All File Changes

v302_base to v303_preview (2014-06-30 to 2014-07-07) v303

• src/hg/hgGene/hgGene.c
  • lines changed 1, context: html, text, full: html, text
    hgGene was missing a call to setUdcCacheDir, so it was using /tmp/udcCachewhere it could have ownership conflicts with files left there by command-line
    programs etc.
    
• src/hg/hgTracks/factorSource.c
  • lines changed 17, context: html, text, full: html, text
    Suppress display of a motif for a TF peak whose highest-scoring motif lies outside the viewing window. refs #13318
  • lines changed 2, context: html, text, full: html, text
    Fixed SEGV in factorSourceLoad: track->items was dereferenced withouta NULL check. Do the NULL check ASAP so we don't even bother with
    all the filtering and joining setup if there are no items in window.
    
• src/hg/hgTracks/hgTracks.c
  • lines changed 1, context: html, text, full: html, text
    fix a crash if an assembly hub doesn't have a freezename. Bug reportedby MarkD
    
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 53, context: html, text, full: html, text
    Reworded a couple sentences in 6/19 news announcement. Fixed lines >100 chars (sorry -- should've been separate commit).
• src/hg/htdocs/indexNews.html
  • lines changed 40, context: html, text, full: html, text
    Reworded a couple sentences in 6/19 news announcement. Fixed missing subject line in archived news item. Added a Read More link to one of the staged announcements. Fixed lines >100 chars (sorry -- should've been separate commit).
• src/hg/lib/cart.c
  • lines changed 13, context: html, text, full: html, text
    Fixes #13530. Users reported that blank cookie values are coming in. Check for them and give appropriate warnings, debugging info, and response when parsing or writing cookie values for webIds.
• src/hg/lib/cartDb.c
  • lines changed 10, context: html, text, full: html, text
    Fixes #13530. Users reported that blank cookie values are coming in. Check for them and give appropriate warnings, debugging info, and response when parsing or writing cookie values for webIds.
• src/hg/lib/gpFx.c
  • lines changed 20, context: html, text, full: html, text
    Fixed two bugs in the way cdsBasesAdded was computed -- that causedsome strange functional assignments for "<DEL>" (large deletion).
    Also fixed a miscall of frameshift instead of stop_gained (from
    insertion) brought to my attention by GoldenHelix's comparison of VEP,
    Annovar and SnpEff: http://blog.goldenhelix.com/?p=2486
    
• src/hg/lib/hgFind.c
  • lines changed 3, context: html, text, full: html, text
    Ugh, c73b60407 introduced a bug: I assumed that if tdb->parent is non-NULL,tdb->parentName would be too -- nope, tdb->parentName is apparently only for
    children of superTracks, not children of views/composites.
    refs #13477
    
