tdreszer: changes by file

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

• src/hg/encode/DAFs/BroadChipSeq.daf
  • 1.1 lines changed: 39, context: html, text, full: html, text
    Broad DAFs need to be checked in and need to use dafVersion 1.1
• src/hg/encode/DAFs/BroadChipSeqControl.daf
  • 1.1 lines changed: 33, context: html, text, full: html, text
    Broad DAFs need to be checked in and need to use dafVersion 1.1
• src/hg/encode/DAFs/DukeDNaseSeq.DAF
  • 1.3 lines changed: 7, context: html, text, full: html, text
    DukeUNC/UT needs base overlap signal
  • 1.2 lines changed: 13, context: html, text, full: html, text
    Duke/UNC/UT should be using dafVersion 1.1 now.
• src/hg/encode/DAFs/UncFAIREseq.DAF
  • 1.4 lines changed: 7, context: html, text, full: html, text
    DukeUNC/UT needs base overlap signal
  • 1.3 lines changed: 13, context: html, text, full: html, text
    Duke/UNC/UT should be using dafVersion 1.1 now.
• src/hg/encode/DAFs/UtaChIPseq.DAF
  • 1.4 lines changed: 7, context: html, text, full: html, text
    DukeUNC/UT needs base overlap signal
  • 1.3 lines changed: 14, context: html, text, full: html, text
    Duke/UNC/UT should be using dafVersion 1.1 now.
• src/hg/encode/DAFs/UtaInput.DAF
  • 1.4 lines changed: 1, context: html, text, full: html, text
    DukeUNC/UT needs base overlap signal
  • 1.3 lines changed: 12, context: html, text, full: html, text
    Duke/UNC/UT should be using dafVersion 1.1 now.
• src/hg/encode/DAFs/UwChIPseq.daf
  • 1.2 lines changed: 1, context: html, text, full: html, text
    UW should provide replicates for peaks to be consistent
• src/hg/encode/DAFs/YDHChipSeq.daf
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Yale signal is bedGraph
• src/hg/encode/DAFs/YDHChipSeqTreatment.daf
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Yale signal is bedGraph
• src/hg/encode/encodeValidate/config/cv.ra
  • 1.130 lines changed: 26, context: html, text, full: html, text
    Added Antibody HA and cell HGF
  • 1.129 lines changed: 1, context: html, text, full: html, text
    Changing H1 ES or H1_ES to H1-hESC for clarity
• src/hg/hgTracks/cytoBandTrack.c
  • 1.11 lines changed: 7, context: html, text, full: html, text
    Cleanup recommended by Angie a week ago.
• src/hg/hgTracks/imageV2.c
  • 1.11 lines changed: 4, context: html, text, full: html, text
    Removed a define dependency
• src/hg/hgTracks/simpleTracks.c
  • 1.107 lines changed: 1, context: html, text, full: html, text
    Bug in imageV2 found by Ann a week ago
• src/hg/js/hui.js
  • 1.35 lines changed: 44, context: html, text, full: html, text
    Fixed matrix CB normalize to do it's best for dimension Z
• src/hg/lib/customTrack.c
  • 1.177 lines changed: 5, context: html, text, full: html, text
    autocreated custom trackNames now exclude all special chars and append a uniquifier number
• src/hg/makeDb/doc/encodeDccHg18/yaleUpdate9-30.notes.txt
  • 1.1 lines changed: 902, context: html, text, full: html, text
    Complete lists of files and tables for ENCODE Yale TFSB release 2 which should occur after the 9-30-2009 data freeze. Notes were too long to include directly in pushQ entry.
• src/hg/makeDb/schema/all.joiner
  • 1.736 lines changed: 9, context: html, text, full: html, text
    Added wgEncodeGencode V3 tables
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
  • 1.543 lines changed: 4, context: html, text, full: html, text
    Oops. Turned off some Yale RNAseq tracks
  • 1.542 lines changed: 61, context: html, text, full: html, text
    Added 5 Yale RNA-seq tracks
  • 1.540 lines changed: 94, context: html, text, full: html, text
    Fixed some colors and converted H1_ES to H1-hESC for clarity
  • 1.539 lines changed: 63, context: html, text, full: html, text
    Three new experiments for YDH-Peggy Farnham
  • 1.538 lines changed: 246, context: html, text, full: html, text
    UW Exon Affy submissions added
  • 1.533 lines changed: 289, context: html, text, full: html, text
    Tracy and Tim have been straightening out UW
  • 1.531 lines changed: 588, context: html, text, full: html, text
    Tracy Ballinger added new UW Dnase-seq and UW ChIPseq tracks
• src/inc/common.h
  • 1.155 lines changed: 3, context: html, text, full: html, text
    Added eraseNonAlphaNum()
• src/lib/common.c
  • 1.133 lines changed: 18, context: html, text, full: html, text
    Added eraseNonAlphaNum()