File Changes for kent

v321_preview to v321_preview2 (2015-08-10 to 2015-08-17) v321

• src/blat/version.doc
  • lines changed 4, context: html, text, full: html, text
    Bumping version number
    
• src/hg/cirm/cdw/cdwAddStep/cdwAddStep.c
  • lines changed 46, context: html, text, full: html, text
    Command line utility to load a cdwStepDef.
    
• src/hg/cirm/cdw/cdwAddStep/makefile
  • lines changed 4, context: html, text, full: html, text
    Command line utility to load a cdwStepDef.
    
• src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c
  • lines changed 21, context: html, text, full: html, text
    Changing image on main page and bumping version number. Adding color picker widget to test page.
    
• src/hg/cirm/cdw/inc/cdwStep.h
  • lines changed 288, context: html, text, full: html, text
    Starting to make file relationship tracker.
    
• src/hg/cirm/cdw/lib/cdwStep.as
  • lines changed 38, context: html, text, full: html, text
    Starting to make file relationship tracker.
    
• src/hg/cirm/cdw/lib/cdwStep.c
  • lines changed 640, context: html, text, full: html, text
    Starting to make file relationship tracker.
    
• src/hg/cirm/cdw/lib/cdwStep.sql
  • lines changed 47, context: html, text, full: html, text
    Starting to make file relationship tracker.
    
• src/hg/cirm/cdw/lib/cdwValid.c
  • lines changed 4, context: html, text, full: html, text
    Making it so that all tags starting with 'GEO_' are allowed. Also added cell_type, submission_date, and update_date to the allowed tags.
    
• src/hg/cirm/cdw/lib/makefile
  • lines changed 2, context: html, text, full: html, text
    Starting to make file relationship tracker.
    
• src/hg/cirm/cdw/oneShot/cdwSnyderomeStepLink/cdwSnyderomeStepLink.c
  • lines changed 139, context: html, text, full: html, text
    Program that helps load Snyderome file graph seems to work for WGS data.
    
  • lines changed 139, context: html, text, full: html, text
    Moving from oneShot to wrangling directory
    
• src/hg/cirm/cdw/oneShot/cdwSnyderomeStepLink/makefile
  • lines changed 4, context: html, text, full: html, text
    Program that helps load Snyderome file graph seems to work for WGS data.
    
  • lines changed 4, context: html, text, full: html, text
    Moving from oneShot to wrangling directory
    
• src/hg/cirm/cdw/wrangle/cdwSnyderomeStepLink/cdwSnyderomeStepLink.c
  • lines changed 139, context: html, text, full: html, text
    Moving from oneShot to wrangling directory
    
• src/hg/cirm/cdw/wrangle/cdwSnyderomeStepLink/makefile
  • lines changed 4, context: html, text, full: html, text
    Moving from oneShot to wrangling directory
    
• src/hg/cirm/quakeLab/quakeBrainGeo1/manifest.txt
  • lines changed 933, context: html, text, full: html, text
    Checking in program generated manifest.
    
  • lines changed 1, context: html, text, full: html, text
    Adding # to first line
    
• src/hg/cirm/quakeLab/quakeBrainGeo1/meta.txt
  • lines changed 3944, context: html, text, full: html, text
    Initial cut of quake brain PNAS paper metadata.
    
  • lines changed 544, context: html, text, full: html, text
    Adding cell_type field, access field, and starting to unpack age-related fields from GEO tag.
    
  • lines changed 42, context: html, text, full: html, text
    Unpacking GEO_Sample_age into age/age-units/life_stage fields
    
  • lines changed 89, context: html, text, full: html, text
    Removing extranious third level GEO_Sample_c1_chip_id tag
    
  • lines changed 22, context: html, text, full: html, text
    Removing a bunch of uninformative or incorrect GEO fields.
    
  • lines changed 36, context: html, text, full: html, text
    Adding donor and cell_count tag. Reworking body_part tag to be at finer level. Getting rid of some GEO tags that contained no new info.
    
  • lines changed 434, context: html, text, full: html, text
    Removing now redundand GEO_Sample_cell_type.
    
  • lines changed 16, context: html, text, full: html, text
    Fixed age_units/age_unit typo
    
  • lines changed 1, context: html, text, full: html, text
    Adding data_set_id tag
    
• src/hg/cirm/quakeLab/quakeBrainGeo1/quakeRnaPipeline2.txt
  • lines changed 1, context: html, text, full: html, text
    First cut of the pipeline description.
    
• src/hg/das/das.c
  • lines changed 8, context: html, text, full: html, text
    Making help text not appear as XML to the browser.
    
  • lines changed 14, context: html, text, full: html, text
    Fixing crash on fetching ctgPos2 features.
    
• src/hg/htdocs/style/makefile
  • lines changed 2, context: html, text, full: html, text
    Adding style to support a color picker jquery widget.
    
• src/hg/js/makefile
  • lines changed 4, context: html, text, full: html, text
    Adding d3pie.js 3rd party module for current CIRM use, and colorPicker in anticipation of future use.
    
  • lines changed 5, context: html, text, full: html, text
    Fixing simple merge conflict.
    
• src/inc/genoFind.h
  • lines changed 1, context: html, text, full: html, text
    Bumping version number
    
• src/inc/jsonWrite.h
  • lines changed 12, context: html, text, full: html, text
    Improving opening module level comment.
    
• src/inc/tagStorm.h
  • lines changed 6, context: html, text, full: html, text
    Improving documentation a little.
    
• src/isPcr/isPcr/tests/input/in.fa
  • lines changed 2001, context: html, text, full: html, text
    Rearranging test directory as we add more.
    
• src/isPcr/isPcr/tests/input/in.primers
  • lines changed 1, context: html, text, full: html, text
    Rearranging test directory as we add more.
    
• src/isPcr/isPcr/tests/input/testFlip.in
  • lines changed 1, context: html, text, full: html, text
    Rearranging test directory as we add more.
    
• src/isPcr/isPcr/tests/simple/in.fa
  • lines changed 2001, context: html, text, full: html, text
    Rearranging test directory as we add more.
    
• src/isPcr/isPcr/tests/simple/in.primers
  • lines changed 1, context: html, text, full: html, text
    Rearranging test directory as we add more.
    
• src/isPcr/isPcr/tests/simple/testFlip.in
  • lines changed 1, context: html, text, full: html, text
    Rearranging test directory as we add more.
    
• src/jkOwnLib/ffSeedExtend.c
  • lines changed 22, context: html, text, full: html, text
    Removing some unused code.
    
• src/jkOwnLib/gfBlatLib.c
  • lines changed 2, context: html, text, full: html, text
    Fixing fastMap bogus double-sided gaps redmine #15317
    
• src/jkOwnLib/gfPcrLib.c
  • lines changed 9, context: html, text, full: html, text
    Think I fixed #15643
    
• src/makefile
  • lines changed 2, context: html, text, full: html, text
    Removing some encode3 stuff from build.
    
• src/tagStorm/tagStormFromTab/tagStormFromTab.c
  • lines changed 72, context: html, text, full: html, text
    Adding div option.