File Changes for wong

v260_base to v261_preview (2011-12-06 to 2011-12-13) v261

• python/lib/ucscgenomics/mkChangeNotes.py
  • lines changed 9, context: html, text, full: html, text
    added some attributes needed externally
  • lines changed 24, context: html, text, full: html, text
    added verbose messagings to mkChange Notes
• src/hg/encode/DAFs/2.0/uwChipSeq.daf
  • lines changed 1, context: html, text, full: html, text
    updated uw chipseq dafs
• src/hg/encode/DAFs/2.0/uwTfbs.daf
  • lines changed 1, context: html, text, full: html, text
    updated uw chipseq dafs
• src/hg/encode/encodeMkChangeNotes/encodeMkChangeNotes
  • lines changed 2, context: html, text, full: html, text
    added verbose messagings to mkChange Notes
• src/hg/encode/encodeMkChangeNotes/test/CurrentMkChangeNotes.py
  • lines changed 33, context: html, text, full: html, text
    added verbose messagings to mkChange Notes
• src/hg/encode/encodeMkFilesList/encodeMkFilesList
  • lines changed 1, context: html, text, full: html, text
    sorted the md5sum files array
• src/hg/encode/encodeQaCheckHgdownloadFiles/encodeQaCheckHgdownloadFiles
  • lines changed 73, context: html, text, full: html, text
    first draft of tool to check if files exist in hgdownload
  • lines changed 53, context: html, text, full: html, text
    changed it to a recursive crawler so it can get all subdirectory contents
• src/hg/encode/encodeQaCheckHgdownloadFiles/makefile
  • lines changed 27, context: html, text, full: html, text
    first draft of tool to check if files exist in hgdownload
• src/hg/encode/encodeQaInit/encodeQaInit
  • lines changed 8, context: html, text, full: html, text
    first draft of tool to check if files exist in hgdownload
  • lines changed 8, context: html, text, full: html, text
    added ability to print out full files and tables list
  • lines changed 2, context: html, text, full: html, text
    corrected sample commands
  • lines changed 2, context: html, text, full: html, text
    added verbose mode to the local mkChangeNotes
• src/hg/encode/encodeValidate/doEncodeValidate.pl
  • lines changed 60, context: html, text, full: html, text
    reworked the validateBed subroutine
  • lines changed 11, context: html, text, full: html, text
    changed the bed validation rules a bit
  • lines changed 17, context: html, text, full: html, text
    added in chrom Size check and streamlined another check
  • lines changed 5, context: html, text, full: html, text
    added in more info for error message
  • lines changed 18, context: html, text, full: html, text
    streamlined the validateBed routine
• src/hg/encode/qaTableCheck/makefile
  • lines changed 27, context: html, text, full: html, text
    added in first draft of program to check a list of tables against the ones on the RR
• src/hg/encode/qaTableCheck/qaTableCheck
  • lines changed 54, context: html, text, full: html, text
    added in first draft of program to check a list of tables against the ones on the RR
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeOpenChromChip.release2.notes
  • lines changed 708, context: html, text, full: html, text
    added release2 notes for open chrom tracks
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeOpenChromFaire.release2.notes
  • lines changed 487, context: html, text, full: html, text
    added release2 notes for open chrom tracks
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 3, context: html, text, full: html, text
    added cd20 protocol to the donor children
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCaltechRnaSeq.ra
  • lines changed 217, context: html, text, full: html, text
    replaced the bad fastqs
  • lines changed 9, context: html, text, full: html, text
    added md5sums
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGencodeV9.ra
  • lines changed 18, context: html, text, full: html, text
    removing duplicate metaDb entry
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibGenotype.ra
  • lines changed 2, context: html, text, full: html, text
    corrected space and added md5sum
  • lines changed 2, context: html, text, full: html, text
    revoking a bad table, and a replaced table
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra
  • lines changed 217, context: html, text, full: html, text
    added md5sums
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromChip.ra
  • lines changed 3, context: html, text, full: html, text
    restored some lines so the revoked table would get properly displayed in mkChangeNotes
  • lines changed 271, context: html, text, full: html, text
    added None treatment valeus to objects missing them
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwHistone.ra
  • lines changed 2, context: html, text, full: html, text
    updated md5sum
  • lines changed 3334, context: html, text, full: html, text
    batch added a lot of new tracks
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwTfbs.ra
  • lines changed 1, context: html, text, full: html, text
    added in bai in fileName
  • lines changed 1, context: html, text, full: html, text
    Revert "added in bai in fileName" This reverts commit 3445aea17002c3c53f9ac99eccccb17710df7b65.
