Commits for cricket

v257_preview2 to v257_base (2011-09-13 to 2011-09-19) v257

• Put replicate 5 in the attic and changed short labels according to Kate instructions on track 43
  • src/hg/encode/DAFs/2.0/affyRnaChip.daf - lines changed 38, context: html, text, full: html, text
  • src/hg/encode/DAFs/2.0/cshlLongElements.daf - lines changed 76, context: html, text, full: html, text
  • src/hg/encode/DAFs/2.0/cshlLongSpikeIns.daf - lines changed 42, context: html, text, full: html, text
  • src/hg/encode/DAFs/2.0/gisDnaPet.daf - lines changed 73, context: html, text, full: html, text
  • src/hg/encode/DAFs/2.0/haibMethylRrbs.daf - lines changed 34, context: html, text, full: html, text
  • src/hg/encode/DAFs/2.0/sunySwitchgear.daf - lines changed 35, context: html, text, full: html, text
  • src/hg/encode/DAFs/2.0/wgEncodeAffyRnaChip.daf - lines changed 38, context: html, text, full: html, text
  • src/hg/encode/DAFs/2.0/wgEncodeGisDnaPet.daf - lines changed 73, context: html, text, full: html, text
  • src/hg/encode/DAFs/2.0/wgEncodeHaibMethylRrbs.daf - lines changed 34, context: html, text, full: html, text
  • src/hg/encode/DAFs/2.0/wgEncodeSunySwitchgear.daf - lines changed 35, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra - lines changed 71, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.ra - lines changed 101, context: html, text, full: html, text
• Moving to the next generation of DAFs
  • src/hg/encode/DAFs/3.0/wgEncodeAffyRnaChip.daf - lines changed 38, context: html, text, full: html, text
  • src/hg/encode/DAFs/3.0/wgEncodeGisDnaPet.daf - lines changed 73, context: html, text, full: html, text
  • src/hg/encode/DAFs/3.0/wgEncodeHaibMethylRrbs.daf - lines changed 34, context: html, text, full: html, text
  • src/hg/encode/DAFs/3.0/wgEncodeSunySwitchgear.daf - lines changed 35, context: html, text, full: html, text
• Moving the hg19 into the new directory
  • src/hg/encode/DAFs/3.0/hg19/wgEncodeAffyRnaChip.daf - lines changed 38, context: html, text, full: html, text
  • src/hg/encode/DAFs/3.0/hg19/wgEncodeGisDnaPet.daf - lines changed 73, context: html, text, full: html, text
  • src/hg/encode/DAFs/3.0/hg19/wgEncodeHaibMethylRrbs.daf - lines changed 34, context: html, text, full: html, text
  • src/hg/encode/DAFs/3.0/hg19/wgEncodeSunySwitchgear.daf - lines changed 35, context: html, text, full: html, text
  • src/hg/encode/DAFs/3.0/wgEncodeAffyRnaChip.daf - lines changed 38, context: html, text, full: html, text
  • src/hg/encode/DAFs/3.0/wgEncodeGisDnaPet.daf - lines changed 73, context: html, text, full: html, text
  • src/hg/encode/DAFs/3.0/wgEncodeHaibMethylRrbs.daf - lines changed 34, context: html, text, full: html, text
  • src/hg/encode/DAFs/3.0/wgEncodeSunySwitchgear.daf - lines changed 35, context: html, text, full: html, text
• I meant to make these changes on .new.ra
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyAlbanyGeneSt.ra - lines changed 3, context: html, text, full: html, text
• Getting rid of the - in H1-hESC
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyAlbanyGeneSt.new.ra - lines changed 6, context: html, text, full: html, text
• Trying to make release 2 have the path information
  • src/hg/encode/encodeMkChangeNotes/encodeMkChangeNotes - lines changed 1, context: html, text, full: html, text
• I know the spikeins do not have bai files, they are not for display
  • src/hg/makeDb/doc/encodeDccHg19/wgEncodeCshlLongRnaSeq.release1.notes - lines changed 7, context: html, text, full: html, text
• Resolving merge conflict
  • src/hg/makeDb/doc/encodeDccHg19/wgEncodeCshlLongRnaSeq.release1.notes - lines changed 7, context: html, text, full: html, text
• BioRep should not be just for transcriptome project
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 2, context: html, text, full: html, text
• Adding the bioRep and labId to the Protocol Docs
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra - lines changed 276, context: html, text, full: html, text
• removing 3 orphan objects, see track #43
