tdreszer: changes by commit

branch to review (2009-12-14 to 2010-01-04) v222

• Shortened some tags because tableNames are over-flowing
  • src/hg/encode/encodeValidate/config/cv.ra 1.156 - lines changed: 3, context: html, text, full: html, text
• Shortened more tags because tableNames and sorting
  • src/hg/encode/encodeValidate/config/cv.ra 1.157 - lines changed: 8, context: html, text, full: html, text
• Added 4 more HAIB ChIP submissions
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.722 - lines changed: 151, context: html, text, full: html, text
• Plug up a runtime warning warning
  • src/hg/utils/automation/Encode.pm 1.53 - lines changed: 2, context: html, text, full: html, text
• Need this to note the obscure hg.conf setting required to test changes
  • src/hg/js/README 1.1 - lines changed: 0, context: html, text, full: html, text
• Simplified controlled vocab validation, tableNames based on cv tags not terms, tag 'None' not included in naem, special case replicate subGroup
  • src/hg/encode/encodeValidate/doEncodeValidate.pl 1.208 - lines changed: 114, context: html, text, full: html, text
• Added 2 cell types for Broad
  • src/hg/encode/encodeValidate/config/cv.ra 1.158 - lines changed: 49, context: html, text, full: html, text
• Fix BTO term for myotubes
  • src/hg/encode/encodeValidate/config/cv.ra 1.159 - lines changed: 2, context: html, text, full: html, text
• Exception for chrM should not be an option. If end > chromSize and chrM, then make sure start <= chromSize
  • src/hg/encode/validateFiles/validateFiles.c 1.32 - lines changed: 5, context: html, text, full: html, text
• Never do in 1 checkin what can be spread out into 2
  • src/hg/encode/validateFiles/validateFiles.c 1.33 - lines changed: 14, context: html, text, full: html, text
• Kayla found some mangled names
  • src/hg/makeDb/doc/encodeDccHg18/broadChipSeq.notes.txt 1.8 - lines changed: 51, context: html, text, full: html, text
• Warning only for javascriipt developers
  • src/hg/hgTracks/imageV2.c 1.18 - lines changed: 6, context: html, text, full: html, text
• Fix captitaliZation in paths
  • src/hg/makeDb/doc/encodeDccHg18/broadChipSeq.notes.txt 1.9 - lines changed: 287, context: html, text, full: html, text
• Special case code for cleaning up tablenames that are too long
  • src/hg/encode/encodeValidate/doEncodeValidate.pl 1.209 - lines changed: 8, context: html, text, full: html, text
• Added 'privateData' option and require tab delimit instead of white space delimit
  • src/hg/encode/validateFiles/validateFiles.c 1.34 - lines changed: 21, context: html, text, full: html, text
• Changed verbose messages from js developers only to hgwdev only
  • src/hg/hgTracks/imageV2.c 1.19 - lines changed: 1, context: html, text, full: html, text
• Broads 14 for Jan 2010
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.726 - lines changed: 264, context: html, text, full: html, text
• Notes for the 2nd release of UW DNase
  • src/hg/makeDb/doc/encodeDccHg18/uwDnaseSeq.release2.notes.txt 1.1 - lines changed: 0, context: html, text, full: html, text
• Fix UW ChipSeq settings
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.728 - lines changed: 1, context: html, text, full: html, text
• Fix my mistake in 'variables' line
  • src/hg/encode/DAFs/HAIBChIPseq.daf 1.3 - lines changed: 1, context: html, text, full: html, text
• Fix dataVersion on Broad during the 13th hour
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.730 - lines changed: 1, context: html, text, full: html, text
• Added 14 new tier 3 cell lines for Snyder and Stam labs
  • src/hg/encode/encodeValidate/config/cv.ra 1.166 - lines changed: 154, context: html, text, full: html, text