All File Changes

v312_preview2 to v312_base (2015-02-09 to 2015-02-16) v312

• src/hg/checkTableCoords/checkTableCoords.c
  • lines changed 1, context: html, text, full: html, text
    fix checkTableCoords to actually set the exit code if it finds errors
    
• src/hg/checkTableCoords/tests/makefile
  • lines changed 1, context: html, text, full: html, text
    don't output error message on error that is supposed to occur
    
• src/hg/cirm/cdw/cdwMakeValidFile/cdwMakeValidFile.c
  • lines changed 51, context: html, text, full: html, text
    Putting in validators for cram, jpg, text, and html files.
    
• src/hg/cirm/cdw/cdwQuery/cdwQuery.c
  • lines changed 32, context: html, text, full: html, text
    Expanding wildcards in field list, so allowing select *. Also implementing count(*) function.
    
  • lines changed 125, context: html, text, full: html, text
    Reworking to get metadata tags from cdwMetaTags table rather than tagStorm file.
    
  • lines changed 92, context: html, text, full: html, text
    Moving tagStormFromDatabase into cdwTabStorm library function. Making count(*) queries work.
    
  • lines changed 1, context: html, text, full: html, text
    Sorting field list.
    
• src/hg/cirm/cdw/cdwSubmit/cdwSubmit.c
  • lines changed 2, context: html, text, full: html, text
    Fixing cdwFileName for manifest.txt and meta.txt files.
    
  • lines changed 34, context: html, text, full: html, text
    Adding support for cram, jpg, html, and text files. Checking all tags are defined in meta.txt.
    
  • lines changed 94, context: html, text, full: html, text
    Saving metadata tags in cdwMetaTags table.
    
  • lines changed 20, context: html, text, full: html, text
    Updating metadata on old files during resubmissions.
    
• src/hg/cirm/cdw/cdwSwapInSymLink/cdwSwapInSymLink.c
  • lines changed 68, context: html, text, full: html, text
    Utility to swap symlinks into warehouse for submitted files seems to work mostly.
    
• src/hg/cirm/cdw/cdwSwapInSymLink/makefile
  • lines changed 4, context: html, text, full: html, text
    Utility to swap symlinks into warehouse for submitted files seems to work mostly.
    
• src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c
  • lines changed 2, context: html, text, full: html, text
    Just changing some text visible to user to be more consistent.
    
  • lines changed 199, context: html, text, full: html, text
    Reworking away from a submission oriented view to an executive summary. Also letting you query with RQL.
    
• src/hg/cirm/cdw/fix/cdwFixCdwFileNamePath/cdwFixCdwFileNamePath.c
  • lines changed 55, context: html, text, full: html, text
    Fixing cdwFileName.
    
• src/hg/cirm/cdw/fix/cdwFixCdwFileNamePath/makefile
  • lines changed 4, context: html, text, full: html, text
    Fixing cdwFileName.
    
• src/hg/cirm/cdw/fix/cdwFixUpdateTime/cdwFixUpdateTime.c
  • lines changed 62, context: html, text, full: html, text
    Fix utility to restore update times seems to work.
    
• src/hg/cirm/cdw/fix/cdwFixUpdateTime/makefile
  • lines changed 4, context: html, text, full: html, text
    Fix utility to restore update times seems to work.
    
• src/hg/cirm/cdw/inc/cdw.h
  • lines changed 71, context: html, text, full: html, text
    Adding cdwMetaTags table, and a field that refers to it in cdwFile.
    
• src/hg/cirm/cdw/inc/cdwLib.h
  • lines changed 7, context: html, text, full: html, text
    Moving cdwTagStorm to library and polishing it a little.
    
• src/hg/cirm/cdw/inc/cdwValid.h
  • lines changed 18, context: html, text, full: html, text
    Implementing file recognizers for jpg and cram files. Restricting tags to just ones that are documented.
    
