File Changes for wong

v262_base to v263_preview (2012-01-24 to 2012-01-31) v263

• python/lib/ucscgenomics/mkChangeNotes.py
  • lines changed 8, context: html, text, full: html, text
    added md5sum repush options for those rare situations where something changes md5sums between releases, but retains the same filename, also added the outputting of an attic files list
  • lines changed 3, context: html, text, full: html, text
    attic for single release mode
• python/lib/ucscgenomics/ucscUtils.py
  • lines changed 27, context: html, text, full: html, text
    changed over to Needleman-Wunsch for alignment of lists
  • lines changed 27, context: html, text, full: html, text
    This somehow included cv.ra changes that I don't remember adding in. Revert "changed over to Needleman-Wunsch for alignment of lists" This reverts commit c6bd349fa19566d37c1ac02a42865a9031420acb.
  • lines changed 27, context: html, text, full: html, text
    moved to Needleman-Wunsch for alignment of lists, left in code to convert to Smith-Waterman if this proves to be a bad decision
• src/hg/encode/encodeMkFilesList/encodeMkFilesList
  • lines changed 71, context: html, text, full: html, text
    many efficiency improvements
  • lines changed 8, context: html, text, full: html, text
    fixed a bug where a link that used to be a file in the history persisted between passes of the history
• src/hg/encode/encodeQaCheckHgdownloadFiles/makefile
  • lines changed 1, context: html, text, full: html, text
    changed makefile clean messages to reflect the script itself
• src/hg/encode/encodeQaInit/makefile
  • lines changed 1, context: html, text, full: html, text
    changed clean message
• src/hg/encode/encodeQaPrepareRelease/encodeQaPrepareRelease
  • lines changed 35, context: html, text, full: html, text
    now prints sorted makefile for metaDb, and more status messages so you know what's going on
  • lines changed 8, context: html, text, full: html, text
    fixed a bug where if it is release 1, and no betaMetaDb.ra exists, the program would crash.
• src/hg/encode/encodeQaPrepareRelease/makefile
  • lines changed 1, context: html, text, full: html, text
    changed makefile clean messages to reflect the script itself
• src/hg/encode/encodeQaSqlRelease/makefile
  • lines changed 1, context: html, text, full: html, text
    changed makefile clean messages to reflect the script itself
• src/hg/encode/qaEncodeTracks2/makefile
  • lines changed 27, context: html, text, full: html, text
    adding in makefile for qaEncodeTracks
• src/hg/encode/qaTableCheck/makefile
  • lines changed 1, context: html, text, full: html, text
    changed makefile clean messages to reflect the script itself
• src/hg/encode/qaUpdateMetadata/makefile
  • lines changed 1, context: html, text, full: html, text
    changed makefile clean messages to reflect the script itself
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeHaibTfbs.release2.notes
  • lines changed 261, context: html, text, full: html, text
    updated the notes for haib tfbs
  • lines changed 163, context: html, text, full: html, text
    corrected notes
  • lines changed 12, context: html, text, full: html, text
    updated notes
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 336, context: html, text, full: html, text
    correct comment locations - Willy
  • lines changed 3, context: html, text, full: html, text
    Willy's copy was liek an hour old, putting in other changes back
• src/hg/makeDb/trackDb/cv/public/cv.ra
  • lines changed 324, context: html, text, full: html, text
    changed over to Needleman-Wunsch for alignment of lists
  • lines changed 324, context: html, text, full: html, text
    This somehow included cv.ra changes that I don't remember adding in. Revert "changed over to Needleman-Wunsch for alignment of lists" This reverts commit c6bd349fa19566d37c1ac02a42865a9031420acb.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra
  • lines changed 695, context: html, text, full: html, text
    adding in lots of replacement files
  • lines changed 29, context: html, text, full: html, text
    added in md5sums
  • lines changed 29, context: html, text, full: html, text
    revoking the old U87 experiments
  • lines changed 2141, context: html, text, full: html, text
    renaming Control to Reverse crosslinks
  • lines changed 2, context: html, text, full: html, text
    updated md5sum
  • lines changed 63, context: html, text, full: html, text
    expIds and one correction
  • lines changed 7, context: html, text, full: html, text
    update dates on things I missed
  • lines changed 1066, context: html, text, full: html, text
    updating gzipped files wth md5sums of the internal contents
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromChip.ra
  • lines changed 119, context: html, text, full: html, text
    uppdated md5sums for new files and internal contents of gzips
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromDnase.ra
  • lines changed 166, context: html, text, full: html, text
    uppdated md5sums for new files and internal contents of gzips
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromFaire.ra
  • lines changed 81, context: html, text, full: html, text
    uppdated md5sums for new files and internal contents of gzips
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromSynth.ra
  • lines changed 18, context: html, text, full: html, text
    uppdated md5sums for new files and internal contents of gzips
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra
  • lines changed 880, context: html, text, full: html, text
    changed md5sums of gzips to internal contents
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDgf.ra
  • lines changed 106, context: html, text, full: html, text
    uppdated md5sums for new files and internal contents of gzips
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDnase.ra
  • lines changed 574, context: html, text, full: html, text
    uppdated md5sums for new files and internal contents of gzips
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwHistone.ra
  • lines changed 688, context: html, text, full: html, text
    uppdated md5sums for new files and internal contents of gzips
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwTfbs.ra
  • lines changed 421, context: html, text, full: html, text
    uppdated md5sums for new files and internal contents of gzips
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/makefile
  • lines changed 2, context: html, text, full: html, text
    sorting the makefile for cleanliness' sake
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/makefile
  • lines changed 4, context: html, text, full: html, text
    sorting the makefile for cleanliness' sake
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.release2.html
  • lines changed 30, context: html, text, full: html, text
    pre-qa fixes for haib tfbs
  • lines changed 1, context: html, text, full: html, text
    fixed link to not be going to a directory
  • lines changed 182, context: html, text, full: html, text
    made it more searchable
  • lines changed 1, context: html, text, full: html, text
    fixed missing period
  • lines changed 12, context: html, text, full: html, text
    added in release notes
  • lines changed 7, context: html, text, full: html, text
    fixed release notes
  • lines changed 7, context: html, text, full: html, text
    corrected capitalization of ChIP-seq
  • lines changed 27, context: html, text, full: html, text
    added in Flo's changes to the description page
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.release2.ra
  • lines changed 1, context: html, text, full: html, text
    pre-qa fixes for haib tfbs
  • lines changed 72, context: html, text, full: html, text
    revoking old U87 tracks
  • lines changed 96, context: html, text, full: html, text
    adding in remapped U87 tracks
  • lines changed 12, context: html, text, full: html, text
    fixed long labels
  • lines changed 12, context: html, text, full: html, text
    short labels for haib tfbs
  • lines changed 28, context: html, text, full: html, text
    renaming Control to Reverse crosslinks