  • lines changed 533, context: html, text, full: html, text
    batch added tfbs tracks
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
  • lines changed 2, context: html, text, full: html, text
    added alpha .ra for mapability
  • lines changed 0, context: html, text, full: html, text
    removed extra space
  • lines changed 2, context: html, text, full: html, text
    made changes to revoke in a patch.ra for qa to review over
  • lines changed 1, context: html, text, full: html, text
    added in include statement for new haib genotype trackDb
  • lines changed 2, context: html, text, full: html, text
    checking patch for uwhistone
  • lines changed 3, context: html, text, full: html, text
    changed trackDb to include the release2 and 3 histone
  • lines changed 3, context: html, text, full: html, text
    fixed a mispelling
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCaltechRnaSeq.new.html
  • lines changed 4, context: html, text, full: html, text
    changed headers to h4 for sub-categories
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGisChiaPet.ra
  • lines changed 7, context: html, text, full: html, text
    uncommented out a track that works now
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibGenotype.new.html
  • lines changed 82, context: html, text, full: html, text
    renamed files to new release convention
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibGenotype.new.ra
  • lines changed 743, context: html, text, full: html, text
    renamed files to new release convention
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibGenotype.release2.html
  • lines changed 82, context: html, text, full: html, text
    renamed files to new release convention
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibGenotype.release2.ra
  • lines changed 743, context: html, text, full: html, text
    renamed files to new release convention
  • lines changed 6, context: html, text, full: html, text
    commenting out version 1 data
  • lines changed 8, context: html, text, full: html, text
    revoking a bad table, and a replaced table
  • lines changed 9, context: html, text, full: html, text
    changed html and added stanza back in
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.new.html
  • lines changed 166, context: html, text, full: html, text
    copying over html to new.html
  • lines changed 166, context: html, text, full: html, text
    renaming to new release convention
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.patch.ra
  • lines changed 6839, context: html, text, full: html, text
    made changes to revoke in a patch.ra for qa to review over
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.ra
  • lines changed 28, context: html, text, full: html, text
    Revert "the K562/BCL3 objects need to be revoke also" This reverts commit bf663af7e2a654939d6c8395a50661e48658f0a5.
  • lines changed 64, context: html, text, full: html, text
    Revert "revokeing HEY1 tracks in trackDb, this will leak out at the the of the week." This reverts commit bda0bda2243900af9728abec0406bf9b3d8e3614.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.release2.html
  • lines changed 166, context: html, text, full: html, text
    renaming to new release convention
  • lines changed 19, context: html, text, full: html, text
    added in html about shRNA verfication data
  • lines changed 1, context: html, text, full: html, text
    forgot a comma
  • lines changed 8, context: html, text, full: html, text
    corrected paragraph for validation
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.release2.ra
  • lines changed 1, context: html, text, full: html, text
    added in html about shRNA verfication data
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromFaire.new.ra
  • lines changed 1, context: html, text, full: html, text
    fixed a broken label
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.html
  • lines changed 92, context: html, text, full: html, text
    moved html over to release2
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.new.html
  • lines changed 92, context: html, text, full: html, text
    renamed histone html to release3
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.new.ra
  • lines changed 5242, context: html, text, full: html, text
    renamed new.ra to patch.ra
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.patch.ra
  • lines changed 5242, context: html, text, full: html, text
    renamed new.ra to patch.ra
  • lines changed 1, context: html, text, full: html, text
    checking patch for uwhistone
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.ra
  • lines changed 5241, context: html, text, full: html, text
    renamed histone to release2.ra
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.release2.html
  • lines changed 92, context: html, text, full: html, text
    moved html over to release2
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.release2.ra
  • lines changed 5241, context: html, text, full: html, text
    renamed histone to release2.ra
  • lines changed 1, context: html, text, full: html, text
    moved histone over to release2
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.release3.html
  • lines changed 92, context: html, text, full: html, text
    renamed histone html to release3
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.release3.ra
  • lines changed 5242, context: html, text, full: html, text
    added in release3 ra for histone
  • lines changed 805, context: html, text, full: html, text
    batch added a lot of new tracks
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwTfbs.new.html
  • lines changed 91, context: html, text, full: html, text
    renamed to have release number
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwTfbs.new.ra
  • lines changed 3502, context: html, text, full: html, text
    renamed to have release number
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwTfbs.release2.html
  • lines changed 91, context: html, text, full: html, text
    renamed to have release number
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwTfbs.release2.ra
  • lines changed 3502, context: html, text, full: html, text
    renamed to have release number
  • lines changed 1, context: html, text, full: html, text
    created release3 trackDb
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwTfbs.release3.ra
  • lines changed 3502, context: html, text, full: html, text
    created release3 trackDb
  • lines changed 92, context: html, text, full: html, text
    batch added tfbs tracks