• src/hg/cirm/cdw/lib/cdw.as
  • lines changed 1, context: html, text, full: html, text
    Fixing typo in comment.
    
  • lines changed 9, context: html, text, full: html, text
    Adding cdwMetaTags table, and a field that refers to it in cdwFile.
    
• src/hg/cirm/cdw/lib/cdw.c
  • lines changed 169, context: html, text, full: html, text
    Adding cdwMetaTags table, and a field that refers to it in cdwFile.
    
• src/hg/cirm/cdw/lib/cdw.sql
  • lines changed 12, context: html, text, full: html, text
    Adding cdwMetaTags table, and a field that refers to it in cdwFile.
    
• src/hg/cirm/cdw/lib/cdwLib.c
  • lines changed 2, context: html, text, full: html, text
    Fixing a part/file_part mixup, and ''/NULL mixup.
    
  • lines changed 136, context: html, text, full: html, text
    Moving cdwTagStorm to library and polishing it a little.
    
  • lines changed 140, context: html, text, full: html, text
    Moving cdwTagStorm function to it's own file and expanding it to include additional tags.
    
• src/hg/cirm/cdw/lib/cdwTagStorm.c
  • lines changed 234, context: html, text, full: html, text
    Moving cdwTagStorm function to it's own file and expanding it to include additional tags.
    
  • lines changed 30, context: html, text, full: html, text
    Adding map_to_ribosome and map_to_repeat tags.
    
  • lines changed 36, context: html, text, full: html, text
    Adding map_to_ contaminant tags.
    
  • lines changed 44, context: html, text, full: html, text
    Adding info from cdwBamFile
    
• src/hg/cirm/cdw/lib/cdwValid.c
  • lines changed 97, context: html, text, full: html, text
    Implementing file recognizers for jpg and cram files. Restricting tags to just ones that are documented.
    
  • lines changed 3, context: html, text, full: html, text
    Adding seq_sample, data_set_id, and keywords to acceptable tags.
    
• src/hg/cirm/cdw/lib/makefile
  • lines changed 2, context: html, text, full: html, text
    Moving cdwTagStorm function to it's own file and expanding it to include additional tags.
    
• src/hg/cirm/quakeLab/quakeFakeMouseManifest/quakeFakeMouseManifest.c
  • lines changed 21, context: html, text, full: html, text
    Coming up with a unique identifier for the sample-level data. Changing tag names to fit documentation where they differed.
    
  • lines changed 9, context: html, text, full: html, text
    Adjusting metadata to new cdw way.
    
• src/hg/genePredCheck/genePredCheck.c
  • lines changed 25, context: html, text, full: html, text
    Created a program to filter genePreds file. Currently filters
    based on genePredCheck validation errors.
    
• src/hg/hgTracks/rmskJoinedTrack.c
  • lines changed 2, context: html, text, full: html, text
    fix left label offset difficulty refs #9741
    
• src/hg/hgc/hgc.c
  • lines changed 3, context: html, text, full: html, text
    Ensembl link could be elsewhere, allow trackDb override default refs #14462
    
• src/hg/htdocs/goldenPath/help/hg38.chrom.sizes
  • lines changed 455, context: html, text, full: html, text
    Adding hg38.chrom.sizes to goldenPath/help/ next to hg18 and hg19
    
• src/hg/htdocs/goldenPath/help/hubQuickStart.html
  • lines changed 9, context: html, text, full: html, text
    Adding wget lines to Hub Quick Start pages, and links to new Assembly QuickStart page
    
• src/hg/htdocs/goldenPath/help/hubQuickStartGroups.html
  • lines changed 10, context: html, text, full: html, text
    Adding wget lines to Hub Quick Start pages, and links to new Assembly QuickStart page
    
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 5, context: html, text, full: html, text
    encoding email address. we're getting spam, maybe from open email address
    
  • lines changed 35, context: html, text, full: html, text
    Adding announcement of snp142 release, refs #14189
    
  • lines changed 8, context: html, text, full: html, text
    Adding notice of the retirement of snp135/137 to 142 release, refs #14189
    
