Commits for cricket

v263_preview2 to v263_base (2011-02-07 to 2012-02-14) v263

• Added protocol TAP-Only and found the missing subId 4061 data, see ticket 1634
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlShortRnaSeq.ra - lines changed 406, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.release2.ra - lines changed 375, context: html, text, full: html, text
• Cleaning out old comments mostly, a few more changes according to ticket 1634
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.release2.html - lines changed 90, context: html, text, full: html, text
• Name change to add Tap protocol into the names
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisRnaPet.ra - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.release2.ra - lines changed 116, context: html, text, full: html, text
• This was part of the name change to Tap, I am not sure how it didn't get checked in
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlShortRnaSeq.ra - lines changed 818, context: html, text, full: html, text
• Restructured the paragraphs
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV10.html - lines changed 149, context: html, text, full: html, text
• Fixing merge conflict, this will likely need more review, the merge went very badly
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV10.html - lines changed 46, context: html, text, full: html, text
• Adding the Tap protocol to yet more object names
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlShortRnaSeq.ra - lines changed 1427, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.release2.ra - lines changed 186, context: html, text, full: html, text
• Clean up BJ Rep 1 rename issue
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlShortRnaSeq.ra - lines changed 9, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.release2.ra - lines changed 6, context: html, text, full: html, text
• Fixing the ExonV7 files to have Tap in the name
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlShortRnaSeq.ra - lines changed 872, context: html, text, full: html, text
• Finding the missing files from 4468 submission
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlShortRnaSeq.ra - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.release2.ra - lines changed 1, context: html, text, full: html, text
• Resubmit of Contigs as Tap with no floats in the score field
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlShortRnaSeq.ra - lines changed 267, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.release2.ra - lines changed 26, context: html, text, full: html, text
• md5sums
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlShortRnaSeq.ra - lines changed 1432, context: html, text, full: html, text
• Proposed Changes to Take new file types and protocol
  • src/hg/encode/DAFs/3.0/hg19/wgEncodeUncBsuProt.daf - lines changed 20, context: html, text, full: html, text
• Trying to fix issues in the ticket for Katrina, this is a work in progress that I am checking in for her to put on beta
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV10.html - lines changed 57, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV10.ra - lines changed 13, context: html, text, full: html, text
• Adding terms for Proteogenomics protocols
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 7, context: html, text, full: html, text
• Still trying to resolve color with Katrina
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV10.ra - lines changed 19, context: html, text, full: html, text
• Changing the Display Section to match other encode tracks
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV10.html - lines changed 21, context: html, text, full: html, text
• Merging UncBsuProt and UncBsuProtFasp into UncBsuProt.release2
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUncBsuProt.ra - lines changed 46, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUncBsuProtFasp.obsolete.ra - lines changed 40, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUncBsuProtFasp.ra - lines changed 40, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProt.new.ra - lines changed 108, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProt.release2.html - lines changed 174, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProt.release2.ra - lines changed 110, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProtFasp.html - lines changed 175, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProtFasp.ra - lines changed 32, context: html, text, full: html, text
• Removing protocol as a expID
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUncBsuProt.ra - lines changed 1, context: html, text, full: html, text
• Adding DCC accessions
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlShortRnaSeq.ra - lines changed 9, context: html, text, full: html, text
• The TssHmm will now be displayed
  • src/hg/encode/DAFs/3.0/hg19/wgEncodeRikenCage.daf - lines changed 20, context: html, text, full: html, text
• Cleaned up attic labels to fix the notes file
  • src/hg/makeDb/doc/encodeDccHg19/wgEncodeCshlShort.release2.notes - lines changed 871, context: html, text, full: html, text
  • src/hg/makeDb/doc/encodeDccHg19/wgEncodeCshlShortRnaSeq.release2.notes - lines changed 925, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlShortRnaSeq.ra - lines changed 4, context: html, text, full: html, text
• Standard Naming
  • src/hg/makeDb/doc/encodeDccHg19/wgEncodeCshlShort.release1.notes - lines changed 196, context: html, text, full: html, text
  • src/hg/makeDb/doc/encodeDccHg19/wgEncodeCshlShortRnaSeq.release1.notes - lines changed 196, context: html, text, full: html, text
• Fixed labels and made tags not start with numerals
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.release2.ra - lines changed 169, context: html, text, full: html, text
• Changing the 2 H1-hesc contigs files to have V2 and have -1 instead of .
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlShortRnaSeq.ra - lines changed 11, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.release2.ra - lines changed 5, context: html, text, full: html, text
• Adding the V2 Contigs to the notes file and the mdb
  • src/hg/makeDb/doc/encodeDccHg19/wgEncodeCshlShortRnaSeq.release2.notes - lines changed 7, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlShortRnaSeq.ra - lines changed 3, context: html, text, full: html, text
• wgEncodeRikenCage.release3.ra
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.release3.ra - lines changed 3, context: html, text, full: html, text
• Updating the dafs to what we are using now
  • src/hg/encode/DAFs/3.0/hg19/wgEncodeCshlLongRnaSeq.daf - lines changed 22, context: html, text, full: html, text
  • src/hg/encode/DAFs/3.0/hg19/wgEncodeCshlShortRnaSeq.daf - lines changed 1, context: html, text, full: html, text
• Fixed errant tabs according to code review
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProt.release2.ra - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
• html changes according to preQA ticket http://redmine.soe.ucsc.edu/issues/1634#note-96
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.release2.html - lines changed 9, context: html, text, full: html, text
• Changing hard links to relative links
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeCaltechRnaSc.html - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.release2.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.release2.html - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProt.release2.html - lines changed 1, context: html, text, full: html, text