Commits for kent

v313_preview to v313_preview2 (2015-02-23 to 2015-03-02) v313

• Doing a better job of prepping vcf files
  
  • src/hg/cirm/cdw/cdwMakeTrackViz/cdwMakeTrackViz.c - lines changed 6, context: html, text, full: html, text
• Expanding size fields can take in browse tracks table. Bumping version.
  
  • src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c - lines changed 15, context: html, text, full: html, text
• Changing to case-ignoring sort since that's the usual in a database and we're mixing database and local order.
  
  • src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c - lines changed 4, context: html, text, full: html, text
• A new module for tables on the web mostly.
  
  • src/hg/inc/tablesTables.h - lines changed 12, context: html, text, full: html, text
  • src/hg/lib/tablesTables.c - lines changed 27, context: html, text, full: html, text
• Refactoring. Moving functions to library modules. Breaking up some larger functions.
  
  • src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c - lines changed 225, context: html, text, full: html, text
• More large function break-apart.
  
  • src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c - lines changed 69, context: html, text, full: html, text
• MOstly commenting and renaming.
  
  • src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c - lines changed 28, context: html, text, full: html, text
• Harmonized order of parameters to two show tables routines and bumped version number.
  
  • src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c - lines changed 20, context: html, text, full: html, text
• Adding several routines that work across a column into library including one to see if column is entirely numeric, another to figure out how wide it is, and a third to sort on a column.
  
  • src/inc/fieldedTable.h - lines changed 9, context: html, text, full: html, text
  • src/lib/fieldedTable.c - lines changed 98, context: html, text, full: html, text
• Added functions to get all fields associated with a sqlResult as a slName list or as an array of char *'s.
  
  • src/hg/inc/jksql.h - lines changed 9, context: html, text, full: html, text
  • src/hg/lib/jksql.c - lines changed 26, context: html, text, full: html, text
• Adding a ton of useful web table handling stuff from cdwWebBrowse.c to hg/lib/tablesTables.c and it's header.
  
  • src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c - lines changed 343, context: html, text, full: html, text
  • src/hg/inc/tablesTables.h - lines changed 37, context: html, text, full: html, text
  • src/hg/lib/tablesTables.c - lines changed 338, context: html, text, full: html, text
• Adding new tablesTables module.
  
  • src/hg/lib/makefile - lines changed 1, context: html, text, full: html, text
• Added a little more explanitory text. Added enriched_in column.
  
  • src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c - lines changed 9, context: html, text, full: html, text
• Wrangle tool to help create inputs.txt for baldwin lab submission.
  
  • src/hg/cirm/cdw/wrangle/cdwWrangleIsaacInput/cdwWrangleIsaacInput.c - lines changed 93, context: html, text, full: html, text
  • src/hg/cirm/cdw/wrangle/cdwWrangleIsaacInput/makefile - lines changed 4, context: html, text, full: html, text
• Utility to gather stats on vcf files seems to work.
  
  • src/hg/cirm/cdw/utils/cdwVcfStats/cdwVcfStats.c - lines changed 245, context: html, text, full: html, text
  • src/hg/cirm/cdw/utils/cdwVcfStats/makefile - lines changed 4, context: html, text, full: html, text
• Rmoving snpPassCount
  
  • src/hg/cirm/cdw/utils/cdwVcfStats/cdwVcfStats.c - lines changed 6, context: html, text, full: html, text
• Adding context parameter to wraps. Minor polish here and there.
  
  • src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c - lines changed 180, context: html, text, full: html, text
• Adding context parameter to wraps. Minor polish here and there.
  
  • src/hg/inc/tablesTables.h - lines changed 10, context: html, text, full: html, text
  • src/hg/lib/tablesTables.c - lines changed 12, context: html, text, full: html, text
• Removing stray '=' in ra output. Counting depth for record rather than genotype.
  
  • src/hg/cirm/cdw/utils/cdwVcfStats/cdwVcfStats.c - lines changed 27, context: html, text, full: html, text
• Adding cdwVcfFileFromRa auto-generated parser to help process output of cdwVcfStats.
  
  • src/hg/cirm/cdw/inc/cdwVcfFileFromRa.h - lines changed 18, context: html, text, full: html, text
  • src/hg/cirm/cdw/lib/cdwVcfFileFromRa.c - lines changed 261, context: html, text, full: html, text
  • src/hg/cirm/cdw/lib/makefile - lines changed 1, context: html, text, full: html, text
• Adding cdwVcfFile table.
  
  • src/hg/cirm/cdw/inc/cdw.h - lines changed 90, context: html, text, full: html, text
  • src/hg/cirm/cdw/lib/cdw.as - lines changed 30, context: html, text, full: html, text
  • src/hg/cirm/cdw/lib/cdw.c - lines changed 258, context: html, text, full: html, text
  • src/hg/cirm/cdw/lib/cdw.sql - lines changed 32, context: html, text, full: html, text
• Allowing chrom fields in metadata.
  
  • src/hg/cirm/cdw/lib/cdwValid.c - lines changed 1, context: html, text, full: html, text
• Integrating VCF file statistics into system.
  
  • src/hg/cirm/cdw/inc/cdwLib.h - lines changed 8, context: html, text, full: html, text
  • src/hg/cirm/cdw/lib/cdwLib.c - lines changed 51, context: html, text, full: html, text
• Doing enrichments on VCF files.
  
  • src/hg/cirm/cdw/cdwMakeEnrichments/cdwMakeEnrichments.c - lines changed 3, context: html, text, full: html, text
• Adding viz for narrowPeak and broadPeak files.
  
  • src/hg/cirm/cdw/cdwMakeTrackViz/cdwMakeTrackViz.c - lines changed 8, context: html, text, full: html, text
• Improving handling of VCF files, delegating most of work to cdwVcfStats. Adding -redo command line option.
  
  • src/hg/cirm/cdw/cdwMakeValidFile/cdwMakeValidFile.c - lines changed 43, context: html, text, full: html, text
• Renaming -format option to -out option to be more consistent with other utilities.
  
  • src/hg/cirm/cdw/cdwQuery/cdwQuery.c - lines changed 6, context: html, text, full: html, text
• Adding cdwVcfFile and cdwTrackViz to list of tables things get ripped out of.
  
  • src/hg/cirm/cdw/cdwReallyRemoveFiles/cdwReallyRemoveFiles.c - lines changed 4, context: html, text, full: html, text
• Ifdefing out some currently unused code.
  
  • src/hg/cirm/cdw/cdwSubmit/cdwSubmit.c - lines changed 4, context: html, text, full: html, text
• Making time out same as genome browser's menu time out.
  
  • src/hg/cirm/cdw/cdwWebBrowse/cdwNavBar.html - lines changed 1, context: html, text, full: html, text