All File Changes

v285_preview to v285_preview2 (2013-06-04 to 2013-06-11) v285

• src/hg/hgGene/hgGeneData/links.ra
  • lines changed 1, context: html, text, full: html, text
    change TreeFam link out URL refs #10874
• src/hg/hgGenome/hgGenome.c
  • lines changed 3, context: html, text, full: html, text
    notify folks that genome graphs doesn't work with assembly hubs
• src/hg/hgTracks/gencodeTracks.c
  • lines changed 3, context: html, text, full: html, text
    fix bug in fixsqli
• src/hg/hgTracks/mainMain.c
  • lines changed 1, context: html, text, full: html, text
    redundant setUdcCacheDir call removed
• src/hg/hgUserSuggestion/hgUserSuggestion.c
  • lines changed 14, context: html, text, full: html, text
    Minor editing per CR review 10985 feedback
  • lines changed 35, context: html, text, full: html, text
    Bug 11006 hgUserSuggestion CGI need to check proper suggestion setting in hg.conf first.
• src/hg/hgVai/hgVai.c
  • lines changed 465, context: html, text, full: html, text
    Added support for remaining dbNSFP sources; added longLabels to VEP output header lines. refs #6152
• src/hg/hgVai/libifyMe.c
  • lines changed 10, context: html, text, full: html, text
    Valuable feedback from code review -- thanks Tim! refs 10977
  • lines changed 29, context: html, text, full: html, text
    Added support for remaining dbNSFP sources; added longLabels to VEP output header lines. refs #6152
• src/hg/hgVai/libifyMe.h
  • lines changed 1, context: html, text, full: html, text
    Valuable feedback from code review -- thanks Tim! refs 10977
  • lines changed 5, context: html, text, full: html, text
    Added support for remaining dbNSFP sources; added longLabels to VEP output header lines. refs #6152
• src/hg/hgVarAnnogrator/hgVarAnnogrator.c
  • lines changed 2, context: html, text, full: html, text
    Oops, hgVarAnnogrator is catching up with 2b5eb866 -- since it's notin top-level build, it's too easy to overlook things that break it.
    I intend to replace it with a less variant-centric CGI when hgVai is stable.
    
• src/hg/hgc/hgc.c
  • lines changed 1, context: html, text, full: html, text
    increase the size of buffer that was being exceeded on SOD1
• src/hg/htdocs/ENCODE/usageResources.html
  • lines changed 2, context: html, text, full: html, text
    Adding link to pdf for ENCODE Open Helix page, refs #11023
• src/hg/htdocs/goldenPath/credits.html
  • lines changed 33, context: html, text, full: html, text
    Corrections to credits.html from code review, refs #10978
• src/hg/htdocs/goldenPath/help/genomeEuro.html
  • lines changed 27, context: html, text, full: html, text
    Added section about saved sessions and custom tracks on genome-euro (redmine #7481,9767)
• src/hg/htdocs/goldenPath/help/haplotypes.html
  • lines changed 4, context: html, text, full: html, text
    Grammar tweaks pointed out by Jonathan in code review. refs 10979
• src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
  • lines changed 90, context: html, text, full: html, text
    first pass at documentation for assembly hubs and track item search refs #8072
  • lines changed 1, context: html, text, full: html, text
    clean up twoBit and trix pages a bit. Still need a lot of work
• src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.html
  • lines changed 6, context: html, text, full: html, text
    first pass at documentation for assembly hubs and track item search refs #8072
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 22, context: html, text, full: html, text
    first pass at documentation for assembly hubs and track item search refs #8072
  • lines changed 1, context: html, text, full: html, text
    add new html files for trix and twoBit.
• src/hg/htdocs/goldenPath/help/trix.html
  • lines changed 45, context: html, text, full: html, text
    add new html files for trix and twoBit.
  • lines changed 13, context: html, text, full: html, text
    clean up twoBit and trix pages a bit. Still need a lot of work
• src/hg/htdocs/goldenPath/help/twoBit.html
  • lines changed 58, context: html, text, full: html, text
    add new html files for trix and twoBit.
  • lines changed 26, context: html, text, full: html, text
    clean up twoBit and trix pages a bit. Still need a lot of work
• src/hg/htdocs/images/server_selector.jpg
  • lines changed 0, context: html, text, full: html, text
    Updated the server selector image to reflect the dropping of 'Use' from the Mirrors menu
• src/hg/inc/annoFormatVep.h
  • lines changed 4, context: html, text, full: html, text
    Added support for remaining dbNSFP sources; added longLabels to VEP output header lines. refs #6152
• src/hg/inc/hubConnect.h
  • lines changed 1, context: html, text, full: html, text
    Valuable feedback from code review -- thanks Tim! refs 10977
• src/hg/inc/hui.h
  • lines changed 1, context: html, text, full: html, text
    QA advises OK for V2 track to use V3 table display format (better even) so retiring trackDb setting that allowed two display modes. refs #10097
• src/hg/inc/trackDb.h
  • lines changed 1, context: html, text, full: html, text
    Revert "Added support for multi-view composites of type pgSnp. There are no config options for pgSnp, so disable the config pop-up in configurableByAjax. refs #683"This reverts commit 275a4e6b9d4eef6b3408e29198d94883b0e809ca.
    -- Tim pointed out in code review that there is a much better way to avoid the warnBox at the end of cfgTypeFromTdb. refs #10977 #683
    
