File Changes for wong

v263_base to v264_preview (2012-02-14 to 2012-02-21) v264

• python/lib/ucscgenomics/mkChangeNotes.py
  • lines changed 1, context: html, text, full: html, text
    forgot to also remove revoked tables from the change table status set, possibly need to remove attic, but i'll do it if the problem comes up
  • lines changed 17, context: html, text, full: html, text
    changed the reporting of changed tables state to be a critical error
• src/hg/encode/encodeMkFilesList/encodeMkFilesList
  • lines changed 2, context: html, text, full: html, text
    the threading of the md5sums was causing problems with the database objects not being able to be clones, so i dosconnect fom the database, then reconnect after making the md5sums
  • lines changed 70, context: html, text, full: html, text
    changed the gzip md5sum function to check internally for the contents, but report the external md5sum to the metaDb
• src/hg/encode/encodeQaCheckHgdownloadFiles/encodeQaCheckHgdownloadFiles
  • lines changed 2, context: html, text, full: html, text
    changed it to show the server and foldername onthe same line
• src/hg/encode/encodeQaInit/encodeQaInit
  • lines changed 10, context: html, text, full: html, text
    changed it to complain and die upon subId setting to reviewing failure
• src/hg/encode/qaAddTrackReferences/makefile
  • lines changed 28, context: html, text, full: html, text
    first draft of qaAddTrackReferences
• src/hg/encode/qaAddTrackReferences/qaAddTrackReferences
  • lines changed 423, context: html, text, full: html, text
    first draft of qaAddTrackReferences
  • lines changed 60, context: html, text, full: html, text
    removed unnecessary lines
  • lines changed 17, context: html, text, full: html, text
    changed how collective name is put in the author list. It's always put at the front now.
• src/hg/encode/qaEncodeTracks2/qaEncodeTracks
  • lines changed 8, context: html, text, full: html, text
    uncomment parser line, and reomved Test \d: from test names
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeHaibTfbs.release2.notes
  • lines changed 135, context: html, text, full: html, text
    updated notes again
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeUwHistone.release3.notes
  • lines changed 30, context: html, text, full: html, text
    corrected notes, last time was premature
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 16, context: html, text, full: html, text
    added in provisional views for haib Bisulfite
  • lines changed 2, context: html, text, full: html, text
    for the merge
  • lines changed 16, context: html, text, full: html, text
    removing temporary provisional views
  • lines changed 1, context: html, text, full: html, text
    changing tag to conform to norm
  • lines changed 95, context: html, text, full: html, text
    added in antibody target to the decsription field (Willy)
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeBroadHistone.ra
  • lines changed 687, context: html, text, full: html, text
    correcting for the gzip bug error in mkFilesList
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlShortRnaSeq.ra
  • lines changed 145, context: html, text, full: html, text
    more internal gzip bug fixes
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibBisulfate.ra
  • lines changed 115, context: html, text, full: html, text
    added in provisional views for haib Bisulfite
  • lines changed 157, context: html, text, full: html, text
    more fake stanzas
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibRnaSeq.ra
  • lines changed 21, context: html, text, full: html, text
    expIds and accessions for rna seq
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra
  • lines changed 9, context: html, text, full: html, text
    some merge problem needs this
  • lines changed 9, context: html, text, full: html, text
    more lab found errors
  • lines changed 21, context: html, text, full: html, text
    renaming some files before they are released
  • lines changed 9, context: html, text, full: html, text
    reverted a metaDB change, becuase hte objects already went out in release 1
  • lines changed 191, context: html, text, full: html, text
    renamed objects to now have antibody vendor id
  • lines changed 183, context: html, text, full: html, text
    added in FoxM1 experiment
  • lines changed 17, context: html, text, full: html, text
    added in md5sums
  • lines changed 37, context: html, text, full: html, text
    expIds for haib
  • lines changed 1076, context: html, text, full: html, text
    more internal gzip bug fixes
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromDnase.ra
  • lines changed 113, context: html, text, full: html, text
    md5sums for open chrom dnase
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDgf.ra
  • lines changed 98, context: html, text, full: html, text
    correcting for the gzip bug error in mkFilesList
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwHistone.ra
  • lines changed 271, context: html, text, full: html, text
    expIds and other mdb fixes
  • lines changed 3, context: html, text, full: html, text
    more metadata corrections
  • lines changed 627, context: html, text, full: html, text
    fixed internal gzip md5sum
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwTfbs.ra
  • lines changed 409, context: html, text, full: html, text
    more internal gzip bug fixes
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
  • lines changed 2, context: html, text, full: html, text
    added in the rest of the bisulfate test track
  • lines changed 1, context: html, text, full: html, text
    forgot alpha tag
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibBisulfate.html
  • lines changed 125, context: html, text, full: html, text
    added in the rest of the bisulfate test track
  • lines changed 74, context: html, text, full: html, text
    flo's version of haib bisulfate
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibBisulfate.ra
  • lines changed 84, context: html, text, full: html, text
    added in the rest of the bisulfate test track
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibRnaSeq.html
  • lines changed 41, context: html, text, full: html, text
    pre=qa fixes and reformed references
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibRnaSeq.ra
  • lines changed 1, context: html, text, full: html, text
    changed view limit according to lab
  • lines changed 47, context: html, text, full: html, text
    changed short labels according to lab
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.release2.ra
  • lines changed 8, context: html, text, full: html, text
    renaming some files before they are released
  • lines changed 64, context: html, text, full: html, text
    renamed objects to now have antibody vendor id
  • lines changed 45, context: html, text, full: html, text
    added in FoxM1 experiment
  • lines changed 1, context: html, text, full: html, text
    changed filter to all for treatment
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.release3.html
  • lines changed 1, context: html, text, full: html, text
    fixed tense
  • lines changed 17, context: html, text, full: html, text
    fixed html and order of cells in list
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.release3.ra
  • lines changed 42, context: html, text, full: html, text
    I have no idea how that one got commented out
  • lines changed 1, context: html, text, full: html, text
    fixed html and order of cells in list
  • lines changed 2, context: html, text, full: html, text
    fixed alphabetization
  • lines changed 1, context: html, text, full: html, text
    this time for real on alphabetize
  • lines changed 1, context: html, text, full: html, text
    fixed capitalization
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwTfbs.release3.html
  • lines changed 3, context: html, text, full: html, text
    pre-qa fixes
• src/hg/utils/automation/HgDb.pm
  • lines changed 2, context: html, text, full: html, text
    correcting some errors
  • lines changed 1, context: html, text, full: html, text
    removed line that was left from debugging