Commits for cline

v253_preview to v253_preview2 (2011-06-14 to 2011-06-21) v253

• Checking in a fresh version of the uncBsuProt metadata
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUncBsuProt.ra - lines changed 7, context: html, text, full: html, text
• Housekeeping changes: (1) finished converting the tags to uppercase, so that no one mistakenly enters mixed-case tags in code review (without an excuse) again, (2) added tags to th stanzas that don't have tags, to give the validator a nice, general schema to work with, and (3) removed a handful of stanzas that have been commented out for eons, as well as a couple recent ones which I know to not be needed anymore
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 616, context: html, text, full: html, text
• Addressing code review feedback from Jim. A lot of this involves dealing with single-token lines in the ra stanzas (i.e. a label but no contents), which is apparently undefined in the formal ra specification
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 107, context: html, text, full: html, text
• Addressing code review feedback from Katrina
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 24, context: html, text, full: html, text
• (1) Addressing Jim's code review comments, (2) housekeeping: making all tags uppercase and making sure all stanzas have tags, plus removing some cruft that's not needed anymore
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 113, context: html, text, full: html, text
• (1) bug fix: one stanza had lost its type and description, causing anything that displays cv material to blow up (2) I had somehow stomped on Venkat's new colors, and reinstated them to the best of my ability
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 42, context: html, text, full: html, text
• Added three new protocols for the Stam lab
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 6, context: html, text, full: html, text
• Fixing a missing step in adding a new protocol document for the Stam lab
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 1, context: html, text, full: html, text
• Updated with a new version provided by Jainab. The differences seem to pertain to how the data is now filtered by default, with the displayed data now having an estimated FDR of 5%, not 10%.
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProt.html - lines changed 35, context: html, text, full: html, text
• Added DCC accessions for a few new subtracks
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUncBsuProt.ra - lines changed 17, context: html, text, full: html, text
• Minor correction on how the EValue is computed
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProt.html - lines changed 1, context: html, text, full: html, text
• Still cleaning up from last week's code review...
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 11, context: html, text, full: html, text