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra - lines changed 78, context: html, text, full: html, text
• Finishing the dropping of the 3 orphan files
  • src/hg/makeDb/doc/encodeDccHg19/wgEncodeCshlLongRnaSeq.release1.notes - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra - lines changed 53, context: html, text, full: html, text
• removing run from the file, storing in labExpId
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisChiaPet.ra - lines changed 17, context: html, text, full: html, text
• Making the 3.0 daf directory for mm9
  • src/hg/encode/DAFs/3.0/mm9/wgEncodeCaltechHist.daf - lines changed 62, context: html, text, full: html, text
  • src/hg/encode/DAFs/3.0/mm9/wgEncodeCaltechHistone.daf - lines changed 62, context: html, text, full: html, text
  • src/hg/encode/DAFs/3.0/mm9/wgEncodeCaltechTfbs.daf - lines changed 62, context: html, text, full: html, text
  • src/hg/encode/DAFs/3.0/mm9/wgEncodeLicrHistone.daf - lines changed 59, context: html, text, full: html, text
  • src/hg/encode/DAFs/3.0/mm9/wgEncodeLicrRnaSeq.daf - lines changed 58, context: html, text, full: html, text
  • src/hg/encode/DAFs/3.0/mm9/wgEncodeLicrTfbs.daf - lines changed 57, context: html, text, full: html, text
  • src/hg/encode/DAFs/3.0/mm9/wgEncodePsuHistone.daf - lines changed 68, context: html, text, full: html, text
  • src/hg/encode/DAFs/3.0/mm9/wgEncodePsuTfbs.daf - lines changed 67, context: html, text, full: html, text
  • src/hg/encode/DAFs/3.0/mm9/wgEncodeSydhHist.daf - lines changed 63, context: html, text, full: html, text
  • src/hg/encode/DAFs/3.0/mm9/wgEncodeSydhRnaSeq.daf - lines changed 57, context: html, text, full: html, text
  • src/hg/encode/DAFs/3.0/mm9/wgEncodeSydhTfbs.daf - lines changed 63, context: html, text, full: html, text
  • src/hg/encode/DAFs/3.0/mm9/wgEncodeUwDfg.daf - lines changed 76, context: html, text, full: html, text
  • src/hg/encode/DAFs/3.0/mm9/wgEncodeUwDnase.daf - lines changed 63, context: html, text, full: html, text
  • src/hg/encode/DAFs/3.0/mm9/wgEncodeUwRnaSeq.daf - lines changed 69, context: html, text, full: html, text
  • src/hg/encode/DAFs/3.0/mm9/wgEncodeUwTfbs.daf - lines changed 65, context: html, text, full: html, text
• Starting the 3.0 DAF directory for hg19
  • src/hg/encode/DAFs/3.0/hg19/wgEncodeAffyRnaChip.daf - lines changed 2, context: html, text, full: html, text
  • src/hg/encode/DAFs/3.0/hg19/wgEncodeBroadHistone.daf - lines changed 54, context: html, text, full: html, text
  • src/hg/encode/DAFs/3.0/hg19/wgEncodeBroadHmm.daf - lines changed 23, context: html, text, full: html, text
  • src/hg/encode/DAFs/3.0/hg19/wgEncodeCaltechRnaSeq.daf - lines changed 146, context: html, text, full: html, text
  • src/hg/encode/DAFs/3.0/hg19/wgEncodeCshlLongRnaSeq.daf - lines changed 62, context: html, text, full: html, text
  • src/hg/encode/DAFs/3.0/hg19/wgEncodeCshlShortRnaSeq.daf - lines changed 81, context: html, text, full: html, text
  • src/hg/encode/DAFs/3.0/hg19/wgEncodeDukeAffyExon.daf - lines changed 23, context: html, text, full: html, text
  • src/hg/encode/DAFs/3.0/hg19/wgEncodeGencodeV7.daf - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
  • src/hg/encode/DAFs/3.0/hg19/wgEncodeGisChiaPet.daf - lines changed 60, context: html, text, full: html, text
  • src/hg/encode/DAFs/3.0/hg19/wgEncodeGisDnaPet.daf - lines changed 1, context: html, text, full: html, text
  • src/hg/encode/DAFs/3.0/hg19/wgEncodeGisRnaPet.daf - lines changed 72, context: html, text, full: html, text
  • src/hg/encode/DAFs/3.0/hg19/wgEncodeHaibGenotype.daf - lines changed 44, context: html, text, full: html, text
  • src/hg/encode/DAFs/3.0/hg19/wgEncodeHaibMethyl27.daf - lines changed 40, context: html, text, full: html, text
  • src/hg/encode/DAFs/3.0/hg19/wgEncodeHaibMethyl450.daf - lines changed 39, context: html, text, full: html, text
  • src/hg/encode/DAFs/3.0/hg19/wgEncodeHaibMethylRrbs.daf - lines changed 1, context: html, text, full: html, text
  • src/hg/encode/DAFs/3.0/hg19/wgEncodeHaibRnaSeq.daf - lines changed 65, context: html, text, full: html, text
