kate: changes by commit

review to branch (2009-10-06 to 2009-10-13) v217

• Update chipseq tests for latest DAF & label conventions. Assure they fail if expected files differ. Disable methylseq test for now.
  • src/hg/encode/encodeValidate/test/expected/chipseq/trackDb.ra 1.6 - lines changed: 30, context: html, text, full: html, text
  • src/hg/encode/encodeValidate/test/input/chipseq/StanfordChip.DAF 1.7 - lines changed: 1, context: html, text, full: html, text
  • src/hg/encode/encodeValidate/test/makefile 1.24 - lines changed: 7, context: html, text, full: html, text
• Add support for specifying track group in DAF
  • src/hg/encode/encodeValidate/config/fields.ra 1.21 - lines changed: 5, context: html, text, full: html, text
  • src/hg/encode/encodeValidate/doEncodeValidate.pl 1.197 - lines changed: 5, context: html, text, full: html, text
• Change name of chipseq test so it differs from real track so it can test out composite trackDb output
  • src/hg/encode/encodeValidate/test/expected/chipseq/README.txt 1.4 - lines changed: 6, context: html, text, full: html, text
  • src/hg/encode/encodeValidate/test/expected/chipseq/load.ra 1.5 - lines changed: 5, context: html, text, full: html, text
  • src/hg/encode/encodeValidate/test/expected/chipseq/trackDb.ra 1.7 - lines changed: 28, context: html, text, full: html, text
  • src/hg/encode/encodeValidate/test/input/chipseq/StanfordChip.DAF 1.8 - lines changed: 2, context: html, text, full: html, text
• Allow metadata extraction w/o requiring file validation settings, for backwards compatibility
  • src/hg/encode/encodeValidate/doEncodeValidate.pl 1.199 - lines changed: 3, context: html, text, full: html, text
• Add color by cell type (from cv.ra) to trackDb file
  • src/hg/encode/encodeValidate/doEncodeValidate.pl 1.200 - lines changed: 7, context: html, text, full: html, text
• Add testing of color by cell type from cv.ra
  • src/hg/encode/encodeValidate/test/expected/chipseq/README.txt 1.5 - lines changed: 9, context: html, text, full: html, text
  • src/hg/encode/encodeValidate/test/expected/chipseq/load.ra 1.6 - lines changed: 10, context: html, text, full: html, text
  • src/hg/encode/encodeValidate/test/expected/chipseq/trackDb.ra 1.8 - lines changed: 21, context: html, text, full: html, text
  • src/hg/encode/encodeValidate/test/input/chipseq/StanfordChip-Test-Jun08.DDF 1.3 - lines changed: 4, context: html, text, full: html, text
• Replace Andy's entries
  • src/hg/encode/encodeValidate/config/labs.ra 1.9 - lines changed: 2, context: html, text, full: html, text
• Add new required setting
  • src/hg/encode/DAFs/UMassTfbsAll.daf 1.2 - lines changed: 1, context: html, text, full: html, text
  • src/hg/encode/DAFs/UMassTfbsValid.daf 1.3 - lines changed: 1, context: html, text, full: html, text