Commits for cricket

v254_base to v255_preview (2011-07-19 to 2011-07-26) v255

• Adding the typeOfTerm type, removing parentTable and fileIndex, changing the names of geoSeries and geoSample to have accession in the name. Mostly I am trying to get the CV to match what we have in the database so that the validators work.
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 37, context: html, text, full: html, text
• Changed var names that failed in the validation process. Riken: dateResubmitted, GisChiaPet: docId submitPath, UncBsu: dccInternalNotes, Caltech:dateSubmitted
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCaltechRnaSeq.ra - lines changed 149, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisChiaPet.ra - lines changed 193, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisRnaPet.ra - lines changed 15, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeRikenCage.ra - lines changed 50, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUncBsuProt.ra - lines changed 3, context: html, text, full: html, text
• Changed dccNotes to dccInternalNotes
  • src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeHudsonalphaMethylSeq.ra - lines changed 16, context: html, text, full: html, text
• Summary of changes: Commented out all of the variations of BJ tert until we figure it out (ticket 4536). Added views for all of the GencodeV7 data that will be coming in, changed an old view to specify GencodeV3c. Cleaned up typeOfTerms by removing parentTable and fileIndex which have been retired, changing geoSeries and geoSample to be geo*Accession to comply wiht validator, added type as a typeOfTerm. There were many changes to protocol links to try to fix those in ticket 4408. Added a new control RevXLink.
  • src/hg/makeDb/trackDb/cv/beta/cv.ra - lines changed 156, context: html, text, full: html, text
• Reviewed the provisinal tags
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 8, context: html, text, full: html, text
• Long and short labels, removed V3c and added V7, fixed the cv line
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra - lines changed 5116, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.ra - lines changed 826, context: html, text, full: html, text
• Changed defualts for order and visibility of views
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.ra - lines changed 2, context: html, text, full: html, text
• Changed None to none
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 1, context: html, text, full: html, text
• Changed geoSeries and geoSample to have Accession and swapped Paired for Alignments
  • src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeCaltechRnaSeq.ra - lines changed 555, context: html, text, full: html, text
• Changing geoSample to geoSampleAccession and swapping Paired for Alignments
  • src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeCaltechRnaSeq.ra - lines changed 1, context: html, text, full: html, text
• Changed Contigs and Junctions to be bed 6 for display purposes
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.new.ra - lines changed 27, context: html, text, full: html, text
• adding mean+whiskers for signals and filter at 200 for Junctions
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.ra - lines changed 4, context: html, text, full: html, text