  • lines changed 21, context: html, text, full: html, text
    Adding news update about blat on assembly hubs
    
• src/hg/htdocs/indexNews.html
  • lines changed 6, context: html, text, full: html, text
    encoding email address. we're getting spam, maybe from open email address
    
  • lines changed 56, context: html, text, full: html, text
    Adding announcement of snp142 release, refs #14189
    
  • lines changed 8, context: html, text, full: html, text
    Adding notice of the retirement of snp135/137 to 142 release, refs #14189
    
  • lines changed 35, context: html, text, full: html, text
    Forgot to remove main proteomics announcement when I activated the short version
    
  • lines changed 62, context: html, text, full: html, text
    Adding news update about blat on assembly hubs
    
• src/hg/htdocs/mirror.html
  • lines changed 2, context: html, text, full: html, text
    added a little space after Official Mirrors section. It was too cramped at bottom of box
    
• src/hg/htdocs/style/cirm.css
  • lines changed 8194, context: html, text, full: html, text
    Adding cirm css initially as a clone of encode3.css. Hmm. So huge!
    
• src/hg/htdocs/style/cirmUcsc.css
  • lines changed 58, context: html, text, full: html, text
    Adding cirm css initially as a clone of encode3.css. Hmm. So huge!
    
• src/hg/htdocs/style/makefile
  • lines changed 1, context: html, text, full: html, text
    Adding cirm css initially as a clone of encode3.css. Hmm. So huge!
    
• src/hg/htdocs/training/vids/index.html
  • lines changed 1, context: html, text, full: html, text
    Minor edit per code review. refs #14816
    
• src/hg/inc/genePred.h
  • lines changed 7, context: html, text, full: html, text
    Created a program to filter genePreds file. Currently filters
    based on genePredCheck validation errors.
    
• src/hg/inc/spDb.h
  • lines changed 8, context: html, text, full: html, text
    some modifications to support the GENCODE as UCSC genes switch
    
• src/hg/inc/trackHub.h
  • lines changed 2, context: html, text, full: html, text
    Ease compile
    
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    New version number v312
    
• src/hg/js/cdwPersona.js
  • lines changed 45, context: html, text, full: html, text
    Making the little authentication by persona stuff work for cdw web works.
    
• src/hg/js/makefile
  • lines changed 1, context: html, text, full: html, text
    Making the little authentication by persona stuff work for cdw web works.
    
• src/hg/js/model/hgAi/hgAiModel.js
  • lines changed 5, context: html, text, full: html, text
    In hgAi, don't show the loading image and message that says to keep the window
    open unless output will appear in the browser window (not in a file). Thx Matt. refs #14579
    
• src/hg/js/react/hgAi/hgAi.jsx
  • lines changed 5, context: html, text, full: html, text
    In hgAi, don't show the loading image and message that says to keep the window
    open unless output will appear in the browser window (not in a file). Thx Matt. refs #14579
    
• src/hg/lib/genePred.c
  • lines changed 83, context: html, text, full: html, text
    Created a program to filter genePreds file. Currently filters
    based on genePredCheck validation errors.
    
• src/hg/lib/hui.c
  • lines changed 2, context: html, text, full: html, text
    Fix use of boolean caught by Max. Note this is refactored (not new) code.
    
• src/hg/lib/spDb.c
  • lines changed 16, context: html, text, full: html, text
    some modifications to support the GENCODE as UCSC genes switch
    
• src/hg/makeDb/doc/calJac3.txt
  • lines changed 73, context: html, text, full: html, text
    lastz alignment to panTro4 per user request refs #14793
    
• src/hg/makeDb/doc/hg38/hg38.txt
  • lines changed 9, context: html, text, full: html, text
    add the instructions to build a lift file to convert dbVar hg38 chrom
    names to our chrom names
    