• src/hg/js/README
  • lines changed 6, context: html, text, full: html, text
    Made changes to README and makefile in accordance with code review, refs #10978
  • lines changed 4, context: html, text, full: html, text
    Revised makefile to not print a warning when placing files in js/{user}, due to developer request
  • lines changed 2, context: html, text, full: html, text
    Updated README to more accurately reflect the creation of symlinks for .js files
• src/hg/js/makefile
  • lines changed 8, context: html, text, full: html, text
    Made changes to README and makefile in accordance with code review, refs #10978
  • lines changed 1, context: html, text, full: html, text
    Revised makefile to not print a warning when placing files in js/{user}, due to developer request
• src/hg/js/staticDoc.js
  • lines changed 3, context: html, text, full: html, text
    Added a URL rewrite rule for ftp links on hgdownload, refs #10888
• src/hg/lib/annoFormatVep.c
  • lines changed 304, context: html, text, full: html, text
    Added support for remaining dbNSFP sources; added longLabels to VEP output header lines. refs #6152
• src/hg/lib/annoStreamDb.c
  • lines changed 280, context: html, text, full: html, text
    Added a chunked-query mode to annoStreamDb, similar to that of annoStreamBigBed,so that we can quickly drain sqlResults from smaller queries instead of keeping
    a genome-wide sqlResult open for the whole time we're processing -- that was
    making mysql have mysterious hangs on hgwdev. (http://bugs.mysql.com/bug.php?id=50399)
    
• src/hg/lib/gwasCatalog.sql
  • lines changed 1, context: html, text, full: html, text
    make title field 1024 instead of 255 because it was getting truncated.
• src/hg/lib/haplotypes.c
  • lines changed 16, context: html, text, full: html, text
    Fixed rounding to 100 when percent above 99.5. Ref #10653.
• src/hg/lib/hgSeq.c
  • lines changed 5, context: html, text, full: html, text
    Generating sequence names as <db>_<track>_<itemName> works great exceptfor bed3 tracks that have NULL names. Use an incrementing count to
    generate distinct names instead. fixes #10995
    
• src/hg/lib/hubConnect.c
  • lines changed 1, context: html, text, full: html, text
    Valuable feedback from code review -- thanks Tim! refs 10977
• src/hg/lib/hui.c
  • lines changed 9, context: html, text, full: html, text
    QA advises OK for V2 track to use V3 table display format (better even) so retiring trackDb setting that allowed two display modes. refs #10097
  • lines changed 1, context: html, text, full: html, text
    Revert "Added support for multi-view composites of type pgSnp. There are no config options for pgSnp, so disable the config pop-up in configurableByAjax. refs #683"This reverts commit 275a4e6b9d4eef6b3408e29198d94883b0e809ca.
    -- Tim pointed out in code review that there is a much better way to avoid the warnBox at the end of cfgTypeFromTdb. refs #10977 #683
    
