tdreszer: changes by commit

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

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