Commits for cricket

v266_preview2 to v266_base (2012-04-17 to 2012-04-24) v266

• Taking Riken out of the RNA-seq super track per Kate request
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.release3.ra - lines changed 1, context: html, text, full: html, text
• Removing the _ in a label where it is supposed to be a space
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 2, context: html, text, full: html, text
• Changing the - to underbar or space
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeGisChiaPet.ra - lines changed 7, context: html, text, full: html, text
• Trying to get the metaCheck to resolve and deal with old revoke policy weirdness
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeRikenCage.ra - lines changed 370, context: html, text, full: html, text
• Trying to clean up this track for release, see notes in ticket 6579, working on short labels, long labels, dealing with the DCC Rep issue, removing origAssembly and labProtocolId as redundant information, removing the duplicate trackDb entries
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeRikenCage.ra - lines changed 1247, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.release3.ra - lines changed 2581, context: html, text, full: html, text
• Adding missing accession numbers
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisChiaPet.ra - lines changed 5, context: html, text, full: html, text
• Riken changes to merge with Matts
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeRikenCage.ra - lines changed 731, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.release3.ra - lines changed 424, context: html, text, full: html, text
• Getting rid of extraFields
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.ra - lines changed 6, context: html, text, full: html, text
• Changing rank and label for a few to line them up with the meta data
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.release3.ra - lines changed 8, context: html, text, full: html, text
• trying to show the Generation 0 information in the label, also ditched the errang hg19 line and changed bedRnaElements to bed 6 which I Thought was already done
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.release3.ra - lines changed 248, context: html, text, full: html, text
• Non of these .c files are made. We suspect they were generated by autosql and commited without thought
  • src/hg/lib/encode/encodeErge5race.c - lines changed 204, context: html, text, full: html, text
  • src/hg/lib/encode/encodeErgeBinding.c - lines changed 204, context: html, text, full: html, text
  • src/hg/lib/encode/encodeErgeDNAseI.c - lines changed 204, context: html, text, full: html, text
  • src/hg/lib/encode/encodeErgeExpProm.c - lines changed 204, context: html, text, full: html, text
  • src/hg/lib/encode/encodeErgeInVitroFoot.c - lines changed 204, context: html, text, full: html, text
  • src/hg/lib/encode/encodeErgeMethProm.c - lines changed 204, context: html, text, full: html, text
  • src/hg/lib/encode/encodeErgeStableTransf.c - lines changed 204, context: html, text, full: html, text
  • src/hg/lib/encode/encodeErgeSummary.c - lines changed 204, context: html, text, full: html, text
  • src/hg/lib/encode/encodeErgeTransTransf.c - lines changed 204, context: html, text, full: html, text
  • src/hg/lib/encode/encodePrimateAlleles.c - lines changed 303, context: html, text, full: html, text
  • src/hg/lib/encode/unused/encodeErge5race.c - lines changed 204, context: html, text, full: html, text
  • src/hg/lib/encode/unused/encodeErgeBinding.c - lines changed 204, context: html, text, full: html, text
  • src/hg/lib/encode/unused/encodeErgeDNAseI.c - lines changed 204, context: html, text, full: html, text
  • src/hg/lib/encode/unused/encodeErgeExpProm.c - lines changed 204, context: html, text, full: html, text
  • src/hg/lib/encode/unused/encodeErgeInVitroFoot.c - lines changed 204, context: html, text, full: html, text
  • src/hg/lib/encode/unused/encodeErgeMethProm.c - lines changed 204, context: html, text, full: html, text
  • src/hg/lib/encode/unused/encodeErgeStableTransf.c - lines changed 204, context: html, text, full: html, text
  • src/hg/lib/encode/unused/encodeErgeSummary.c - lines changed 204, context: html, text, full: html, text
  • src/hg/lib/encode/unused/encodeErgeTransTransf.c - lines changed 204, context: html, text, full: html, text
  • src/hg/lib/encode/unused/encodePrimateAlleles.c - lines changed 303, context: html, text, full: html, text
