All File Changes

v330_preview to v330_preview2.1 (2016-03-07 to 2016-03-14) v330

• confs/hgwdev.hg.conf
  • lines changed 2, context: html, text, full: html, text
    Installing updated hg.conf files from UCSC servers
    
• confs/preview.hg.conf
  • lines changed 238, context: html, text, full: html, text
    Installing updated hg.conf files from UCSC servers
    
• src/hg/cirm/cdw/wrangle/addMetaDataToJson/addMetaDataToJson
  • lines changed 15, context: html, text, full: html, text
    Fixing the meta data file so it only reads one line as suggested by Jim in #16789, refs #16182
    
• src/hg/cirm/cdw/wrangle/condenseMatrix/condenseMatrix
  • lines changed 49, context: html, text, full: html, text
    Made the dependency files depend on an environment varialbe CIRM as suggested by Max, refs #16244
    
• src/hg/cirm/cdw/wrangle/condenseMatrix/makefile
  • lines changed 3, context: html, text, full: html, text
    Made the dependency files depend on an environment varialbe CIRM as suggested by Max, refs #16244
    
• src/hg/expMatrixClustersForDendrogram/makefile
  • lines changed 3, context: html, text, full: html, text
    Changing the program name as suggested by Jim in #16789, refs #16182
    
• src/hg/expMatrixToJson/expMatrixClustersForDendrogram.c
  • lines changed 636, context: html, text, full: html, text
    Changing the program name as suggested by Jim in #16789, refs #16182
    
• src/hg/expMatrixToJson/expMatrixToJson.c
  • lines changed 160, context: html, text, full: html, text
    Modified the clustering algorithm, added in a sibling comparison function that decides the first born child. Refs #16216
    
  • lines changed 10, context: html, text, full: html, text
    Changing variable names, refs #16216
    
  • lines changed 636, context: html, text, full: html, text
    Changing the program name as suggested by Jim in #16789, refs #16182
    
• src/hg/expMatrixToJson/tests/makefile
  • lines changed 3, context: html, text, full: html, text
    Changing the test directory makefile a bit. Still looking for an easy way to implement changes suggested by Angie, refs #16216
    
• src/hg/hgBlat/hgBlat.c
  • lines changed 1, context: html, text, full: html, text
    fix typo in hgBlat code comment
    
• src/hg/hgTracks/gtexTracks.c
  • lines changed 52, context: html, text, full: html, text
    Fixes to mouseover on gene model and label so gene description is displayed properly. refs #15645
    
  • lines changed 1, context: html, text, full: html, text
    1. Use max median score from gtexInfo table for max viewlimits guidance. 2. Fix placement of gender labels. refs #15645
    
  • lines changed 3, context: html, text, full: html, text
    Doh check null
    
  • lines changed 1, context: html, text, full: html, text
    Add comment.
    
• src/hg/hgTracks/hgTracks.c
  • lines changed 6, context: html, text, full: html, text
    Fixes #16982. nextItem was crashing for custom track big*
    
• src/hg/hgTracks/simpleTracks.c
  • lines changed 4, context: html, text, full: html, text
    fix problem with chain line disappearing when way zoomed in #15209 note
    35
    
  • lines changed 1, context: html, text, full: html, text
    Fixes to mouseover on gene model and label so gene description is displayed properly. refs #15645
    
  • lines changed 1, context: html, text, full: html, text
    Updated OMIM display, more linkouts, resolving merge conflict, refs #16796
    
• src/hg/hgVai/hgVai.c
  • lines changed 33, context: html, text, full: html, text
    Libified hgVai's code to find the latest snpNNN table so that other spots in the code could use it instead of hardcoding version numbers. Thx Matt for pointing out the hardcoding.
    refs #16777
    
• src/hg/hgc/gencodeClick.c
  • lines changed 4, context: html, text, full: html, text
    make wgEncodeGencodeExonSupport table optional, as it will not be available in back-mapped genomes
    
• src/hg/hgc/hgc.c
  • lines changed 10, context: html, text, full: html, text
    Libified hgVai's code to find the latest snpNNN table so that other spots in the code could use it instead of hardcoding version numbers. Thx Matt for pointing out the hardcoding.
    refs #16777
    
  • lines changed 7, context: html, text, full: html, text
    Fixes #16975. hgc: we need to only use nonVirtPosition in certain more-specific conditions.
    