  • lines changed 13, context: html, text, full: html, text
    Merge branch 'master' into tfclusters
• src/hg/lib/jksql.c
  • lines changed 6, context: html, text, full: html, text
    adding support for logOnly setting
• src/hg/lib/lsSnpPdbChimera.c
  • lines changed 1, context: html, text, full: html, text
    fixing where clause oops in fixsqli stuff
• src/hg/lib/mdb.c
  • lines changed 2, context: html, text, full: html, text
    Turns out the single index on both var and val does work fin. The thing that triggers the inefficiency is the length of val that is included. It was val(32) and that was slow. Setting it to val(64) and it is blinfdlingly fast on mysql 5.6.10. Ref 10910.
• src/hg/lib/metaDb.sql
  • lines changed 2, context: html, text, full: html, text
    Combined key may be better than separate keys on cache starved RR. Ref #10910.
• src/hg/lib/tests/annoGratorTester.c
  • lines changed 6, context: html, text, full: html, text
    Added support for remaining dbNSFP sources; added longLabels to VEP output header lines. refs #6152
  • lines changed 29, context: html, text, full: html, text
    Added a chunked-query mode to annoStreamDb, similar to that of annoStreamBigBed,so that we can quickly drain sqlResults from smaller queries instead of keeping
    a genome-wide sqlResult open for the whole time we're processing -- that was
    making mysql have mysterious hangs on hgwdev. (http://bugs.mysql.com/bug.php?id=50399)
    
• src/hg/lib/tests/expected/annoGrator/gpFx.txt
  • lines changed 9, context: html, text, full: html, text
    Added support for remaining dbNSFP sources; added longLabels to VEP output header lines. refs #6152
• src/hg/lib/tests/expected/annoGrator/pgSnpKgDbToGpFx.txt
  • lines changed 39, context: html, text, full: html, text
    Added a chunked-query mode to annoStreamDb, similar to that of annoStreamBigBed,so that we can quickly drain sqlResults from smaller queries instead of keeping
    a genome-wide sqlResult open for the whole time we're processing -- that was
    making mysql have mysterious hangs on hgwdev. (http://bugs.mysql.com/bug.php?id=50399)
    
• src/hg/lib/tests/expected/annoGrator/vepOut.txt
  • lines changed 3, context: html, text, full: html, text
    Added support for remaining dbNSFP sources; added longLabels to VEP output header lines. refs #6152
• src/hg/lib/tests/input/annoGrator/pgForTestingGpFx.pgSnp.tab
  • lines changed 10, context: html, text, full: html, text
    Added a chunked-query mode to annoStreamDb, similar to that of annoStreamBigBed,so that we can quickly drain sqlResults from smaller queries instead of keeping
    a genome-wide sqlResult open for the whole time we're processing -- that was
    making mysql have mysterious hangs on hgwdev. (http://bugs.mysql.com/bug.php?id=50399)
    
• src/hg/lib/trackDbCustom.c
  • lines changed 4, context: html, text, full: html, text
    Revert "Added support for multi-view composites of type pgSnp. There are no config options for pgSnp, so disable the config pop-up in configurableByAjax. refs #683"This reverts commit 275a4e6b9d4eef6b3408e29198d94883b0e809ca.
    -- Tim pointed out in code review that there is a much better way to avoid the warnBox at the end of cfgTypeFromTdb. refs #10977 #683
    
