hg/oneShot/freen/hg7.out
- lines changed 224, context: html, text, full: html, text
Cleaning out old cruft from freen dir. Making freen test named pipes.
- src/hg/pslCDnaFilter/tests/makefile
- lines changed 2, context: html, text, full: html, text
all tests now using binaries from DESTBINDIR, refs #9104 #10630
- src/hg/pslDiff/tests/makefile
- lines changed 4, context: html, text, full: html, text
all tests now using binaries from DESTBINDIR, refs #9104 #10630
- src/hg/pslHisto/tests/makefile
- lines changed 1, context: html, text, full: html, text
all tests now using binaries from DESTBINDIR, refs #9104 #10630
- src/hg/pslPartition/tests/makefile
- lines changed 1, context: html, text, full: html, text
all tests now using binaries from DESTBINDIR, refs #9104 #10630
- src/hg/pslSelect/tests/makefile
- lines changed 3, context: html, text, full: html, text
all tests now using binaries from DESTBINDIR, refs #9104 #10630
- src/hg/pslStats/tests/makefile
- lines changed 1, context: html, text, full: html, text
all tests now using binaries from DESTBINDIR, refs #9104 #10630
- src/hg/pslSwap/tests/makefile
- lines changed 10, context: html, text, full: html, text
all tests now using binaries from DESTBINDIR, refs #9104 #10630
- src/hg/ratStuff/mafSplit/test/makefile
- lines changed 4, context: html, text, full: html, text
all tests now using binaries from DESTBINDIR, refs #9104 #10630
- src/hg/spideyToPsl/tests/makefile
- lines changed 18, context: html, text, full: html, text
all tests now using binaries from DESTBINDIR, refs #9104 #10630
- src/hg/utils/automation/unplacedScaffolds.pl
- lines changed 14, context: html, text, full: html, text
per Angie's code review comment, protect the . in .1 sed regex, refs #10539
- src/hg/utils/bedToPsl/tests/makefile
- lines changed 4, context: html, text, full: html, text
all tests now using binaries from DESTBINDIR, refs #9104 #10630
- src/hg/utils/gff3ToGenePred/tests/makefile
- lines changed 1, context: html, text, full: html, text
all tests now using binaries from DESTBINDIR, refs #9104 #10630
- src/hg/utils/gff3ToPsl/tests/makefile
- lines changed 7, context: html, text, full: html, text
all tests now using binaries from DESTBINDIR, refs #9104 #10630
- src/hg/utils/gtfToGenePred/gtfToGenePred.c
- lines changed 22, context: html, text, full: html, text
added option to ignore GTF groups that have no exons
- src/hg/utils/gtfToGenePred/tests/expected/ignoreGroupWithoutExons.gp
- lines changed 4, context: html, text, full: html, text
added option to ignore GTF groups that have no exons
- src/hg/utils/gtfToGenePred/tests/input/geneFeature.gtf
- lines changed 21, context: html, text, full: html, text
added option to ignore GTF groups that have no exons
- src/hg/utils/gtfToGenePred/tests/makefile
- lines changed 7, context: html, text, full: html, text
added option to ignore GTF groups that have no exons
- lines changed 18, context: html, text, full: html, text
all tests now using binaries from DESTBINDIR, refs #9104 #10630
- src/hg/utils/overlapSelect/tests/makefile
- lines changed 3, context: html, text, full: html, text
all tests now using binaries from DESTBINDIR, refs #9104 #10630
- src/hg/utils/pslMap/tests/makefile
- lines changed 22, context: html, text, full: html, text
all tests now using binaries from DESTBINDIR, refs #9104 #10630
- src/hg/utils/refSeqGet/tests/makefile
- lines changed 1, context: html, text, full: html, text
all tests now using binaries from DESTBINDIR, refs #9104 #10630
- src/inc/annoAssembly.h
- lines changed 24, context: html, text, full: html, text
Refactoring to remove dependencies on annoGratorQuery from streamers,grators and formatters. Instead, provide basic assembly info and
explicitly pass streamers(/grators) along with the rows that they
produced into formatters. ref #6152
- src/inc/annoColumn.h
- lines changed 26, context: html, text, full: html, text
Ripping out unused annoColumn -- it's really an output option for tab-sep or CT output and could simply be an slName list. refs #6152
- src/inc/annoFormatter.h
- lines changed 19, context: html, text, full: html, text
Refactoring to remove dependencies on annoGratorQuery from streamers,grators and formatters. Instead, provide basic assembly info and
explicitly pass streamers(/grators) along with the rows that they
produced into formatters. ref #6152
- src/inc/annoGrateWig.h
- lines changed 1, context: html, text, full: html, text
Refactoring to remove dependencies on annoGratorQuery from streamers,grators and formatters. Instead, provide basic assembly info and