• src/hg/makeDb/doc/hg38/lastzRuns.txt
  • lines changed 368, context: html, text, full: html, text
    done with lastz alignments for anoCar2 cheMyd1 chrPic2 xipMac1 punNye1 mayZeb1 danRer10 petMar2 refs #14560
    
  • lines changed 849, context: html, text, full: html, text
    done with oryAfe1 cerSim1 chrAsi1 eptFus1 tupChi1 equCab2 camFer1 vicPac2 turTru2 orcOrc1 speTri2 refs #14560
    
  • lines changed 1408, context: html, text, full: html, text
    done with cerSim1 chrAsi1 tupChi1 camFer1 turTru2 orcOrc1 speTri2 and starting runs for pteAle1 susScr3 loxAfr3 hetGla2 pteVam1 felCat8 ailMel1 musFur1 cavPor3 dasNov3 oryCun2 panHod1 lepWed1 odoRosDiv1 myoDav1 refs #14560
    
  • lines changed 1155, context: html, text, full: html, text
    wrapping up pteAle1 loxAfr3 hetGla2 pteVam1 felCat8 ailMel1 musFur1 cavPor3 dasNov3 oryCun2 panHod1 lepWed1 odoRosDiv1 myoDav1 camFer1 vicPac2 equCab2 and starting capHir1 myoLuc2 eleEdw1 triMan1 jacJac1 chiLan1 conCri1 octDeg1 ochPri3 eriEur2 echTel2 refs #14560
    
  • lines changed 177, context: html, text, full: html, text
    copleted loxAfr3 hetGla2 pteVam1 cavPor3 dasNov3 oryCun2 panHod1 lepWed1 odoRosDiv1 continuing pteAle1 susScr3 felCat8 ailMel1 musFur1 myoDav1 capHir1 myoLuc2 eleEdw1 jacJac1 chiLan1 conCri1 octDeg1 ochPri3 eriEur2 echTel2 refs #14560
    
  • lines changed 462, context: html, text, full: html, text
    starting rn6 criGri1 mesAur1 micOch1 sorAra2 macEug2 refs #14560
    
  • lines changed 932, context: html, text, full: html, text
    completed pteAle1 susScr3 felCat8 ailMel1 micFur1 myoDav1 chiLan1 octDeg1 eriEur2 echTel2 starting capHir1 eleEdw1 triMan1 jacJac1 ochPri3 rn6 sarHar1 apaSpi1 pelSin1 ornAna1 allMis1 colLiv1 galGal4 anaPla1 melGal1 falChe1 falPer1 amaVit1 refs #14560
    
  • lines changed 45, context: html, text, full: html, text
    finished myoLuc2 eleEdw1 continuing capHir1 triMan1 chiLan1 eriEur2 mesAur1 micOch1 sorAra2 refs #14560
    
• src/hg/makeDb/doc/panTro4.txt
  • lines changed 23, context: html, text, full: html, text
    lastz alignment to panTro4 per user request refs #14793
    
• src/hg/makeDb/doc/tarSyr2/initialBuild.txt
  • lines changed 1, context: html, text, full: html, text
    tarSyr2 doesn't have any native ESTs don't bother with them refs #14820
    
• src/hg/makeDb/doc/tarSyr2/multiz17way.txt
  • lines changed 17, context: html, text, full: html, text
    forgot to load the phastCons track refs #14410
    
• src/hg/makeDb/doc/ucscGenes/hg38.ucscGenes16.csh
  • lines changed 945, context: html, text, full: html, text
    more futzing around building UCSC genes from Gencode
    
• src/hg/makeDb/outside/gencode/gencodeLoad.mk
  • lines changed 4, context: html, text, full: html, text
    suggestions from code review: use HOME rather than hardcode markd users. Add error call to remind about updating import of TSL before next release
    
• src/hg/makeDb/trackDb/chainNet.html
  • lines changed 1, context: html, text, full: html, text
    remove redundent o_db in the net description refs #14410
    
