tdreszer: changes by commit

branch to review (2009-04-14 to 2009-04-21) v204

• Add fragLength so to be specified by replicate
  • src/hg/encode/encodeValidate/config/fields.ra 1.16 - lines changed: 5, context: html, text, full: html, text
• Exclude bigWig from option to limit data output to some number of rows
  • src/hg/hgTables/filterFields.c 1.73 - lines changed: 9, context: html, text, full: html, text
• Added fileDb.ra definition
  • src/hg/utils/automation/Encode.pm 1.40 - lines changed: 1, context: html, text, full: html, text
• Added link to hgTrackUi into the preamble text.
  • src/hg/encode/encodeLoad/doEncodeLoad.pl 1.62 - lines changed: 4, context: html, text, full: html, text
• Added a lot of metadata settings for Broad, Duke/UNC/UT-A, Elnitski, HudsunAlpha, Yale
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.245 - lines changed: 475, context: html, text, full: html, text
• I misunderstood what Jim Wanted. 'Limit data output to' some number of rows should work with bigWig
  • src/hg/hgTables/filterFields.c 1.74 - lines changed: 1, context: html, text, full: html, text
• Support for DDF level fragLength for Alignments to RawSignal. Now creating metadata setting for trackDb and new fileDb.ra
  • src/hg/encode/encodeValidate/doEncodeValidate.pl 1.177 - lines changed: 120, context: html, text, full: html, text
• Added a lot more metadata settings for Most of Mike's tracks
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.249 - lines changed: 218, context: html, text, full: html, text
• validateInt had a bad error message when alpha was entered
  • src/hg/js/utils.js 1.18 - lines changed: 1, context: html, text, full: html, text
• HTC-116 was removed as this should be the already existing HCT-116
  • src/hg/encode/encodeValidate/config/cv.ra 1.89 - lines changed: 4, context: html, text, full: html, text
• A small number of new metadata tags and a very large number of changed ones. Turns out that the metadata generation code did not calc the dataUnrestricted properly
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.251 - lines changed: 683, context: html, text, full: html, text
• If dateSubmitted is ddf ctime, then dateRestricted should use the same.
  • src/hg/encode/encodeValidate/doEncodeValidate.pl 1.178 - lines changed: 4, context: html, text, full: html, text
• Updated to of UNC FAIRE peak tracks
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.254 - lines changed: 14, context: html, text, full: html, text