  • lines changed 2, context: html, text, full: html, text
    Avoid warnBox at the end of cfgTypeFromTdb for pgSnp tracks with views. Thanks Tim! refs #10977 #683
• src/hg/lib/trackHub.c
  • lines changed 1, context: html, text, full: html, text
    fill in browserName for hgPos records so hgFind will highlight the element refs #10426
• src/hg/lib/ucscToEnsembl.as
  • lines changed 6, context: html, text, full: html, text
    to add proper description and field labels for the table browser refs #10746
• src/hg/makeDb/doc/allMis1.txt
  • lines changed 59, context: html, text, full: html, text
    repeat masking finally done with new RM libraries continuing with genscan and cpgIsland builds refs #8750
  • lines changed 47, context: html, text, full: html, text
    running genbank refs #8750
• src/hg/makeDb/doc/echTel2.txt
  • lines changed 47, context: html, text, full: html, text
    running genbank refs #9693
• src/hg/makeDb/doc/encodeRegHg19.txt
  • lines changed 46, context: html, text, full: html, text
    Work on downloads. refs #10097
  • lines changed 8, context: html, text, full: html, text
    Finish up downloads and metaDb. refs #10097
• src/hg/makeDb/doc/eriEur2.txt
  • lines changed 1991, context: html, text, full: html, text
    running masking refs #9419
• src/hg/makeDb/doc/hg18.txt
  • lines changed 63, context: html, text, full: html, text
    lastz panTro4 to hg18 refs #10943
• src/hg/makeDb/doc/hg19.txt
  • lines changed 28, context: html, text, full: html, text
    update cosmic to v65 refs #10158
• src/hg/makeDb/doc/oviAri3.txt
  • lines changed 597, context: html, text, full: html, text
    running repeat masker and window masker refs #9409
  • lines changed 79, context: html, text, full: html, text
    done with masking starting cpgIslands genbank and genscan runs refs #9409
• src/hg/makeDb/doc/proteins/121210.txt
  • lines changed 9, context: html, text, full: html, text
    add most current reactome tables to proteome database
• src/hg/makeDb/doc/sorAra2.txt
  • lines changed 122, context: html, text, full: html, text
    starting genbank run refs #9348
  • lines changed 10, context: html, text, full: html, text
    done with genbank run refs #9348
• src/hg/makeDb/doc/taeGut2.txt
  • lines changed 618, context: html, text, full: html, text
    done with masking ready for genbank refs #10190
• src/hg/makeDb/doc/ucscGenes/hg19.ucscGenes14.csh
  • lines changed 146, context: html, text, full: html, text
    ongoing work on UCSC genes for hg19
  • lines changed 23, context: html, text, full: html, text
    clean up some TODO's in UCSC genes, add some notes for next time, fix txCdsToGene to continue after a warning.
• src/hg/makeDb/doc/vicPac2.txt
  • lines changed 2027, context: html, text, full: html, text
    running repeat masking refs #10833
  • lines changed 191, context: html, text, full: html, text
    done with masking starting cpgIslands genscan and genbank runs refs #10833
• src/hg/makeDb/genbank/etc/align.dbs
  • lines changed 1, context: html, text, full: html, text
    Added echTel2 to daily hgwdev build refs #9693
  • lines changed 1, context: html, text, full: html, text
    added sorAra2 - shrew - refs #9348
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 17, context: html, text, full: html, text
    adding sorAra2 common shrew refs #9348
  • lines changed 17, context: html, text, full: html, text
    adding taeGut2 Zebra Finch to genbank run refs #10190
  • lines changed 19, context: html, text, full: html, text
    adding echTel2 tenrec refs #9693
  • lines changed 16, context: html, text, full: html, text
    updating allMis0 to allMis1 refs #8750
  • lines changed 19, context: html, text, full: html, text
    adding oviAri3 Sheep refs #9409
  • lines changed 13, context: html, text, full: html, text
    adding vicPac2 alpaca refs #10833
• src/hg/makeDb/genbank/etc/hgwdev.dbs
  • lines changed 1, context: html, text, full: html, text
    Added echTel2 to daily hgwdev build refs #9693
  • lines changed 1, context: html, text, full: html, text
    added sorAra2 - shrew - refs #9348
• src/hg/makeDb/genbank/etc/rr.dbs
  • lines changed 1, context: html, text, full: html, text
    Adding musFur1 to genBank updates rr.dbs refs #6352
• src/hg/makeDb/hgLoadBed/hgLoadBed.c
  • lines changed 3, context: html, text, full: html, text
    oops sql string needs a NOSQLINJ tag prefix
• src/hg/makeDb/makefile
  • lines changed 4, context: html, text, full: html, text
    adding hgFindSpec and hgTrackDb to the userApps build refs #9149
  • lines changed 4, context: html, text, full: html, text
    including localEnvironment.mk to allow function in userApp environment refs #9149
• src/hg/makeDb/schema/all.joiner
  • lines changed 1, context: html, text, full: html, text
    Added galGal4 to list of ensDb assemblies (redmine #10746)
  • lines changed 1, context: html, text, full: html, text
    add kg6ToKg7 for UCSC genes
• src/hg/makeDb/trackDb/alpaca/vicPac2/description.html
  • lines changed 63, context: html, text, full: html, text
    adding vicPac2 to the browser refs #10833
• src/hg/makeDb/trackDb/alpaca/vicPac2/gap.html
  • lines changed 30, context: html, text, full: html, text
    adding vicPac2 to the browser refs #10833
• src/hg/makeDb/trackDb/alpaca/vicPac2/gold.html
  • lines changed 34, context: html, text, full: html, text
    adding vicPac2 to the browser refs #10833
• src/hg/makeDb/trackDb/alpaca/vicPac2/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    adding vicPac2 to the browser refs #10833
• src/hg/makeDb/trackDb/hedgehog/eriEur2/description.html
  • lines changed 63, context: html, text, full: html, text
    initial files from makeGenomeDb.pl refs #9419
• src/hg/makeDb/trackDb/hedgehog/eriEur2/gap.html
  • lines changed 30, context: html, text, full: html, text
    initial files from makeGenomeDb.pl refs #9419
• src/hg/makeDb/trackDb/hedgehog/eriEur2/gold.html
  • lines changed 34, context: html, text, full: html, text
    initial files from makeGenomeDb.pl refs #9419
• src/hg/makeDb/trackDb/hedgehog/eriEur2/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    initial files from makeGenomeDb.pl refs #9419
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeRegTfbsClustered.ra
  • lines changed 28, context: html, text, full: html, text
    Finish up downloads and metaDb. refs #10097
• src/hg/makeDb/trackDb/human/hg19/wgEncodeReg.ra
  • lines changed 19, context: html, text, full: html, text
    QA advises OK for V2 track to use V3 table display format (better even) so retiring trackDb setting that allowed two display modes. refs #10097
  • lines changed 20, context: html, text, full: html, text
    Merge branch 'master' into tfclusters
  • lines changed 17, context: html, text, full: html, text