• src/hg/makeDb/trackDb/ebola/eboVir3/newSeqs.html
  • lines changed 22, context: html, text, full: html, text
    adding description and placed track in compGeno refs #14278
    
• src/hg/makeDb/trackDb/ebola/eboVir3/trackDb.newSequences.ra
  • lines changed 1, context: html, text, full: html, text
    adding description and placed track in compGeno refs #14278
    
  • lines changed 1, context: html, text, full: html, text
    adding description and placed track in compGeno refs #14278
    
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    Track ordering and visibility changes for snp142 release
    
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    Track ordering and visibility changes for snp142 release
    
  • lines changed 1, context: html, text, full: html, text
    update the ISCA link-out to point to the right place
    
• src/hg/makeDb/trackDb/joinedRmskComposite.ra
  • lines changed 1, context: html, text, full: html, text
    fixup default visibility refs #9741
    
• src/hg/makeDb/trackDb/mouseLemur/micMur1/description.html
  • lines changed 1, context: html, text, full: html, text
    correct assembly date is July 2007 refs #14835
    
• src/hg/oneShot/freen/freen.c
  • lines changed 46, context: html, text, full: html, text
    Freen tests cgiParseNext.
    
• src/hg/oneShot/hubTrackSettings/hubTrackSettings.c
  • lines changed 128, context: html, text, full: html, text
    Inventory public hub track settings. refs #10015
    
• src/hg/oneShot/hubTrackSettings/makefile
  • lines changed 4, context: html, text, full: html, text
    Inventory public hub track settings. refs #10015
    
• src/hg/txGene/txGeneAlias/txGeneAlias.c
  • lines changed 2, context: html, text, full: html, text
    some modifications to support the GENCODE as UCSC genes switch
    
• src/hg/utils/gencodeToKnownGene/gencodeToKnownGene.c
  • lines changed 403, context: html, text, full: html, text
    introductory work on program to create knownGene tables from gencode
    tables
    
• src/hg/utils/gencodeToKnownGene/makefile
  • lines changed 3, context: html, text, full: html, text
    introductory work on program to create knownGene tables from gencode
    tables
    
• src/hg/utils/genePredFilter/genePredFilter.c
  • lines changed 80, context: html, text, full: html, text
    Created a program to filter genePreds file. Currently filters
    based on genePredCheck validation errors.
    
• src/hg/utils/genePredFilter/makefile
  • lines changed 3, context: html, text, full: html, text
    Created a program to filter genePreds file. Currently filters
    based on genePredCheck validation errors.
    
• src/hg/utils/genePredFilter/tests/expected/gencodeHackDbTest.gp
  • lines changed 8, context: html, text, full: html, text
    Created a program to filter genePreds file. Currently filters
    based on genePredCheck validation errors.
    
• src/hg/utils/genePredFilter/tests/expected/gencodeHackTest.gp
  • lines changed 9, context: html, text, full: html, text
    Created a program to filter genePreds file. Currently filters
    based on genePredCheck validation errors.
    
• src/hg/utils/genePredFilter/tests/input/gencodeHack.gp
  • lines changed 10, context: html, text, full: html, text
    Created a program to filter genePreds file. Currently filters
    based on genePredCheck validation errors.
    
• src/hg/utils/genePredFilter/tests/makefile
  • lines changed 20, context: html, text, full: html, text
    Created a program to filter genePreds file. Currently filters
    based on genePredCheck validation errors.
    
  • lines changed 4, context: html, text, full: html, text
    turn off verbose options to keep automatic tests happy
    
• src/hg/utils/makefile
  • lines changed 2, context: html, text, full: html, text
    Created a program to filter genePreds file. Currently filters
    based on genePredCheck validation errors.
    
• src/inc/cheapcgi.h
  • lines changed 13, context: html, text, full: html, text
    Adding cgiEncodeHash and cgiParseNext functions.
    
• src/inc/common.h
  • lines changed 6, context: html, text, full: html, text
    Added wildExpandList() function.
    
