kate: changes by commit

branch to review (2009-03-31 to 2009-04-07) v203

• Change vis defaults on Yale for consistency
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.229 - lines changed: 1, context: html, text, full: html, text
• Install cv.ra as part of 'make alpha'
  • src/hg/encode/encodeValidate/makefile 1.15 - lines changed: 1, context: html, text, full: html, text
• Fleshing out Methods a bit to summarize analysis and meaning of scoring; expanding acronyms; removing repetitious parts
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeSunyalbanyRnaGeneChip.html 1.14 - lines changed: 40, context: html, text, full: html, text
• Add material about signal and pvalue
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeBroadChipSeq.html 1.12 - lines changed: 16, context: html, text, full: html, text
• Adjust name of HCT cell line to match cv.ra
  • src/hg/encode/encodeValidate/test/expected/methylseq/load.ra 1.2 - lines changed: 2, context: html, text, full: html, text
  • src/hg/encode/encodeValidate/test/expected/methylseq/trackDb.ra 1.2 - lines changed: 5, context: html, text, full: html, text
  • src/hg/encode/encodeValidate/test/input/methylseq/HudsonAlphaMethylSeq.DDF 1.3 - lines changed: 2, context: html, text, full: html, text
• Cosmetics (whitespace in trackDb)
  • src/hg/encode/encodeValidate/doEncodeValidate.pl 1.174 - lines changed: 20, context: html, text, full: html, text
• Add info about replicates
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeSunyalbanyRnaGeneChip.html 1.15 - lines changed: 2, context: html, text, full: html, text
• Set subtrack defaults based on cell type (only Tier1 default on). Change at wrangler's discretion
  • src/hg/encode/encodeValidate/doEncodeValidate.pl 1.175 - lines changed: 8, context: html, text, full: html, text
  • src/hg/encode/encodeValidate/test/expected/methylseq/README.txt 1.3 - lines changed: 5, context: html, text, full: html, text
  • src/hg/encode/encodeValidate/test/expected/methylseq/load.ra 1.4 - lines changed: 16, context: html, text, full: html, text
  • src/hg/encode/encodeValidate/test/expected/methylseq/trackDb.ra 1.4 - lines changed: 12, context: html, text, full: html, text
  • src/hg/encode/encodeValidate/test/input/methylseq/GM12878.txt.BED 1.1 - lines changed: 100, context: html, text, full: html, text
  • src/hg/encode/encodeValidate/test/input/methylseq/GM12878.txt.peaks 1.1 - lines changed: 4999, context: html, text, full: html, text
• Subtracks are no longer by default set to be configurable, due to performance issues. Change at wrangler's discretion
  • src/hg/encode/encodeValidate/doEncodeValidate.pl 1.176 - lines changed: 7, context: html, text, full: html, text
  • src/hg/encode/encodeValidate/test/expected/chipseq/trackDb.ra 1.5 - lines changed: 6, context: html, text, full: html, text
  • src/hg/encode/encodeValidate/test/expected/methylseq/trackDb.ra 1.5 - lines changed: 2, context: html, text, full: html, text
• Update freeze date
  • src/hg/utils/automation/Encode.pm 1.38 - lines changed: 1, context: html, text, full: html, text
• Removing inacurrate replicate info after all
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeSunyalbanyRnaGeneChip.html 1.16 - lines changed: 2, context: html, text, full: html, text