  • lines changed 52, context: html, text, full: html, text
    Updated OMIM display, more linkouts, resolving merge conflict, refs #16796
    
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 4, context: html, text, full: html, text
    Adding hub template html refs #15816
    
• src/hg/htdocs/goldenPath/help/vcf.html
  • lines changed 37, context: html, text, full: html, text
    Adding a third example to VCF file format page about putting VCFs into hubs, Melissa Cline input from MLQ refs #16959
    
  • lines changed 1, context: html, text, full: html, text
    Small typo fix browswer --> browse refs #16959
    
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 62, context: html, text, full: html, text
    Adding announcement for Multi-region feature, refs #12242
    
  • lines changed 1, context: html, text, full: html, text
    Adding missing word to announcement. no redmine.
    
• src/hg/htdocs/indexNews.html
  • lines changed 108, context: html, text, full: html, text
    Adding announcement for Multi-region feature, refs #12242
    
  • lines changed 1, context: html, text, full: html, text
    Adding missing word to announcement. no redmine.
    
• src/hg/inc/hdb.h
  • lines changed 9, context: html, text, full: html, text
    Libified hgVai's code to find the latest snpNNN table so that other spots in the code could use it instead of hardcoding version numbers. Thx Matt for pointing out the hardcoding.
    refs #16777
    
• src/hg/inc/spDb.h
  • lines changed 1, context: html, text, full: html, text
    Fix to handle 10-digit UniProt IDs, see http://www.uniprot.org/help/accession_numbers
    
• src/hg/js/d3.dendrograms.js
  • lines changed 329, context: html, text, full: html, text
    Some minor changes, cleaning up the code a bit and adding in more comments where needed. Refs #16341
    
  • lines changed 521, context: html, text, full: html, text
    Commenting the code a bunch, refs #16341
    
• src/hg/js/makefile
  • lines changed 1, context: html, text, full: html, text
    Updating the /kent/src/hg/js makefile to include d3.dendrograms.js refs #16341
    
• src/hg/lib/chromGraphFactory.c
  • lines changed 19, context: html, text, full: html, text
    Libified hgVai's code to find the latest snpNNN table so that other spots in the code could use it instead of hardcoding version numbers. Thx Matt for pointing out the hardcoding.
    refs #16777
    
• src/hg/lib/gtexUi.c
  • lines changed 4, context: html, text, full: html, text
    1. Use max median score from gtexInfo table for max viewlimits guidance. 2. Fix placement of gender labels. refs #15645
    
• src/hg/lib/hdb.c
  • lines changed 42, context: html, text, full: html, text
    Libified hgVai's code to find the latest snpNNN table so that other spots in the code could use it instead of hardcoding version numbers. Thx Matt for pointing out the hardcoding.
    refs #16777
    
• src/hg/makeDb/doc/galVar1/initialBuild.txt
  • lines changed 86, context: html, text, full: html, text
    done with masking no redmine
    
• src/hg/makeDb/doc/hg19.txt
  • lines changed 44, context: html, text, full: html, text
    GENCODE V24lift37
    
• src/hg/makeDb/doc/hg38/hg38.txt
  • lines changed 5, context: html, text, full: html, text
    fixed documented error that keeps getting propigated with copy and paste
    
    fixed incorrect comment that keeps getting propigated forward
    
• src/hg/makeDb/doc/mm10.txt
  • lines changed 4, context: html, text, full: html, text
    fixed documented error that keeps getting propigated with copy and paste
    
    fixed incorrect comment that keeps getting propigated forward
    
• src/hg/makeDb/doc/uniProt/sp160229.txt
  • lines changed 69, context: html, text, full: html, text
    Makedoc for latest swissprot, refs #15315
    
