Commits for wong

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

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