File Changes for cricket

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

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