explicitly pass streamers(/grators) along with the rows that they
produced into formatters. ref #6152
- src/inc/annoGrator.h
- lines changed 3, context: html, text, full: html, text
Refactoring to remove dependencies on annoGratorQuery from streamers,grators and formatters. Instead, provide basic assembly info and
explicitly pass streamers(/grators) along with the rows that they
produced into formatters. ref #6152
- src/inc/annoGratorQuery.h
- lines changed 19, context: html, text, full: html, text
Refactoring to remove dependencies on annoGratorQuery from streamers,grators and formatters. Instead, provide basic assembly info and
explicitly pass streamers(/grators) along with the rows that they
produced into formatters. ref #6152
- src/inc/annoRow.h
- lines changed 1, context: html, text, full: html, text
Added determination of data type by asObject comparison instead ofkludges like special annoRowType or checking a few column names. refs #6152
- src/inc/annoStreamBigBed.h
- lines changed 1, context: html, text, full: html, text
Refactoring to remove dependencies on annoGratorQuery from streamers,grators and formatters. Instead, provide basic assembly info and
explicitly pass streamers(/grators) along with the rows that they
produced into formatters. ref #6152
- src/inc/annoStreamBigWig.h
- lines changed 1, context: html, text, full: html, text
Refactoring to remove dependencies on annoGratorQuery from streamers,grators and formatters. Instead, provide basic assembly info and
explicitly pass streamers(/grators) along with the rows that they
produced into formatters. ref #6152
- src/inc/annoStreamTab.h
- lines changed 2, context: html, text, full: html, text
Refactoring to remove dependencies on annoGratorQuery from streamers,grators and formatters. Instead, provide basic assembly info and
explicitly pass streamers(/grators) along with the rows that they
produced into formatters. ref #6152
- src/inc/annoStreamVcf.h
- lines changed 2, context: html, text, full: html, text
Refactoring to remove dependencies on annoGratorQuery from streamers,grators and formatters. Instead, provide basic assembly info and
explicitly pass streamers(/grators) along with the rows that they
produced into formatters. ref #6152
- src/inc/annoStreamer.h
- lines changed 28, context: html, text, full: html, text
Refactoring to remove dependencies on annoGratorQuery from streamers,grators and formatters. Instead, provide basic assembly info and
explicitly pass streamers(/grators) along with the rows that they
produced into formatters. ref #6152
- lines changed 12, context: html, text, full: html, text
Ripping out unused annoColumn -- it's really an output option for tab-sep or CT output and could simply be an slName list. refs #6152
- lines changed 2, context: html, text, full: html, text
Added indentifying name to annoStreamer for output header info and better error messages. refs #6152
- src/inc/asParse.h
- lines changed 14, context: html, text, full: html, text
Added determination of data type by asObject comparison instead ofkludges like special annoRowType or checking a few column names. refs #6152
- lines changed 10, context: html, text, full: html, text
Adding index and auto keywords to autoSql columns.
- lines changed 4, context: html, text, full: html, text
Added -addBin option at Angie's request.
- src/inc/cheapcgi.h
- lines changed 1, context: html, text, full: html, text
Fixed type of next pointer in cgiParsedVars. Ref #10621
- lines changed 3, context: html, text, full: html, text
adding support for HTTPS by not hardwiring the protocol and port in the URL but detecting when https is in use
- src/inc/common.mk
- lines changed 8, context: html, text, full: html, text
polishing some of the snake track code, added support for HAL snakes in assembly hubs. refs #10637
- lines changed 2, context: html, text, full: html, text
a tweak to common.mk to look for stdc++ library, and to snakeTrack to keep track of mapName
- lines changed 8, context: html, text, full: html, text
all tests now using binaries from DESTBINDIR, refs #9104 #10630
- src/inc/fieldedTable.h
- lines changed 4, context: html, text, full: html, text
Adding a separate parameter for file name to report errors on for benefit of edwSubmit which want's to report pre-upload URL where error occurs.
- src/inc/obscure.h
- lines changed 3, context: html, text, full: html, text
Adding shuffleArrayOfChars library function.
