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 3, context: html, text, full: html, text
    Improving status output.
  • 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 111, context: html, text, full: html, text
    Adding bigWig support.
  • lines changed 5, context: html, text, full: html, text
    Adding bigBedVariants.
  • 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.
  • lines changed 4, context: html, text, full: html, text
    Improving status output.
• 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 1, context: html, text, full: html, text
    Improving status output.
  • 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.
  • lines changed 7, context: html, text, full: html, text
    A little more polish
• 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.
  • lines changed 36, context: html, text, full: html, text
    Adding indexes.
• 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.
  • lines changed 33, context: html, text, full: html, text
    Adding indexes.
• 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.
  • lines changed 1, context: html, text, full: html, text
    Making Eurie a user.
• 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]
  • lines changed 1, context: html, text, full: html, text
    load of gencode V15
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV13.ra
  • lines changed 1, context: html, text, full: html, text
    load of gencode V15
• 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
  • lines changed 2, context: html, text, full: html, text
    load of gencode V15
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV9.ra
  • lines changed 1, context: html, text, full: html, text
    load of gencode V15
• 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
  • lines changed 5, context: html, text, full: html, text
    Removing warning.
• 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
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    add browser.cgiTime option to allow turning off timing information from CGIs, refs #10611
• src/utils/bigBedNamedItems/makefile
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    added mising -lz that caused failures on fedora
• src/utils/est2genomeToPsl/tests/makefile
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    all tests now using binaries from DESTBINDIR, refs #9104 #10630
• src/utils/faFilter/tests/makefile
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    all tests now using binaries from DESTBINDIR, refs #9104 #10630
• src/utils/faRandomize/tests/makefile
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    all tests now using binaries from DESTBINDIR, refs #9104 #10630
• src/utils/pslLiftSubrangeBlat/tests/makefile
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    all tests now using binaries from DESTBINDIR, refs #9104 #10630
• src/utils/qa/checkTableStatus.csh
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    Changed to report on rrnfs1 now that we are using it instead of hgnfs1.
• src/utils/qa/weeklybld/buildEnv.csh
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    v283 preview1

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• files changed: 302