braney: changes by commit

branch to review (2009-09-02 to 2009-09-09) v214

• fixed bug where replicate 2 was labeled as replicate 1
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.506 - lines changed: 1, context: html, text, full: html, text
• wgEncodeGisRnaSeqAlignmentsK562Cytosol
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.507 - lines changed: 26, context: html, text, full: html, text
• add validateFiles command line
  • src/hg/encode/DAFs/GisDnaPet.daf 1.4 - lines changed: 2, context: html, text, full: html, text
• ln to right place with bigBed files
  • src/hg/encode/encodeLoad/doEncodeLoad.pl 1.70 - lines changed: 1, context: html, text, full: html, text
• if there's no wiggle on a chrom, just assume minSpan is 1 since we won't end up using this value anyway. TIME TO GET RID OF THESE WIGGLES!!
  • src/hg/lib/wiggleUtils.c 1.55 - lines changed: 3, context: html, text, full: html, text
• add encode/validateFiles to utils. THis probably should be part of something ENCODE specific (or maybe not).
  • src/hg/makefile 1.153 - lines changed: 1, context: html, text, full: html, text
• always include 0 option
  • src/hg/lib/hui.c 1.235 - lines changed: 19, context: html, text, full: html, text
  • src/hg/lib/wiggleCart.c 1.21 - lines changed: 21, context: html, text, full: html, text
• always include 0 logic
  • src/hg/hgTracks/wigCommon.h 1.7 - lines changed: 2, context: html, text, full: html, text
  • src/hg/hgTracks/wigTrack.c 1.92 - lines changed: 10, context: html, text, full: html, text
• add is alwaysZero
  • src/hg/inc/hui.h 1.137 - lines changed: 9, context: html, text, full: html, text
  • src/hg/inc/wiggle.h 1.86 - lines changed: 7, context: html, text, full: html, text
• get the right kind of bed in there
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.513 - lines changed: 2, context: html, text, full: html, text