File Changes for kent

v324_preview to v324_preview2 (2015-10-12 to 2015-10-19) v324

• src/hg/cirm/cdw/cdwChangeAccess/cdwChangeAccess.c
  • lines changed 12, context: html, text, full: html, text
    Making a meaningful usage message.
    
• src/hg/cirm/cdw/cdwGroupFile/cdwGroupFile.c
  • lines changed 4, context: html, text, full: html, text
    Making -dry option produce some output to stdout.
    
• src/hg/cirm/cdw/cdwMakeFileTags/cdwMakeFileTags.c
  • lines changed 9, context: html, text, full: html, text
    Dealing with strings longer than 255 characters in tag values.
    
• src/hg/cirm/cdw/cdwMakeValidFile/cdwMakeValidFile.c
  • lines changed 39, context: html, text, full: html, text
    Adding a basic validataor for tab separated files and applying it to validate kallisto_abundance
    
• src/hg/cirm/cdw/cdwSubmit/cdwSubmit.c
  • lines changed 2, context: html, text, full: html, text
    Adding kallisto_abundance format.
    
• src/hg/cirm/cdw/inc/cdwLib.h
  • lines changed 4, context: html, text, full: html, text
    Making this include a file it depends on.
    
• src/hg/cirm/cdw/lib/cdwValid.c
  • lines changed 11, context: html, text, full: html, text
    Adding eight new tags and a new SRA_ prefix for unchecked tags from the short read archive.
    
• src/hg/cirm/quakeLab/quakeBrainGeo1/meta.txt
  • lines changed 25, context: html, text, full: html, text
    Adding sub_tissue field from Spyro's spreadsheet.
    
• src/hg/makeDb/schema/dbSnoop/dbSnoop.c
  • lines changed 4, context: html, text, full: html, text
    Fixing kind of subtle bug in ordering of indexes in output.
    
• src/hg/oneShot/freen/freen.c
  • lines changed 26, context: html, text, full: html, text
    Seeing if an apostrophe in a printf format string adds commas at thousands millions, etd in big numbers in the C library the way it now does in bash. It does not yet work in C.
    
• src/inc/cda.h
  • lines changed 9, context: html, text, full: html, text
    Fixing copyright on some old essentially public domain files.
    
• src/inc/cheapcgi.h
  • lines changed 7, context: html, text, full: html, text
    Fixing copyright on some old essentially public domain files.
    
• src/inc/codebias.h
  • lines changed 6, context: html, text, full: html, text
    Fixing copyright on some old essentially public domain files.
    
• src/inc/crudeali.h
  • lines changed 6, context: html, text, full: html, text
    Fixing copyright on some old essentially public domain files.
    
• src/inc/ens.h
  • lines changed 6, context: html, text, full: html, text
    Fixing copyright on some old essentially public domain files.
    
• src/inc/flydna.h
  • lines changed 6, context: html, text, full: html, text
    Fixing copyright on some old essentially public domain files.
    
• src/inc/fof.h
  • lines changed 10, context: html, text, full: html, text
    Fixing copyright on some old essentially public domain files.
    
• src/inc/fuzzyFind.h
  • lines changed 5, context: html, text, full: html, text
    Fixing copyright on some old essentially public domain files.
    
• src/inc/gdf.h
  • lines changed 6, context: html, text, full: html, text
    Fixing copyright on some old essentially public domain files.
    
• src/inc/gff.h
  • lines changed 6, context: html, text, full: html, text
    Fixing copyright on some old essentially public domain files.
    
• src/inc/hgGene.h
  • lines changed 10, context: html, text, full: html, text
    Fixing copyright on some old essentially public domain files.
    
• src/inc/hgap.h
  • lines changed 6, context: html, text, full: html, text
    Fixing copyright on some old essentially public domain files.
    
• src/inc/hgdb.h
  • lines changed 6, context: html, text, full: html, text
    Fixing copyright on some old essentially public domain files.
    
• src/inc/hmmstats.h
  • lines changed 10, context: html, text, full: html, text
    Fixing copyright on some old essentially public domain files.
    