    Trim experimental track versions. refs #10097
• src/hg/makeDb/trackDb/human/hg19/wgEncodeRegTfbsClustered.html
  • lines changed 2, context: html, text, full: html, text
    Correcting broken links to lab, noticed in V3 of TFBS Clustered, refs #10097
• src/hg/makeDb/trackDb/human/hg19/wgEncodeRegTfbsClustered.release2.html
  • lines changed 2, context: html, text, full: html, text
    Correcting broken links to lab, noticed in V3 of TFBS Clustered, refs #10097
• src/hg/makeDb/trackDb/human/hg19/wgEncodeRegTfbsClusteredV3.html
  • lines changed 1, context: html, text, full: html, text
    Correcting typol, bank->blank, Code Review refs #10981
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 4, context: html, text, full: html, text
    removing score filter for variants tracks
  • lines changed 2, context: html, text, full: html, text
    taking back score filter change
  • lines changed 1, context: html, text, full: html, text
    taking back score filter change
  • lines changed 1, context: html, text, full: html, text
    moved UniProt Annotations out of the first place in the Genes group
  • lines changed 2, context: html, text, full: html, text
    moving spAnnot to experimental
  • lines changed 3, context: html, text, full: html, text
    moving spAnnot to experimental
• src/hg/makeDb/trackDb/makefile
  • lines changed 1, context: html, text, full: html, text
    adding taeGut2 zebra finch to the browser refs #10190
  • lines changed 6, context: html, text, full: html, text
    adding eriEur2 to the build refs #9419
  • lines changed 1, context: html, text, full: html, text
    adding oviAri3 to the browser refs #9409
  • lines changed 2, context: html, text, full: html, text
    adding vicPac2 to the browser refs #10833
• src/hg/makeDb/trackDb/sheep/oviAri3/description.html
  • lines changed 63, context: html, text, full: html, text
    adding oviAri3 to the browser refs #9409
• src/hg/makeDb/trackDb/sheep/oviAri3/gap.html
  • lines changed 30, context: html, text, full: html, text
    adding oviAri3 to the browser refs #9409
• src/hg/makeDb/trackDb/sheep/oviAri3/gold.html
  • lines changed 34, context: html, text, full: html, text
    adding oviAri3 to the browser refs #9409
• src/hg/makeDb/trackDb/sheep/oviAri3/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    adding oviAri3 to the browser refs #9409
• src/hg/makeDb/trackDb/tagTypes.tab
  • lines changed 1, context: html, text, full: html, text
    QA advises OK for V2 track to use V3 table display format (better even) so retiring trackDb setting that allowed two display modes. refs #10097
• src/hg/makeDb/trackDb/zebraFinch/taeGut2/description.html
  • lines changed 63, context: html, text, full: html, text
    initial files from makeGenomeDb.pl refs #10190
• src/hg/makeDb/trackDb/zebraFinch/taeGut2/gap.html
  • lines changed 32, context: html, text, full: html, text
    initial files from makeGenomeDb.pl refs #10190
• src/hg/makeDb/trackDb/zebraFinch/taeGut2/gold.html
  • lines changed 34, context: html, text, full: html, text
    initial files from makeGenomeDb.pl refs #10190
• src/hg/makeDb/trackDb/zebraFinch/taeGut2/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    initial files from makeGenomeDb.pl refs #10190
• src/hg/makefile
  • lines changed 3, context: html, text, full: html, text
    including localEnvironment.mk to allow function in userApp environment refs #9149
• src/hg/mouseStuff/makefile
  • lines changed 4, context: html, text, full: html, text
    including localEnvironment.mk to allow function in userApp environment refs #9149
• src/hg/ratStuff/makefile
  • lines changed 3, context: html, text, full: html, text
    including localEnvironment.mk to allow function in userApp environment refs #9149
• src/hg/txCds/txCdsToGene/txCdsToGene.c
  • lines changed 3, context: html, text, full: html, text
    clean up some TODO's in UCSC genes, add some notes for next time, fix txCdsToGene to continue after a warning.
• src/hg/utils/automation/doRepeatMasker.pl
  • lines changed 8, context: html, text, full: html, text
    better cleaning of RMPart refs #10998
• src/hg/utils/automation/doSimpleRepeat.pl
  • lines changed 3, context: html, text, full: html, text
    better cleaning of the TrfPart directory refs #10998
• src/hg/utils/automation/unplacedScaffolds.pl
  • lines changed 1, context: html, text, full: html, text
    construct chrom.sizes file after 2bit is done refs #10272
• src/hg/utils/makefile
  • lines changed 4, context: html, text, full: html, text
    including localEnvironment.mk to allow function in userApp environment refs #9149
• src/hg/utils/overlapSelect/makefile
  • lines changed 4, context: html, text, full: html, text
    add the include localEnvironment.mk to allow build in userApps environment refs #9149
• src/hg/utils/phyloTrees/105way.commonNames.nh
  • lines changed 105, context: html, text, full: html, text
    adding takFla1 yellowbelly pufferfish refs #10272
• src/hg/utils/phyloTrees/105way.nh
  • lines changed 105, context: html, text, full: html, text
    adding takFla1 yellowbelly pufferfish refs #10272
  • lines changed 1, context: html, text, full: html, text
    vicPac1 updates to vicPac2 refs #10272
• src/hg/utils/phyloTrees/105way.scientificNames.nh
  • lines changed 105, context: html, text, full: html, text
    adding takFla1 yellowbelly pufferfish refs #10272
• src/hg/utils/phyloTrees/commonNames.sh
  • lines changed 1, context: html, text, full: html, text
    adding takFla1 yellowbelly pufferfish refs #10272
  • lines changed 1, context: html, text, full: html, text
    vicPac1 updates to vicPac2 refs #10272
• src/hg/utils/phyloTrees/makefile
  • lines changed 8, context: html, text, full: html, text
    adding takFla1 yellowbelly pufferfish refs #10272
• src/hg/utils/phyloTrees/scientificNames.sh
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    adding takFla1 yellowbelly pufferfish refs #10272
• src/hg/utils/phyloTrees/vertebrates.txt
  • lines changed 4, context: html, text, full: html, text
    adding takFla Takifugu flavidus Yellowbelly puffer fish refs #10272
• src/hg/utils/pslMap/README
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    fixed typo.
• src/hg/utils/pslMap/makefile
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    add the include localEnvironment.mk to allow build in userApps environment refs #9149
• src/inc/annoAssembly.h
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    Added a chunked-query mode to annoStreamDb, similar to that of annoStreamBigBed,so that we can quickly drain sqlResults from smaller queries instead of keeping
    a genome-wide sqlResult open for the whole time we're processing -- that was
    making mysql have mysterious hangs on hgwdev. (http://bugs.mysql.com/bug.php?id=50399)
    
