kate: changes by file

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

• src/hg/encode/encodeValidate/doEncodeValidate.pl
  • 1.176 lines changed: 7, 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
  • 1.175 lines changed: 8, context: html, text, full: html, text
    Set subtrack defaults based on cell type (only Tier1 default on). Change at wrangler's discretion
  • 1.174 lines changed: 20, context: html, text, full: html, text
    Cosmetics (whitespace in trackDb)
• src/hg/encode/encodeValidate/makefile
  • 1.15 lines changed: 1, context: html, text, full: html, text
    Install cv.ra as part of 'make alpha'
• src/hg/encode/encodeValidate/test/expected/chipseq/trackDb.ra
  • 1.5 lines changed: 6, 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/test/expected/methylseq/README.txt
  • 1.3 lines changed: 5, 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/test/expected/methylseq/load.ra
  • 1.4 lines changed: 16, context: html, text, full: html, text
    Set subtrack defaults based on cell type (only Tier1 default on). Change at wrangler's discretion
  • 1.2 lines changed: 2, context: html, text, full: html, text
    Adjust name of HCT cell line to match cv.ra
• src/hg/encode/encodeValidate/test/expected/methylseq/trackDb.ra
  • 1.5 lines changed: 2, 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
  • 1.4 lines changed: 12, context: html, text, full: html, text
    Set subtrack defaults based on cell type (only Tier1 default on). Change at wrangler's discretion
  • 1.2 lines changed: 5, context: html, text, full: html, text
    Adjust name of HCT cell line to match cv.ra
• src/hg/encode/encodeValidate/test/input/methylseq/GM12878.txt.BED
  • 1.1 lines changed: 100, 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/test/input/methylseq/GM12878.txt.peaks
  • 1.1 lines changed: 4999, 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/test/input/methylseq/HudsonAlphaMethylSeq.DDF
  • 1.3 lines changed: 2, context: html, text, full: html, text
    Adjust name of HCT cell line to match cv.ra
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
  • 1.229 lines changed: 1, context: html, text, full: html, text
    Change vis defaults on Yale for consistency
• src/hg/makeDb/trackDb/human/hg18/wgEncodeBroadChipSeq.html
  • 1.12 lines changed: 16, context: html, text, full: html, text
    Add material about signal and pvalue
• src/hg/makeDb/trackDb/human/hg18/wgEncodeSunyalbanyRnaGeneChip.html
  • 1.16 lines changed: 2, context: html, text, full: html, text
    Removing inacurrate replicate info after all
  • 1.15 lines changed: 2, context: html, text, full: html, text
    Add info about replicates
  • 1.14 lines changed: 40, 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/utils/automation/Encode.pm
  • 1.38 lines changed: 1, context: html, text, full: html, text
    Update freeze date