Commits for cricket

v254_preview2 to v254_base (2011-07-12 to 2011-07-19) v254

• replacing Riken TSS with Riken TSS GencV7
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeRikenCage.ra - lines changed 600, context: html, text, full: html, text
• added bedRnaElements
  • src/hg/encode/encodeMkChangeNotes/encodeMkChangeNotes - lines changed 1, context: html, text, full: html, text
• Finishing touches on track, a new notes file, a new .html file with release notes and the new views described
  • src/hg/makeDb/doc/encodeDccHg19/wgEncodeRikenCage.release2.notes - lines changed 1361, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeRikenCage.ra - lines changed 89, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.new.html - lines changed 141, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.new.ra - lines changed 1, context: html, text, full: html, text
• Removed the numbers from the begeinning of the labels
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.ra - lines changed 1, context: html, text, full: html, text
• Changed fileSortOrder
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeCaltechRnaSeq.new.ra - lines changed 1, context: html, text, full: html, text
• Adding terms for V7 Gencode
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 12, context: html, text, full: html, text
• added geo Series number
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwAffyExonArray.ra - lines changed 2, context: html, text, full: html, text
• This is in repsonse to code review 4578 and 4579. I took out some provisional tags, changed a tab typo, removed some cruft
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 16, context: html, text, full: html, text
• Updated with dropped files
  • src/hg/makeDb/doc/encodeDccHg19/wgEncodeHaibTfbs.release1.notes - lines changed 822, context: html, text, full: html, text
• Replacing TSS with TssGencV7 so that we specify the version from here on out
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 4, context: html, text, full: html, text
• Remove fileiIndex
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeRikenCage.ra - lines changed 2, context: html, text, full: html, text
• Adding 4 submissions with the V7 files
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra - lines changed 221, context: html, text, full: html, text
• Changed .gz to .tgz for paired fastqs, removed V2 where added erroneously, added origAssmbly where added erroneously, trying to remove md5sums for the paired fastqs
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCaltechRnaSeq.ra - lines changed 245, context: html, text, full: html, text
• Adding new readType 2x76D
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 5, context: html, text, full: html, text
• Added in a TssGencV3c as well as the V7 added earlier
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 6, context: html, text, full: html, text
• Removed replicate pooled
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisChiaPet.ra - lines changed 5, context: html, text, full: html, text
• Changed TSS to TssGencV3c for clarification
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCaltechRnaSeq.ra - lines changed 35, context: html, text, full: html, text