- src/inc/twoBit.h
- lines changed 3, context: html, text, full: html, text
Adding twoBitTotalSizeNoN.
- src/inc/userApp.mk
- lines changed 2, context: html, text, full: html, text
it is OK to have the destination binary depend upon the objects, refs #9104
- src/lib/annoAssembly.c
- lines changed 33, context: html, text, full: html, text
Refactoring to remove dependencies on annoGratorQuery from streamers,grators and formatters. Instead, provide basic assembly info and
explicitly pass streamers(/grators) along with the rows that they
produced into formatters. ref #6152
- src/lib/annoColumn.c
- lines changed 41, context: html, text, full: html, text
Ripping out unused annoColumn -- it's really an output option for tab-sep or CT output and could simply be an slName list. refs #6152
- src/lib/annoFormatTab.c
- lines changed 22, context: html, text, full: html, text
Refactoring to remove dependencies on annoGratorQuery from streamers,grators and formatters. Instead, provide basic assembly info and
explicitly pass streamers(/grators) along with the rows that they
produced into formatters. ref #6152
- lines changed 9, context: html, text, full: html, text
Ripping out unused annoColumn -- it's really an output option for tab-sep or CT output and could simply be an slName list. refs #6152
- lines changed 2, context: html, text, full: html, text
Added indentifying name to annoStreamer for output header info and better error messages. refs #6152
- lines changed 1, context: html, text, full: html, text
Added determination of data type by asObject comparison instead ofkludges like special annoRowType or checking a few column names. refs #6152
- src/lib/annoFormatter.c
- lines changed 13, context: html, text, full: html, text
Refactoring to remove dependencies on annoGratorQuery from streamers,grators and formatters. Instead, provide basic assembly info and
explicitly pass streamers(/grators) along with the rows that they
produced into formatters. ref #6152
- src/lib/annoGrateWig.c
- lines changed 2, context: html, text, full: html, text
Refactoring to remove dependencies on annoGratorQuery from streamers,grators and formatters. Instead, provide basic assembly info and
explicitly pass streamers(/grators) along with the rows that they
produced into formatters. ref #6152
- lines changed 2, context: html, text, full: html, text
Added indentifying name to annoStreamer for output header info and better error messages. refs #6152
- src/lib/annoGrator.c
- lines changed 10, context: html, text, full: html, text
Refactoring to remove dependencies on annoGratorQuery from streamers,grators and formatters. Instead, provide basic assembly info and
explicitly pass streamers(/grators) along with the rows that they
produced into formatters. ref #6152
- lines changed 20, context: html, text, full: html, text
Added indentifying name to annoStreamer for output header info and better error messages. refs #6152
- src/lib/annoGratorQuery.c
- lines changed 81, context: html, text, full: html, text
Refactoring to remove dependencies on annoGratorQuery from streamers,grators and formatters. Instead, provide basic assembly info and
explicitly pass streamers(/grators) along with the rows that they
produced into formatters. ref #6152
- src/lib/annoRow.c
- lines changed 1, context: html, text, full: html, text
Added determination of data type by asObject comparison instead ofkludges like special annoRowType or checking a few column names. refs #6152
- src/lib/annoStreamBigBed.c
- lines changed 2, context: html, text, full: html, text
Refactoring to remove dependencies on annoGratorQuery from streamers,grators and formatters. Instead, provide basic assembly info and
explicitly pass streamers(/grators) along with the rows that they
produced into formatters. ref #6152
- lines changed 3, context: html, text, full: html, text
Added indentifying name to annoStreamer for output header info and better error messages. refs #6152
- src/lib/annoStreamBigWig.c
- lines changed 2, context: html, text, full: html, text
Refactoring to remove dependencies on annoGratorQuery from streamers,grators and formatters. Instead, provide basic assembly info and
explicitly pass streamers(/grators) along with the rows that they
produced into formatters. ref #6152
- lines changed 8, context: html, text, full: html, text
Added indentifying name to annoStreamer for output header info and better error messages. refs #6152
- src/lib/annoStreamTab.c
- lines changed 3, context: html, text, full: html, text
Refactoring to remove dependencies on annoGratorQuery from streamers,grators and formatters. Instead, provide basic assembly info and
explicitly pass streamers(/grators) along with the rows that they
produced into formatters. ref #6152