• src/inc/localEnvironment.mk
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    updating userApps to make the fetchSource a separate step refs #9149
• src/inc/memalloc.h
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    adding mutex to make careful alloc, free, etc work with multiple pthreads, which customFactory now uses. The careful mem handler is being used in many cgis now although not hgTracks at this time. Because of the saved-session support going into cart.c, that means that practically anything that uses the cart now can be calling the multi-threaded customtrack loader.
• src/inc/userApp.mk
  • lines changed 1, context: html, text, full: html, text
    updating userApps to make the fetchSource a separate step refs #9149
• src/lib/annoAssembly.c
  • lines changed 10, context: html, text, full: html, text
    Added a chunked-query mode to annoStreamDb, similar to that of annoStreamBigBed,so that we can quickly drain sqlResults from smaller queries instead of keeping
    a genome-wide sqlResult open for the whole time we're processing -- that was
    making mysql have mysterious hangs on hgwdev. (http://bugs.mysql.com/bug.php?id=50399)
    
• src/lib/annoGrator.c
  • lines changed 0, context: html, text, full: html, text
    Added a chunked-query mode to annoStreamDb, similar to that of annoStreamBigBed,so that we can quickly drain sqlResults from smaller queries instead of keeping
    a genome-wide sqlResult open for the whole time we're processing -- that was
    making mysql have mysterious hangs on hgwdev. (http://bugs.mysql.com/bug.php?id=50399)
    