• src/inc/keys.h
  • lines changed 10, context: html, text, full: html, text
    Fixing copyright on some old essentially public domain files.
    
• src/inc/maDbRep.h
  • lines changed 10, context: html, text, full: html, text
    Fixing copyright on some old essentially public domain files.
    
• src/inc/maToFf.h
  • lines changed 10, context: html, text, full: html, text
    Fixing copyright on some old essentially public domain files.
    
• src/inc/memgfx.h
  • lines changed 9, context: html, text, full: html, text
    Fixing copyright on some old essentially public domain files.
    
• src/inc/nib.h
  • lines changed 10, context: html, text, full: html, text
    Fixing copyright on some old essentially public domain files.
    
• src/inc/nt4.h
  • lines changed 5, context: html, text, full: html, text
    Fixing copyright on some old essentially public domain files.
    
• src/inc/oldGff.h
  • lines changed 10, context: html, text, full: html, text
    Fixing copyright on some old essentially public domain files.
    
• src/inc/patSpace.h
  • lines changed 10, context: html, text, full: html, text
    Fixing copyright on some old essentially public domain files.
    
• src/inc/sig.h
  • lines changed 6, context: html, text, full: html, text
    Fixing copyright on some old essentially public domain files.
    
• src/inc/snof.h
  • lines changed 8, context: html, text, full: html, text
    Fixing copyright on some old essentially public domain files.
    
• src/inc/snofmake.h
  • lines changed 5, context: html, text, full: html, text
    Fixing copyright statement.
    
• src/inc/spaceSaver.h
  • lines changed 10, context: html, text, full: html, text
    Fixing copyright on some old essentially public domain files.
    
• src/inc/supStitch.h
  • lines changed 10, context: html, text, full: html, text
    Fixing copyright on some old essentially public domain files.
    
• src/inc/tagStorm.h
  • lines changed 6, context: html, text, full: html, text
    Adding tagStormIndexExtended.
    
• src/inc/trans3.h
  • lines changed 10, context: html, text, full: html, text
    Fixing copyright on some old essentially public domain files.
    
• src/inc/unfin.h
  • lines changed 6, context: html, text, full: html, text
    Fixing copyright on some old essentially public domain files.
    
• src/inc/wormdna.h
  • lines changed 6, context: html, text, full: html, text
    Fixing copyright on some old essentially public domain files.
    
• src/inc/xa.h
  • lines changed 6, context: html, text, full: html, text
    Fixing copyright on some old essentially public domain files.
    
• src/inc/xenalign.h
  • lines changed 6, context: html, text, full: html, text
    Fixing copyright on some old essentially public domain files.
    
• src/lib/portimpl.h
  • lines changed 6, context: html, text, full: html, text
    Fixing copyright on some old essentially public domain files.
    
• src/lib/rqlEval.c
  • lines changed 2, context: html, text, full: html, text
    Adding error message for evaluation non-integer strings as integers.
    
• src/lib/tagStorm.c
  • lines changed 20, context: html, text, full: html, text
    Adding tagStormIndexExtended.
    
• src/tagStorm/tagStormFromTab/tagStormFromTab.c
  • lines changed 164, context: html, text, full: html, text
    Revamping code so that fields that are not in lock step, but that are completely predictable based on key field, can be glommed into a stanza. Changing scoring of partitioning to get partial credit in these predictable but not lock step cases. It tends to result in less partitioning into deep nests of one line stanzas until the end.
    
  • lines changed 9, context: html, text, full: html, text
    Renaming stuff from Locked to Predictable to better reflect new context.
    
  • lines changed 21, context: html, text, full: html, text
    Improving commenting, removing some debugging code, and clamping a weight to be no more than 1.
    
  • lines changed 4, context: html, text, full: html, text
    Turning uglyfs to verbose-2's
    
• src/tagStorm/tagStormJoinTab/tagStormJoinTab.c
  • lines changed 1, context: html, text, full: html, text
    Making it so that it only joins to actual stanza with ID, not child stanzas as well.