- lines changed 1, context: html, text, full: html, text
Added indentifying name to annoStreamer for output header info and better error messages. refs #6152
- src/lib/annoStreamVcf.c
- lines changed 3, context: html, text, full: html, text
Refactoring to remove dependencies on annoGratorQuery from streamers,grators and formatters. Instead, provide basic assembly info and
explicitly pass streamers(/grators) along with the rows that they
produced into formatters. ref #6152
- lines changed 5, context: html, text, full: html, text
Added indentifying name to annoStreamer for output header info and better error messages. refs #6152
- lines changed 1, context: html, text, full: html, text
Added determination of data type by asObject comparison instead ofkludges like special annoRowType or checking a few column names. refs #6152
- src/lib/annoStreamer.c
- lines changed 10, context: html, text, full: html, text
Refactoring to remove dependencies on annoGratorQuery from streamers,grators and formatters. Instead, provide basic assembly info and
explicitly pass streamers(/grators) along with the rows that they
produced into formatters. ref #6152
- lines changed 18, context: html, text, full: html, text
Ripping out unused annoColumn -- it's really an output option for tab-sep or CT output and could simply be an slName list. refs #6152
- lines changed 5, context: html, text, full: html, text
Added indentifying name to annoStreamer for output header info and better error messages. refs #6152
- src/lib/asParse.c
- lines changed 43, context: html, text, full: html, text
Adding index and auto keywords to autoSql columns.
- lines changed 16, context: html, text, full: html, text
Added -addBin option at Angie's request.
- src/lib/bigBed.c
- lines changed 16, context: html, text, full: html, text
fix a couple of problems that Max found in bigBed handling. One is spaces were causing problem in custom track bigBed support (not cloning memory which was being chopped by spaces), and the second problem was that bigBedIntervalQuery was adding one character at a time to a dyString that ended up growing to megabyte, which was very slow and timed out in hgc
- src/lib/cheapcgi.c
- lines changed 18, context: html, text, full: html, text
adding support for HTTPS by not hardwiring the protocol and port in the URL but detecting when https is in use
- src/lib/fieldedTable.c
- lines changed 27, context: html, text, full: html, text
Adding a separate parameter for file name to report errors on for benefit of edwSubmit which want's to report pre-upload URL where error occurs.
- src/lib/gff.c
- src/lib/makefile
- lines changed 1, context: html, text, full: html, text
Refactoring to remove dependencies on annoGratorQuery from streamers,grators and formatters. Instead, provide basic assembly info and
explicitly pass streamers(/grators) along with the rows that they
produced into formatters. ref #6152
- lines changed 1, context: html, text, full: html, text
Ripping out unused annoColumn -- it's really an output option for tab-sep or CT output and could simply be an slName list. refs #6152
- src/lib/obscure.c
- lines changed 16, context: html, text, full: html, text
Adding shuffleArrayOfChars library function.
- src/lib/twoBit.c
- lines changed 13, context: html, text, full: html, text
Adding twoBitTotalSizeNoN.
- src/makefile
- lines changed 1, context: html, text, full: html, text
Improving file list for tag maker.
- lines changed 23, context: html, text, full: html, text
begin to move obsolete programs into the cellar, refs #9104
- src/product/ex.hg.conf
- lines changed 4, context: html, text, full: html, text
add browser.cgiTime option to allow turning off timing information from CGIs, refs #10611
- src/utils/bigBedNamedItems/makefile
- lines changed 1, context: html, text, full: html, text
added mising -lz that caused failures on fedora
- src/utils/est2genomeToPsl/tests/makefile
- lines changed 2, context: html, text, full: html, text
all tests now using binaries from DESTBINDIR, refs #9104 #10630
- src/utils/faFilter/tests/makefile
- lines changed 9, context: html, text, full: html, text
all tests now using binaries from DESTBINDIR, refs #9104 #10630
- src/utils/faRandomize/tests/makefile
- lines changed 4, context: html, text, full: html, text
all tests now using binaries from DESTBINDIR, refs #9104 #10630
- src/utils/pslLiftSubrangeBlat/tests/makefile
- lines changed 6, context: html, text, full: html, text
all tests now using binaries from DESTBINDIR, refs #9104 #10630
- src/utils/qa/checkTableStatus.csh
- lines changed 2, context: html, text, full: html, text
Changed to report on rrnfs1 now that we are using it instead of hgnfs1.
- src/utils/qa/weeklybld/buildEnv.csh
- lines changed: 339617
- files changed: 302