All File Changes

v328_preview to v328_preview2 (2016-01-18 to 2016-01-25) v328

• src/hg/cirm/cdw/wrangle/kallistoToMatrix/kallistoToMatrix
  • lines changed 67, context: html, text, full: html, text
    making kallistoToMatrix always create a gene-TPM output file, refs #16182
    
• src/hg/getRna/getRna.c
  • lines changed 107, context: html, text, full: html, text
    added ability to request specific version in getRna and generate error if that version isn't available
    
• src/hg/hgGene/hgGeneData/section.ra
  • lines changed 2, context: html, text, full: html, text
    Minor edit, Malacards to MalaCards. refs #14417
    
• src/hg/hgGene/malacards.c
  • lines changed 1, context: html, text, full: html, text
    Minor edit, Malacards to MalaCards. refs #14417
    
• src/hg/hgTracks/simpleTracks.c
  • lines changed 5, context: html, text, full: html, text
    Fixes #16700. Fixes broken limitVisibility. pack routine now returns 0 instead of 1 when data is still loading which then delays setting limitedVis until it is ready.
    
• src/hg/hgc/hgc.c
  • lines changed 1, context: html, text, full: html, text
    special URL links for ce11 Ensembl transcripts refs #15209
    
  • lines changed 3, context: html, text, full: html, text
    same special handling for ce11 as was for ce6 refs #15209
    
• src/hg/htdocs/goldenPath/help/multiRegionHelp.html
  • lines changed 210, context: html, text, full: html, text
    Did an editing and polishing pass on this doc. Need to take one more look at it, but that can happen after the release. There are some broken links that may be due to uncommitted files (noted in redmine ticket). refs #16565
    
• src/hg/htdocs/goldenPath/help/net.html
  • lines changed 0, context: html, text, full: html, text
    minor edit from code review. refs# 14581
    
  • lines changed 2, context: html, text, full: html, text
    Minor edit for code review. refs# 125175
    
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 32, context: html, text, full: html, text
    Adding announcement for mm10 snp142 track, refs #15934
    
• src/hg/htdocs/indexNews.html
  • lines changed 84, context: html, text, full: html, text
    Adding announcement for mm10 snp142 track, refs #15934
    
• src/hg/htdocs/training/index.html
  • lines changed 45, context: html, text, full: html, text
    dropped completed NYC workshop, added next couple
    
• src/hg/lib/bigPsl.c
  • lines changed 1, context: html, text, full: html, text
    fixed problem with bigPslToPsl not computing insert counts. Base on previous work that was deemed a waste of time
    
• src/hg/lib/genePred.c
  • lines changed 2, context: html, text, full: html, text
    correct option check for added version genepred ids
    
• src/hg/makeDb/doc/ce11/initialBuild.txt
  • lines changed 24, context: html, text, full: html, text
    rerun genbank and add blatServer refs #15209
    
• src/hg/makeDb/doc/hg38/gbffToCds.pl
  • lines changed 86, context: html, text, full: html, text
    document NCBI RefSeq gene track construction refs #13673
    
• src/hg/makeDb/doc/hg38/gffToIx.pl
  • lines changed 243, context: html, text, full: html, text
    document NCBI RefSeq gene track construction refs #13673
    
• src/hg/makeDb/doc/hg38/ncbiRefSeq.txt
  • lines changed 135, context: html, text, full: html, text
    document NCBI RefSeq gene track construction refs #13673
    
  • lines changed 2, context: html, text, full: html, text
    corrected typo errors refs #13673
    
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 4, context: html, text, full: html, text
    turn on more genbank for ce11 refs #15209
    
• src/hg/makeDb/schema/all.joiner
  • lines changed 1, context: html, text, full: html, text
    adding MicMur2 to the chain list refs #15292
    
• src/hg/makeDb/trackDb/drosophila/droAna1/description.html
  • lines changed 2, context: html, text, full: html, text
    Removing bad url, no Redmine.
    
