File Changes for kent

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

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