• Moving more things into unsed because they were in obsolete or because they are a .sql file with no .as and no .c
  • src/hg/lib/encode/encodeBuPromCerebrum.sql - lines changed 24, context: html, text, full: html, text
  • src/hg/lib/encode/encodeBuPromColon.sql - lines changed 24, context: html, text, full: html, text
  • src/hg/lib/encode/encodeBuPromHeart.sql - lines changed 24, context: html, text, full: html, text
  • src/hg/lib/encode/encodeBuPromKidney.sql - lines changed 24, context: html, text, full: html, text
  • src/hg/lib/encode/encodeBuPromLiver.sql - lines changed 24, context: html, text, full: html, text
  • src/hg/lib/encode/encodeBuPromLung.sql - lines changed 24, context: html, text, full: html, text
  • src/hg/lib/encode/encodeBuPromSkMuscle.sql - lines changed 24, context: html, text, full: html, text
  • src/hg/lib/encode/encodeBuPromSpleen.sql - lines changed 24, context: html, text, full: html, text
  • src/hg/lib/encode/encodeBuPromStomach.sql - lines changed 24, context: html, text, full: html, text
  • src/hg/lib/encode/encodeBuPromTestis.sql - lines changed 24, context: html, text, full: html, text
  • src/hg/lib/encode/obsolete/shortFrags.as - lines changed 31, context: html, text, full: html, text
  • src/hg/lib/encode/obsolete/shortFrags.sql - lines changed 37, context: html, text, full: html, text
  • src/hg/lib/encode/unused/encodeBuPromCerebrum.sql - lines changed 24, context: html, text, full: html, text
  • src/hg/lib/encode/unused/encodeBuPromColon.sql - lines changed 24, context: html, text, full: html, text
  • src/hg/lib/encode/unused/encodeBuPromHeart.sql - lines changed 24, context: html, text, full: html, text
  • src/hg/lib/encode/unused/encodeBuPromKidney.sql - lines changed 24, context: html, text, full: html, text
  • src/hg/lib/encode/unused/encodeBuPromLiver.sql - lines changed 24, context: html, text, full: html, text
  • src/hg/lib/encode/unused/encodeBuPromLung.sql - lines changed 24, context: html, text, full: html, text
  • src/hg/lib/encode/unused/encodeBuPromSkMuscle.sql - lines changed 24, context: html, text, full: html, text
  • src/hg/lib/encode/unused/encodeBuPromSpleen.sql - lines changed 24, context: html, text, full: html, text
  • src/hg/lib/encode/unused/encodeBuPromStomach.sql - lines changed 24, context: html, text, full: html, text
  • src/hg/lib/encode/unused/encodeBuPromTestis.sql - lines changed 24, context: html, text, full: html, text
  • src/hg/lib/encode/unused/shortFrags.as - lines changed 31, context: html, text, full: html, text
  • src/hg/lib/encode/unused/shortFrags.sql - lines changed 37, context: html, text, full: html, text
• Cleaning out duplicate lines
  • src/hg/encode/validateFiles/validateFilesUsage - lines changed 27, context: html, text, full: html, text
• Starting the release notes and the changes to the displayed views
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.release3.html - lines changed 11, context: html, text, full: html, text
• Trying to bring the as files and sql files in line wiht each other, specifically score is uint and reserved is uint and strand is char[1]
  • src/hg/lib/encode/bedLogR.as - lines changed 1, context: html, text, full: html, text
  • src/hg/lib/encode/bedLogR.sql - lines changed 5, context: html, text, full: html, text
  • src/hg/lib/encode/bedRnaJunctions.as - lines changed 2, context: html, text, full: html, text
  • src/hg/lib/encode/bedRrbs.as - lines changed 1, context: html, text, full: html, text
  • src/hg/lib/encode/bedRrbs.sql - lines changed 8, context: html, text, full: html, text
  • src/hg/lib/encode/broadPeak.sql - lines changed 5, context: html, text, full: html, text
  • src/hg/lib/encode/gappedPeak.as - lines changed 1, context: html, text, full: html, text
  • src/hg/lib/encode/gappedPeak.sql - lines changed 6, context: html, text, full: html, text
  • src/hg/lib/encode/narrowPeak.sql - lines changed 1, context: html, text, full: html, text
  • src/hg/lib/encode/tagAlign.as - lines changed 1, context: html, text, full: html, text
  • src/hg/lib/encode/tagAlign.sql - lines changed 2, context: html, text, full: html, text
• Removing extraFields
  • src/hg/makeDb/trackDb/tagTypes.tab - lines changed 1, context: html, text, full: html, text
• Adding the cell lines to the release notes
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.release3.html - lines changed 1, context: html, text, full: html, text