• src/hg/makeDb/genbank/etc/align.dbs
  • lines changed 1, context: html, text, full: html, text
    take braNey1 off the genbank align and load lists
    
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 19, context: html, text, full: html, text
    Added galVar1 - Galeopterus variegatus - Malayan flying lemur ; no redmine
    
• src/hg/makeDb/genbank/etc/hgwdev.dbs
  • lines changed 1, context: html, text, full: html, text
    take braNey1 off the genbank align and load lists
    
• src/hg/makeDb/genbank/src/lib/gbGenome.c
  • lines changed 2, context: html, text, full: html, text
    Added galVar1 Galeopterus variegatus - Malayan flying lemur no redmine
    
• src/hg/makeDb/outside/gencode/gencodeLoad.mk
  • lines changed 46, context: html, text, full: html, text
    GENCODE V24lift37
    
• src/hg/makeDb/outside/hgGtexExonBed/hgGtexExonBed.c
  • lines changed 1, context: html, text, full: html, text
    Fix misspelling. refs #15645
    
• src/hg/makeDb/schema/all.joiner
  • lines changed 2, context: html, text, full: html, text
    Adding tablesIgnored entries for the tables in the Lens Patents track, refs #14486
    
  • lines changed 91, context: html, text, full: html, text
    GENCODE V24lift37
    
• src/hg/makeDb/trackDb/ebola/eboVir3/trackDb.ra
  • lines changed 13, context: html, text, full: html, text
    Ebola needed local overrides so patent tracks end up in the right group, refs #14486
    
• src/hg/makeDb/trackDb/est.new.html
  • lines changed 137, context: html, text, full: html, text
    get rid of weird duplication of genbank trackDb.ra entries
    
• src/hg/makeDb/trackDb/human/hg19/defaultPriority.ra
  • lines changed 1, context: html, text, full: html, text
    turn off intronEst in hg19 by default
    
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
  • lines changed 1, context: html, text, full: html, text
    GENCODE V24lift37
    
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV18.ra
  • lines changed 1, context: html, text, full: html, text
    GENCODE V24lift37
    
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV24lift37.html
  • lines changed 348, context: html, text, full: html, text
    added forgotten wgEncodeGencodeV24lift37 spec files
    
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV24lift37.ra
  • lines changed 272, context: html, text, full: html, text
    added forgotten wgEncodeGencodeV24lift37 spec files
    
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV24.ra
  • lines changed 2, context: html, text, full: html, text
    GENCODE V24lift37
    
• src/hg/makeDb/trackDb/patSeq.html
  • lines changed 5, context: html, text, full: html, text
    html wording change, refs #14486
    
  • lines changed 36, context: html, text, full: html, text
    Changes to Patent Lens track description page, refs #14486
    
  • lines changed 8, context: html, text, full: html, text
    Small changes to Lens Patents track description page to fit our conventions, refs #14486
    
  • lines changed 35, context: html, text, full: html, text
    Primairly white space changes to Lens Patents track description page. refs #14486
    
  • lines changed 3, context: html, text, full: html, text
    refs #14486: added comment why no features on chrM.
    
• src/hg/makeDb/trackDb/trackDb.genbank.new.ra
  • lines changed 231, context: html, text, full: html, text
    get rid of weird duplication of genbank trackDb.ra entries
    
• src/hg/makeDb/trackDb/trackDb.genbank.ra
  • lines changed 1, context: html, text, full: html, text
    get rid of weird duplication of genbank trackDb.ra entries
    
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    get rid of weird duplication of genbank trackDb.ra entries
    
• src/hg/protein/spDbAddVarSplice/spDbAddVarSplice.c
  • lines changed 2, context: html, text, full: html, text
    Fix to handle 10-digit UniProt IDs, see http://www.uniprot.org/help/accession_numbers
    