• src/lib/annoStreamBigBed.c
  • lines changed 5, context: html, text, full: html, text
    Added a chunked-query mode to annoStreamDb, similar to that of annoStreamBigBed,so that we can quickly drain sqlResults from smaller queries instead of keeping
    a genome-wide sqlResult open for the whole time we're processing -- that was
    making mysql have mysterious hangs on hgwdev. (http://bugs.mysql.com/bug.php?id=50399)
    
• src/lib/annoStreamBigWig.c
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    Added support for remaining dbNSFP sources; added longLabels to VEP output header lines. refs #6152
• src/lib/memalloc.c
  • lines changed 25, context: html, text, full: html, text
    adding mutex to make careful alloc, free, etc work with multiple pthreads, which customFactory now uses. The careful mem handler is being used in many cgis now although not hgTracks at this time. Because of the saved-session support going into cart.c, that means that practically anything that uses the cart now can be calling the multi-threaded customtrack loader.
• src/makefile
  • lines changed 2, context: html, text, full: html, text
    including localEnvironment.mk to allow function in userApp environment refs #9149
• src/userApps/Makefile
  • lines changed 23, context: html, text, full: html, text
    updating userApps to make the fetchSource a separate step refs #9149
  • lines changed 18, context: html, text, full: html, text
    add the local environment business refs #9149
  • lines changed 4, context: html, text, full: html, text
    fixup echo -e argument situation refs #9149
  • lines changed 2, context: html, text, full: html, text
    indicate an alternative to using git refs #9149
  • lines changed 1, context: html, text, full: html, text
    fixup clean rule so it will function OK without the kent/src directory existing refs #9149
• src/userApps/README
  • lines changed 1, context: html, text, full: html, text
    updating userApps to make the fetchSource a separate step refs #9149
  • lines changed 29, context: html, text, full: html, text
    indicate an alternative to using git refs #9149
• src/utils/makefile
  • lines changed 4, context: html, text, full: html, text
    including localEnvironment.mk to allow function in userApp environment refs #9149
• src/utils/qa/blatPing.csh
  • lines changed 16, context: html, text, full: html, text
    Fixed problem with only the first 100 blat servers being tested (the outer while loop was setting list2 to nothing but then requiring it to not be empty in order to continue). Also changed to generate output only when errors are found and got rid of email to individuals so that it can be controlled more easily from the qateam crontab. Finally, added the PID to the filename and an instruction for cleanup on interruption. refs #10796
• src/utils/userApps/makefile
  • lines changed 4, context: html, text, full: html, text
    including localEnvironment.mk to allow function in userApp environment refs #9149

• lines changed: 9089
• files changed: 168