braney: changes by commit

review to branch (2009-09-22 to 2009-09-29) v216

• move Gis Pet to variation
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.530 - lines changed: 1, context: html, text, full: html, text
• make barb colors be the same color as the line and box.
  • src/hg/hgTracks/simpleTracks.c 1.105 - lines changed: 1, context: html, text, full: html, text
• drop all the old Hannon lab stuff so I can start over
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.532 - lines changed: 849, context: html, text, full: html, text
• new Hannon lab short RNA data
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.534 - lines changed: 342, context: html, text, full: html, text
• shortened and editing some labels for Affy/CSHL exons
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.535 - lines changed: 22, context: html, text, full: html, text
• Hannon lab short rna edits
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.537 - lines changed: 159, context: html, text, full: html, text
• add a few files to the library (yay! it's even bigger now ;-)
  • src/hg/lib/makefile 1.397 - lines changed: 2, context: html, text, full: html, text
• a header file for bed12 plus a pair of sequences
  • src/hg/inc/bed12wSeq.h 1.1 - lines changed: 96, context: html, text, full: html, text
• bed12 plus a couple of sequences at the end
  • src/hg/lib/bed12wSeq.as 1.1 - lines changed: 18, context: html, text, full: html, text
  • src/hg/lib/bed12wSeq.c 1.1 - lines changed: 294, context: html, text, full: html, text
  • src/hg/lib/bed12wSeq.sql 1.1 - lines changed: 24, context: html, text, full: html, text
• a program to convert a pairedTag file into a bed12 with a couple of sequences
  • src/hg/encode/converters/pairedTagToBed12/makefile 1.1 - lines changed: 18, context: html, text, full: html, text
  • src/hg/encode/converters/pairedTagToBed12/pairedTagToBed12.c 1.1 - lines changed: 83, context: html, text, full: html, text
• a program to convert a tagAlign file into a bed12 with a couple of sequences
  • src/hg/encode/converters/tagToBed12/makefile 1.1 - lines changed: 18, context: html, text, full: html, text
  • src/hg/encode/converters/tagToBed12/tagToBed12.c 1.1 - lines changed: 82, context: html, text, full: html, text
• reload wiggles for Hannon lab
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.541 - lines changed: 18, context: html, text, full: html, text
• added -bed12, -max, and -zero options. Made default counting unit size and unsigned long
  • src/hg/bedItemOverlapCount/bedItemOverlapCount.c 1.15 - lines changed: 122, context: html, text, full: html, text
• oops, default should be to use 32 bits
  • src/hg/bedItemOverlapCount/bedItemOverlapCount.c 1.16 - lines changed: 1, context: html, text, full: html, text
• add LogSignal tracks for Hannon lab
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.544 - lines changed: 181, context: html, text, full: html, text
• add bounds output
  • src/hg/bedItemOverlapCount/bedItemOverlapCount.c 1.17 - lines changed: 17, context: html, text, full: html, text
• added a couple of options to facilitate use in ENCODE pipeline
  • src/hg/bedSplitOnChrom/bedSplitOnChrom.c 1.2 - lines changed: 25, context: html, text, full: html, text
• add a little optimization to avoid hash search on each line
  • src/hg/bedSplitOnChrom/bedSplitOnChrom.c 1.3 - lines changed: 14, context: html, text, full: html, text