  • src/hg/encode/DAFs/3.0/hg19/wgEncodeHaibTfbs.daf - lines changed 59, context: html, text, full: html, text
  • src/hg/encode/DAFs/3.0/hg19/wgEncodeMapability.daf - lines changed 23, context: html, text, full: html, text
  • src/hg/encode/DAFs/3.0/hg19/wgEncodeOpenChromChip.daf - lines changed 62, context: html, text, full: html, text
  • src/hg/encode/DAFs/3.0/hg19/wgEncodeOpenChromDnase.daf - lines changed 63, context: html, text, full: html, text
  • src/hg/encode/DAFs/3.0/hg19/wgEncodeOpenChromFaire.daf - lines changed 60, context: html, text, full: html, text
  • src/hg/encode/DAFs/3.0/hg19/wgEncodeRikenCage.daf - lines changed 70, context: html, text, full: html, text
  • src/hg/encode/DAFs/3.0/hg19/wgEncodeSunyAlbanyGeneSt.daf - lines changed 22, context: html, text, full: html, text
  • src/hg/encode/DAFs/3.0/hg19/wgEncodeSunyAlbanyTiling.daf - lines changed 25, context: html, text, full: html, text
  • src/hg/encode/DAFs/3.0/hg19/wgEncodeSunyRipSeq.daf - lines changed 51, context: html, text, full: html, text
  • src/hg/encode/DAFs/3.0/hg19/wgEncodeSunySwitchgear.daf - lines changed 1, context: html, text, full: html, text
  • src/hg/encode/DAFs/3.0/hg19/wgEncodeSydhHistone.daf - lines changed 58, context: html, text, full: html, text
  • src/hg/encode/DAFs/3.0/hg19/wgEncodeSydhNsome.daf - lines changed 46, context: html, text, full: html, text
  • src/hg/encode/DAFs/3.0/hg19/wgEncodeSydhTfbs.daf - lines changed 56, context: html, text, full: html, text
  • src/hg/encode/DAFs/3.0/hg19/wgEncodeUchicagoTfbs.daf - lines changed 60, context: html, text, full: html, text
  • src/hg/encode/DAFs/3.0/hg19/wgEncodeUmMassWengTfbsValid.daf - lines changed 25, context: html, text, full: html, text
  • src/hg/encode/DAFs/3.0/hg19/wgEncodeUmassDekker5C.daf - lines changed 23, context: html, text, full: html, text
  • src/hg/encode/DAFs/3.0/hg19/wgEncodeUncBsuProt.daf - lines changed 39, context: html, text, full: html, text
  • src/hg/encode/DAFs/3.0/hg19/wgEncodeUw5C.daf - lines changed 28, context: html, text, full: html, text
  • src/hg/encode/DAFs/3.0/hg19/wgEncodeUwAffyExonArray.daf - lines changed 35, context: html, text, full: html, text
  • src/hg/encode/DAFs/3.0/hg19/wgEncodeUwDgf.daf - lines changed 70, context: html, text, full: html, text
  • src/hg/encode/DAFs/3.0/hg19/wgEncodeUwDnase.daf - lines changed 61, context: html, text, full: html, text
  • src/hg/encode/DAFs/3.0/hg19/wgEncodeUwHistone.daf - lines changed 58, context: html, text, full: html, text
  • src/hg/encode/DAFs/3.0/hg19/wgEncodebuOrchid.daf - lines changed 33, context: html, text, full: html, text
• Adding in the commented out fileSortOrder line in case we want to leak this ever
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeAffyRnaChip.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeCaltechRnaSeq.new.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeCshlLongRnaSeq.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeCshlShortRnaSeq.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeGisDnaPet.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeGisPet.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeGisRnaSeq.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeHelicosRnaSeq.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaChipSeq.new.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaMethylSeq.new.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaRnaSeq.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeMapability.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeRikenCage.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeUwChIPSeq.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeUwDGF.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeYaleChIPseq.new.ra - lines changed 1, context: html, text, full: html, text
• Changed the min and max display, dropped the reference to pink and purple, dropped some of the color tools
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.html - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.ra - lines changed 7, context: html, text, full: html, text