• src/hg/utils/automation/doDbSnp.pl
  • lines changed 6, context: html, text, full: html, text
    Removing unnecessary "optimization" that caused several thousand rs's to be lost.
    refs #16777 note 25
    
• src/hg/utils/otto/gwas/checkGwas.sh
  • lines changed 5, context: html, text, full: html, text
    Replaced Unicode handling in GWAS scripts with a call to iconv, refs #16925
    
• src/hg/utils/otto/gwas/gwasWrapper.sh
  • lines changed 1, context: html, text, full: html, text
    Replaced Unicode handling in GWAS scripts with a call to iconv, refs #16925
    
• src/hg/utils/otto/gwas/makefile
  • lines changed 2, context: html, text, full: html, text
    Replaced Unicode handling in GWAS scripts with a call to iconv, refs #16925
    
• src/hg/utils/otto/gwas/perlParser.pl
  • lines changed 20, context: html, text, full: html, text
    Replaced Unicode handling in GWAS scripts with a call to iconv, refs #16925
    
• src/inc/hacTree.h
  • lines changed 5, context: html, text, full: html, text
    Adding in a sibling comparison function to the multi threaded function, refs #16216
    
• src/lib/common.c
  • lines changed 2, context: html, text, full: html, text
    fix after code review, refs #16971
    
• src/lib/hacTree.c
  • lines changed 24, context: html, text, full: html, text
    Adding in a sibling comparison function to the multi threaded function, refs #16216
    
• src/utils/bigWigCluster/bigWigCluster.c
  • lines changed 1, context: html, text, full: html, text
    Changed the underlying library file and had to update this program. The program will run the same, now it passes an extra NULL into one of the library functions.
    
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    v330 preview1 refs #16963
    
  • lines changed 2, context: html, text, full: html, text
    v330 preview2
    
  • lines changed 4, context: html, text, full: html, text
    I made a mistake and ran preview2 too early. I am not trying to extend the system to use $somestageSubversion settings like .1 to extend the tag, and these new settings are defined in buildEnv.csh and used by tag scripts and git reports. Should work for preview and preview2 stages. Base stage works for git reports but does not yet handle _branch properly.
    
  • lines changed 1, context: html, text, full: html, text
    v330 preview2
    
• src/utils/qa/weeklybld/buildGitReports.csh
  • lines changed 6, context: html, text, full: html, text
    I made a mistake and ran preview2 too early. I am not trying to extend the system to use $somestageSubversion settings like .1 to extend the tag, and these new settings are defined in buildEnv.csh and used by tag scripts and git reports. Should work for preview and preview2 stages. Base stage works for git reports but does not yet handle _branch properly.
    
• src/utils/qa/weeklybld/tagNewBranch.csh
  • lines changed 10, context: html, text, full: html, text
    I made a mistake and ran preview2 too early. I am not trying to extend the system to use $somestageSubversion settings like .1 to extend the tag, and these new settings are defined in buildEnv.csh and used by tag scripts and git reports. Should work for preview and preview2 stages. Base stage works for git reports but does not yet handle _branch properly.
    
• src/utils/qa/weeklybld/tagPreview.csh
  • lines changed 1, context: html, text, full: html, text
    I made a mistake and ran preview2 too early. I am not trying to extend the system to use $somestageSubversion settings like .1 to extend the tag, and these new settings are defined in buildEnv.csh and used by tag scripts and git reports. Should work for preview and preview2 stages. Base stage works for git reports but does not yet handle _branch properly.
    
• src/utils/qa/weeklybld/tagPreview2.csh
  • lines changed 1, context: html, text, full: html, text
    I made a mistake and ran preview2 too early. I am not trying to extend the system to use $somestageSubversion settings like .1 to extend the tag, and these new settings are defined in buildEnv.csh and used by tag scripts and git reports. Should work for preview and preview2 stages. Base stage works for git reports but does not yet handle _branch properly.
    

• lines changed: 4633
• files changed: 87