• src/inc/fieldedTable.h
  • lines changed 6, context: html, text, full: html, text
    Added functions to index a field.
    
• src/inc/ra.h
  • lines changed 1, context: html, text, full: html, text
    Adding missing part to the 'only include me once' bracketing of this include file.
    
• src/inc/rql.h
  • lines changed 1, context: html, text, full: html, text
    Switching rql's integral type from int to long long since it's dealing some with file sizes that overflow 32 bits.
    
• src/inc/tagStorm.h
  • lines changed 19, context: html, text, full: html, text
    Adding functions to get all fields mentioned in a tagStorm.
    
  • lines changed 1, context: html, text, full: html, text
    Changed tagStormNew's parameter name from fileName to more generic name, since they are built in memory sometimes too.
    
  • lines changed 8, context: html, text, full: html, text
    Adding function for adding long long integer or double values to storm.
    
• src/lib/cheapcgi.c
  • lines changed 56, context: html, text, full: html, text
    Adding cgiEncodeHash and cgiParseNext functions.
    
• src/lib/fieldedTable.c
  • lines changed 39, context: html, text, full: html, text
    Added functions to index a field.
    
• src/lib/rqlEval.c
  • lines changed 1, context: html, text, full: html, text
    Switching rql's integral type from int to long long since it's dealing some with file sizes that overflow 32 bits.
    
• src/lib/rqlParse.c
  • lines changed 2, context: html, text, full: html, text
    Updating code for long long vs. int.
    
• src/lib/tagStorm.c
  • lines changed 64, context: html, text, full: html, text
    Adding functions to get all fields mentioned in a tagStorm.
    
  • lines changed 2, context: html, text, full: html, text
    Changed tagStormNew's parameter name from fileName to more generic name, since they are built in memory sometimes too.
    
  • lines changed 18, context: html, text, full: html, text
    Adding function for adding long long integer or double values to storm.
    
• src/lib/wildcmp.c
  • lines changed 54, context: html, text, full: html, text
    Added wildExpandList() function.
    
• src/tagStorm/tagStormInfo/c
  • lines changed 0, context: html, text, full: html, text
    Adding a comment.
    
  • lines changed 0, context: html, text, full: html, text
    Removing stray file
    
• src/tagStorm/tagStormInfo/tagStormInfo.c
  • lines changed 1, context: html, text, full: html, text
    Adding a comment.
    
• src/tagStorm/tagStormJoinTab/more.tab
  • lines changed 26, context: html, text, full: html, text
    A test case for the append option.
    
• src/tagStorm/tagStormQuery/tagStormQuery.c
  • lines changed 52, context: html, text, full: html, text
    Making it so that you can have wildcards on the field list, and so that it will abort if the field list in the query contains fields not in the tag storm.
    
  • lines changed 39, context: html, text, full: html, text
    Moving wildExpandList to library.
    
  • lines changed 10, context: html, text, full: html, text
    Supporting count command in addition to select.
    
• src/userApps/fetchKentSource.sh
  • lines changed 1, context: html, text, full: html, text
    adding checkUmask.sh to the userApps build fetch refs #14507
    
• src/utils/makefile
  • lines changed 2, context: html, text, full: html, text
    add faAlign to the utils list since it is used in the Ebola construction refs #14278
    
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 1, context: html, text, full: html, text
    temporarily add donnak to final build report emails to cover Ann outage next week refs #14821
    
  • lines changed 3, context: html, text, full: html, text
    v312 final build refs #14821
    
• src/utils/qa/weeklybld/doNewBranch.csh
  • lines changed 4, context: html, text, full: html, text
    temporarily add donnak to final build report emails to cover Ann outage next week refs #14821buildEnv.csh
    
• src/utils/qa/weeklybld/doNewReview2.csh
  • lines changed 1, context: html, text, full: html, text
    temporarily add donnak to final build report emails to cover Ann outage next week refs #14821buildEnv.csh
    

• lines changed: 18715
• files changed: 136