• src/hg/makeDb/trackDb/human/hg18/wgEncodeChromatinMap.html
  • lines changed 1, context: html, text, full: html, text
    Fixing broken urls, no Redmine
    
  • lines changed 1, context: html, text, full: html, text
    Minor url edit, no Redmine
    
• src/hg/makeDb/trackDb/human/hg18/wgEncodeChromatinMapRelease2.html
  • lines changed 1, context: html, text, full: html, text
    Fixing broken urls, no Redmine
    
  • lines changed 1, context: html, text, full: html, text
    Minor url edit, no Redmine
    
• src/hg/makeDb/trackDb/human/hg19/wgEncodeDukeAffyExon.release3.html
  • lines changed 2, context: html, text, full: html, text
    Fixing broken urls, no Redmine
    
  • lines changed 2, context: html, text, full: html, text
    Minor url edit, no Redmine
    
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromChip.release2.html
  • lines changed 1, context: html, text, full: html, text
    Fixing broken urls, no Redmine
    
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromDnase.release2.html
  • lines changed 1, context: html, text, full: html, text
    Fixing broken urls, no Redmine
    
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromDnase.release3.html
  • lines changed 1, context: html, text, full: html, text
    Fixing broken urls, no Redmine
    
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromFaire.release2.html
  • lines changed 1, context: html, text, full: html, text
    Fixing broken urls, no Redmine
    
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromSynth.release2.html
  • lines changed 1, context: html, text, full: html, text
    Fixing broken urls, no Redmine
    
• src/hg/makeDb/trackDb/human/hg38/primateChainNet.html
  • lines changed 1, context: html, text, full: html, text
    Escaping quotes on primate chain net desc page, refs #15292
    
• src/hg/makeDb/trackDb/mouse/mm10/defaultPriority.ra
  • lines changed 2, context: html, text, full: html, text
    Changing visibility and priority settings for mm10 snp138 ahead of snp142 release, refs #15934
    
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    Changing visibility and priority settings for mm10 snp138 ahead of snp142 release, refs #15934
    
• src/hg/makeDb/trackDb/mouseLemur/micMur2/trackDb.chainNet.ra
  • lines changed 9, context: html, text, full: html, text
    Fixing matrix for micMur2 chain/nets, refs #15292
    
• src/hg/makeDb/trackDb/mouseLemur/micMur2/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    Fixing matrix for micMur2 chain/nets, refs #15292
    
• src/hg/makeDb/trackDb/tarsier/tarSyr2/trackDb.chainNet.ra
  • lines changed 5, context: html, text, full: html, text
    Updating matrix for micMur2, refs #15292
    
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 104, context: html, text, full: html, text
    testing NCBI RefSeq track refs #13673
    
• src/hg/makeDb/trackDb/worm/ce11/trackDb.26way.ra
  • lines changed 4, context: html, text, full: html, text
    Changing labels for ce11 conservation tracks, refs #15209
    
• src/hg/utils/automation/grcParseGff.pl
  • lines changed 44, context: html, text, full: html, text
    current parsing of *_issues.gff incident database refs #16660
    
• src/hg/utils/automation/grcRunIncidentUpdate.sh
  • lines changed 50, context: html, text, full: html, text
    up to date with current scripts refs #16660
    
• src/hg/utils/automation/grcUpdate.sh
  • lines changed 5, context: html, text, full: html, text
    up to date with current scripts refs #16660
    
• src/hg/utils/otto/omim/omimUploadWrapper.sh
  • lines changed 1, context: html, text, full: html, text
    Updating recipients list for OMIM otto build
    
• src/hg/utils/otto/omim/omimWrapper.sh
  • lines changed 1, context: html, text, full: html, text
    Updating recipients list for OMIM otto build
    
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    v328 preview2 refs #16669
    

• lines changed: 1304
• files changed: 48