Commits for kent

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

• 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.
  
  • src/tagStorm/tagStormFromTab/tagStormFromTab.c - lines changed 164, context: html, text, full: html, text
• Renaming stuff from Locked to Predictable to better reflect new context.
  
  • src/tagStorm/tagStormFromTab/tagStormFromTab.c - lines changed 9, context: html, text, full: html, text
• Improving commenting, removing some debugging code, and clamping a weight to be no more than 1.
  
  • src/tagStorm/tagStormFromTab/tagStormFromTab.c - lines changed 21, context: html, text, full: html, text
• Turning uglyfs to verbose-2's
  
  • src/tagStorm/tagStormFromTab/tagStormFromTab.c - lines changed 4, 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/cdwMakeValidFile/cdwMakeValidFile.c - lines changed 39, context: html, text, full: html, text
• Making this include a file it depends on.
  
  • src/hg/cirm/cdw/inc/cdwLib.h - lines changed 4, context: html, text, full: html, text
• Fixing kind of subtle bug in ordering of indexes in output.
  
  • src/hg/makeDb/schema/dbSnoop/dbSnoop.c - lines changed 4, context: html, text, full: html, text
• Fixing copyright on some old essentially public domain files.
  
  • src/inc/cda.h - lines changed 9, context: html, text, full: html, text
  • src/inc/cheapcgi.h - lines changed 7, context: html, text, full: html, text
  • src/inc/codebias.h - lines changed 6, context: html, text, full: html, text
  • src/inc/crudeali.h - lines changed 6, context: html, text, full: html, text
  • src/inc/ens.h - lines changed 6, context: html, text, full: html, text
  • src/inc/flydna.h - lines changed 6, context: html, text, full: html, text
  • src/inc/fof.h - lines changed 10, context: html, text, full: html, text
  • src/inc/fuzzyFind.h - lines changed 5, context: html, text, full: html, text
  • src/inc/gdf.h - lines changed 6, context: html, text, full: html, text
  • src/inc/gff.h - lines changed 6, context: html, text, full: html, text
  • src/inc/hgGene.h - lines changed 10, context: html, text, full: html, text
  • src/inc/hgap.h - lines changed 6, context: html, text, full: html, text
  • src/inc/hgdb.h - lines changed 6, context: html, text, full: html, text
  • src/inc/hmmstats.h - lines changed 10, context: html, text, full: html, text
  • src/inc/keys.h - lines changed 10, context: html, text, full: html, text
  • src/inc/maDbRep.h - lines changed 10, context: html, text, full: html, text
  • src/inc/maToFf.h - lines changed 10, context: html, text, full: html, text
  • src/inc/memgfx.h - lines changed 9, context: html, text, full: html, text
  • src/inc/nib.h - lines changed 10, context: html, text, full: html, text
  • src/inc/nt4.h - lines changed 5, context: html, text, full: html, text
  • src/inc/oldGff.h - lines changed 10, context: html, text, full: html, text
  • src/inc/patSpace.h - lines changed 10, context: html, text, full: html, text
  • src/inc/sig.h - lines changed 6, context: html, text, full: html, text
  • src/inc/snof.h - lines changed 8, context: html, text, full: html, text
  • src/inc/spaceSaver.h - lines changed 10, context: html, text, full: html, text
  • src/inc/supStitch.h - lines changed 10, context: html, text, full: html, text
  • src/inc/trans3.h - lines changed 10, context: html, text, full: html, text
  • src/inc/unfin.h - lines changed 6, context: html, text, full: html, text
  • src/inc/wormdna.h - lines changed 6, context: html, text, full: html, text
  • src/inc/xa.h - lines changed 6, context: html, text, full: html, text
  • src/inc/xenalign.h - lines changed 6, context: html, text, full: html, text
  • src/lib/portimpl.h - lines changed 6, context: html, text, full: html, text
• Fixing copyright statement.
  
  • src/inc/snofmake.h - lines changed 5, context: html, text, full: html, text
• Adding tagStormIndexExtended.
  
  • src/inc/tagStorm.h - lines changed 6, context: html, text, full: html, text
  • src/lib/tagStorm.c - lines changed 20, context: html, text, full: html, text
• Adding error message for evaluation non-integer strings as integers.
  
  • src/lib/rqlEval.c - lines changed 2, context: html, text, full: html, text
• Making it so that it only joins to actual stanza with ID, not child stanzas as well.
  
  • src/tagStorm/tagStormJoinTab/tagStormJoinTab.c - lines changed 1, 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/hg/oneShot/freen/freen.c - lines changed 26, context: html, text, full: html, text
• Adding sub_tissue field from Spyro's spreadsheet.
  
  • src/hg/cirm/quakeLab/quakeBrainGeo1/meta.txt - lines changed 25, 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/cdw/lib/cdwValid.c - lines changed 11, context: html, text, full: html, text
• Making a meaningful usage message.
  
  • src/hg/cirm/cdw/cdwChangeAccess/cdwChangeAccess.c - lines changed 12, context: html, text, full: html, text
• Making -dry option produce some output to stdout.
  
  • src/hg/cirm/cdw/cdwGroupFile/cdwGroupFile.c - lines changed 4, context: html, text, full: html, text
• Dealing with strings longer than 255 characters in tag values.
  
  • src/hg/cirm/cdw/cdwMakeFileTags/cdwMakeFileTags.c - lines changed 9, context: html, text, full: html, text
• Adding kallisto_abundance format.
  
  • src/hg/cirm/cdw/cdwSubmit/cdwSubmit.c - lines changed 2, context: html, text, full: html, text