tdreszer: changes by file

branch to review (2009-12-01 to 2009-12-09) v221

• src/hg/encode/DAFs/HAIBChIPseq.daf
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Added protocol and treatment terms
• src/hg/encode/DAFs/HAIBChIPseqExample.ddf
  • 1.1 lines changed: 9, context: html, text, full: html, text
    Example with protocol and treatment
• src/hg/encode/encodeValidate/doEncodeValidate.pl
  • 1.207 lines changed: 1, context: html, text, full: html, text
    Added protocol as another term
• src/hg/encode/encodeValidate/config/cv.ra
  • 1.152 lines changed: 55, context: html, text, full: html, text
    Added some treatments and protocols for HAIB
  • 1.151 lines changed: 44, context: html, text, full: html, text
    Switched Gliobla and Medullo
  • 1.149 lines changed: 12, context: html, text, full: html, text
    Renamed 6 cell lines by request from Greg Crawford
• src/hg/encode/encodeValidate/config/fields.ra
  • 1.23 lines changed: 5, context: html, text, full: html, text
    Added protocol for HAIB
• src/hg/hgTracks/config.c
  • 1.87 lines changed: 17, context: html, text, full: html, text
    Created static variable advancedJsEnabled to avoid excessive calls to look it up
• src/hg/hgTracks/cytoBandTrack.c
  • 1.12 lines changed: 8, context: html, text, full: html, text
    Tie the chrom imnnage drag jump feature to advancedJavascriptFeatures
• src/hg/hgTracks/hgTracks.c
  • 1.1612 lines changed: 660, context: html, text, full: html, text
    Checkin for FLAT_TRACKS for dragReorder. Also several other features worked out or cleaned up
• src/hg/hgTracks/imageV2.c
  • 1.17 lines changed: 273, context: html, text, full: html, text
    Checkin for FLAT_TRACKS for dragReorder. Also several other features worked out or cleaned up
  • 1.15 lines changed: 2, context: html, text, full: html, text
    Fix bug in imageV2 maps to make them written in creation order
• src/hg/hgTracks/imageV2.h
  • 1.12 lines changed: 78, context: html, text, full: html, text
    Checkin for FLAT_TRACKS for dragReorder. Also several other features worked out or cleaned up
• src/hg/hgTracks/simpleTracks.c
  • 1.116 lines changed: 35, context: html, text, full: html, text
    Checkin for FLAT_TRACKS for dragReorder. Also several other features worked out or cleaned up
• src/hg/hgTracks/wigTrack.c
  • 1.99 lines changed: 5, context: html, text, full: html, text
    Checkin for FLAT_TRACKS for dragReorder. Also several other features worked out or cleaned up
• src/hg/js/hgTracks.js
  • 1.48 lines changed: 156, context: html, text, full: html, text
    Checkin for FLAT_TRACKS for dragReorder. Also several other features worked out or cleaned up
• src/hg/js/hui.js
  • 1.44 lines changed: 1, context: html, text, full: html, text
    Fix for bug Katrina found. All plus/minus buttons were failing when no matrix exists
• src/hg/lib/cart.c
  • 1.114 lines changed: 109, context: html, text, full: html, text
    cartJustify has been added to clean up _imgOrd settings superceded by changed priorities
• src/hg/lib/hui.c
  • 1.251 lines changed: 1, context: html, text, full: html, text
    Fix for bug Katrina found. All plus/minus buttons were failing when no matrix exists
• src/hg/lib/wiggleCart.c
  • 1.35 lines changed: 37, context: html, text, full: html, text
    Restored viewLimitsCompositeOverride so that minLimit,maxLimit can be used to prompt range in view level cfg
• src/hg/makeDb/doc/encodeDccHg18/broadBernstein.txt
  • 1.10 lines changed: 120, context: html, text, full: html, text
    Some Rep2 tagAligns were missing.
• src/hg/makeDb/doc/encodeDccHg18/haibChipSeq.txt
  • 1.5 lines changed: 2, context: html, text, full: html, text
    Keeping the record up to date
  • 1.4 lines changed: 131, context: html, text, full: html, text
    Backlog of work needing check-in
• src/hg/makeDb/doc/encodeDccHg18/uwChIPseq.release1.notes.txt
  • 1.3 lines changed: 2, context: html, text, full: html, text
    Removed one file that Richard noticed was replaced with differently named file
• src/hg/makeDb/doc/encodeDccHg18/uwStam.txt
  • 1.5 lines changed: 6, context: html, text, full: html, text
    Keeping the record up to date
  • 1.4 lines changed: 11, context: html, text, full: html, text
    Backlog check-in
• src/hg/makeDb/doc/encodeDccHg18/yaleDavisHarvardSnyder.txt
  • 1.13 lines changed: 49, context: html, text, full: html, text
    Keeping the record up to date
  • 1.12 lines changed: 306, context: html, text, full: html, text
    Finally most of Yale's tagAligns have been corrected.
• src/hg/makeDb/trackDb/tagTypes.tab
  • 1.4 lines changed: 4, context: html, text, full: html, text
    Added 3 dimensionChecked terms and made subGroup6 allowed on any type
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
  • 1.715 lines changed: 226, context: html, text, full: html, text
    Added protocol and treatment to HAIB TFBS
  • 1.707 lines changed: 20, context: html, text, full: html, text
    Replaced a bunch of viewLimitsMax vars with minLimit and maxLimit. Don't like it but will go along with the current.
  • 1.695 lines changed: 4, context: html, text, full: html, text
    relabel a couple of Yale tracks that should belong to YCD or Stanford
  • 1.693 lines changed: 81, context: html, text, full: html, text
    Added in 2 more experiments for HAIB TFSB
• src/hg/makeDb/trackDb/human/hg18/wgEncodeChromatinMap.html
  • 1.28 lines changed: 1, context: html, text, full: html, text
    Fixed poorly worded release 2 note.
• src/inc/cheapcgi.h
  • 1.68 lines changed: 4, context: html, text, full: html, text
    Added a couple color defines