• src/hg/lib/variant.c
  • lines changed 1, context: html, text, full: html, text
    One more spot to convert from regular allocation to localmem.
• src/hg/makeDb/doc/encodeAwgHg19.txt
  • lines changed 42, context: html, text, full: html, text
    Wrap-up for QA. refs #13230
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeAwgDnaseMasterSites.release1.notes
  • lines changed 41, context: html, text, full: html, text
    Add notes file for QA. refs #13230
• src/hg/makeDb/hgLoadChain/hgLoadChain.c
  • lines changed 6, context: html, text, full: html, text
    fixup index length to be correct for chrom name sizes refs #13548
• src/hg/makeDb/trackDb/animalQtl.html
  • lines changed 4, context: html, text, full: html, text
    Edited journal links per code review (redmine #13534)
• src/hg/makeDb/trackDb/chicken/galGal2/ecoresTetraodon.html
  • lines changed 1, context: html, text, full: html, text
    Changes based on feedback from Code Review, refs #13533
• src/hg/makeDb/trackDb/drosophila/droYak2/description.html
  • lines changed 1, context: html, text, full: html, text
    Changes based on feedback from Code Review, refs #13533
• src/hg/makeDb/trackDb/fugu/fr2/gap.html
  • lines changed 1, context: html, text, full: html, text
    Changes based on feedback from Code Review, refs #13533
• src/hg/makeDb/trackDb/fugu/gap.html
  • lines changed 1, context: html, text, full: html, text
    Changes based on feedback from Code Review, refs #13533
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeAwgDnaseMasterSites.ra
  • lines changed 19, context: html, text, full: html, text
    Adding minimal metadata. refs #13230
  • lines changed 3, context: html, text, full: html, text
    Add m5sums to metadata. refs #13230
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
  • lines changed 1, context: html, text, full: html, text
    Reorg trackDb entry. refs #13230
• src/hg/makeDb/trackDb/human/hg19/wgEncodeAwg.ra
  • lines changed 16, context: html, text, full: html, text
    Retire obsolete version of new track. refs #13230
  • lines changed 2, context: html, text, full: html, text
    Adjust priority to appear with analysis tracks. refs #13230
  • lines changed 23, context: html, text, full: html, text
    Reorg trackDb entry. refs #13230
• src/hg/makeDb/trackDb/human/hg19/wgEncodeAwgDnaseMaster.html
  • lines changed 60, context: html, text, full: html, text
    Retire obsolete track description. refs #1320
• src/hg/makeDb/trackDb/human/hg19/wgEncodeAwgDnaseMasterSites.html
  • lines changed 12, context: html, text, full: html, text
    Add Credits section. refs #13230
• src/hg/makeDb/trackDb/human/hg19/wgEncodeAwgDnaseMasterSites.ra
  • lines changed 23, context: html, text, full: html, text
    Reorg trackDb entry. refs #13230
• src/hg/makeDb/trackDb/human/hg19/wgEncodeAwgSegmentation.html
  • lines changed 10, context: html, text, full: html, text
    Updating changes per code review feedback refs #13514 #13536
• src/hg/makeDb/trackDb/mouse/FaceBase24SampleTypesAvg.html
  • lines changed 35, context: html, text, full: html, text
    Changes to FaceBase track description page. Added full list of cell and embryo types, changed link to RMA normalizaiton paper, fixed up Bruce email, and added https to Facebase links. Most of changes to Methods section are white space changes. refs #12606 #13533
  • lines changed 2, context: html, text, full: html, text
    From code review, removing hyphens to make cell type naming consistent, refs #12606 #13533
• src/hg/makeDb/trackDb/mouse/mm10/defaultPriority.ra
  • lines changed 4, context: html, text, full: html, text
    Changed default priorities so UCSC Genes would appear first (redmine #7343)
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    Changing shortLabel for FaceBase track in both mm9,mm10. Adding liftOver emblem for FaceBase Track on mm10, refs #12606
• src/hg/makeDb/trackDb/mouse/trackDb.ra
  • lines changed 0, context: html, text, full: html, text
    Changing shortLabel for FaceBase track in both mm9,mm10. Adding liftOver emblem for FaceBase Track on mm10, refs #12606
• src/hg/makeDb/trackDb/platypus/ornAna1/description.html
  • lines changed 2, context: html, text, full: html, text
    Changes based on feedback from Code Review, refs #13533
• src/hg/makeDb/trackDb/platypus/ornAna1/gold.html
  • lines changed 2, context: html, text, full: html, text
    Changes based on feedback from Code Review, refs #13533
• src/hg/minIndexLength/makefile
  • lines changed 3, context: html, text, full: html, text
    to measure a database to find safe index length refs #13548
• src/hg/minIndexLength/minIndexLength.c
  • lines changed 41, context: html, text, full: html, text
    to measure a database to find safe index length refs #13548
• src/lib/vcf.c
  • lines changed 2, context: html, text, full: html, text
    Small bugfix: when reference allele had a padding base but alt allelewas symbolic, the first char was trimmed from the symbolic allele too, oops.
    
• src/utils/qa/weeklybld/doNewBranch.csh
  • lines changed 1, context: html, text, full: html, text
    return Ann to the email list for the victim list refs #13448

• lines changed: 522
• files changed: 40