File Changes for wong

v259_base to v260_preview (2011-11-07 to 2011-11-15) v260

• python/lib/ucscgenomics/mkChangeNotes.py
  • lines changed 4, context: html, text, full: html, text
    fixed some error print in solo mode with errors
• src/hg/encode/encodeLoad/doEncodeLoad.pl
  • lines changed 13, context: html, text, full: html, text
    Revert "changed how encodeValidate and friends uses packages to allow for same directory location of the packages" This reverts commit 371b1e65141e2a3ef55220fee8a120e8fa90dc26.
  • lines changed 7, context: html, text, full: html, text
    Revert "removed the need for labs.ra" This reverts commit 8dc382b443d003200c40eb60b1957d6bfcec5493.
• src/hg/encode/encodeLoad/doEncodeUnload.pl
  • lines changed 13, context: html, text, full: html, text
    Revert "changed how encodeValidate and friends uses packages to allow for same directory location of the packages" This reverts commit 371b1e65141e2a3ef55220fee8a120e8fa90dc26.
  • lines changed 2, context: html, text, full: html, text
    Revert "removed the need for labs.ra" This reverts commit 8dc382b443d003200c40eb60b1957d6bfcec5493.
• src/hg/encode/encodeMkChangeNotes/encodeMkChangeNotes
  • lines changed 557, context: html, text, full: html, text
    moved old version to .v09 and moved mkChangeNotes to encodeMkChangeNotes
• src/hg/encode/encodeMkChangeNotes/encodeMkChangeNotes.v09
  • lines changed 565, context: html, text, full: html, text
    moved old version to .v09 and moved mkChangeNotes to encodeMkChangeNotes
• src/hg/encode/encodeMkChangeNotes/test/CurrentMkChangeNotes.py
  • lines changed 637, context: html, text, full: html, text
    changed mkChangeNotes test over to encodeMkChangeNotes and added README
• src/hg/encode/encodeMkChangeNotes/test/CurrentMkChangeNotes.pyc
  • lines changed 0, context: html, text, full: html, text
    changed mkChangeNotes test over to encodeMkChangeNotes and added README
  • lines changed 0, context: html, text, full: html, text
    accidentally added the compiled library
• src/hg/encode/encodeMkChangeNotes/test/README
  • lines changed 25, context: html, text, full: html, text
    changed mkChangeNotes test over to encodeMkChangeNotes and added README
• src/hg/encode/encodeMkChangeNotes/test/mkChangeTest
  • lines changed 83, context: html, text, full: html, text
    changed mkChangeNotes test over to encodeMkChangeNotes and added README
• src/hg/encode/encodeMkChangeNotes/test/testRunner
  • lines changed 61, context: html, text, full: html, text
    changed mkChangeNotes test over to encodeMkChangeNotes and added README
• src/hg/encode/encodeQaInit/encodeQaInit
  • lines changed 1, context: html, text, full: html, text
    added information to an error to say that it is fatal
  • lines changed 4, context: html, text, full: html, text
    added more to error message
  • lines changed 5, context: html, text, full: html, text
    made other error message consistent
  • lines changed 8, context: html, text, full: html, text
    added test headers so you know what's up
• src/hg/encode/encodeQaPrepareRelease/encodeQaPrepareRelease
  • lines changed 406, context: html, text, full: html, text
    first draft of qaPrepareRelease
  • lines changed 1, context: html, text, full: html, text
    removed hardcoded verbose output
  • lines changed 14, context: html, text, full: html, text
    made a check to see that you have a trackDb.ra in the trackDb dir
  • lines changed 3, context: html, text, full: html, text
    rebalanced whitespace, and made meta db diffs more descriptive
  • lines changed 31, context: html, text, full: html, text
    changed metaDb diff output again, alphabetizes and aggregates dropped and new stanzas
• src/hg/encode/encodeQaPrepareRelease/makefile
  • lines changed 27, context: html, text, full: html, text
    first draft of qaPrepareRelease
• src/hg/encode/encodeQaSqlRelease/encodeQaSqlRelease
  • lines changed 2, context: html, text, full: html, text
    changed name in usage statement
• src/hg/encode/encodeValidate/doEncodeValidate.pl
  • lines changed 14, context: html, text, full: html, text
    Revert "changed how encodeValidate and friends uses packages to allow for same directory location of the packages" This reverts commit 371b1e65141e2a3ef55220fee8a120e8fa90dc26.
  • lines changed 28, context: html, text, full: html, text
    Revert "removed the need for labs.ra" This reverts commit 8dc382b443d003200c40eb60b1957d6bfcec5493.
  • lines changed 4, context: html, text, full: html, text
    Revert "removed the code for pi.ra" This reverts commit a8d2cd12a9005d8bb60f1c89c900ea5a76c145b6.
  • lines changed 2, context: html, text, full: html, text
    removed the need to labs.ra in encodeValidate only
  • lines changed 9, context: html, text, full: html, text
    fixed the Error: 1 error
  • lines changed 2, context: html, text, full: html, text
    removed comment referencing pi.ra
• src/hg/encode/encodeValidate/newtest/README
  • lines changed 14, context: html, text, full: html, text
    fleshed out test some more
• src/hg/encode/encodeValidate/newtest/allGood/out/mdb.txt
  • lines changed 3, context: html, text, full: html, text
    fixed some issues with tester. no long need a copy of doEncodeValidate.pl in the directory
• src/hg/encode/encodeValidate/newtest/allGood/out/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    fixed some issues with tester. no long need a copy of doEncodeValidate.pl in the directory
• src/hg/encode/encodeValidate/newtest/badDdfDafs/invalidFiletype/notest.cfg
  • lines changed 49, context: html, text, full: html, text
    fixed some issues with tester. no long need a copy of doEncodeValidate.pl in the directory
• src/hg/encode/encodeValidate/newtest/badDdfDafs/invalidFiletype/test.cfg
  • lines changed 49, context: html, text, full: html, text
    fleshed out test some more
• src/hg/encode/encodeValidate/newtest/baddafs/badDataVersion/out/mdb.txt
  • lines changed 2, context: html, text, full: html, text
    fixed some issues with tester. no long need a copy of doEncodeValidate.pl in the directory
• src/hg/encode/encodeValidate/newtest/baddafs/badDataVersion/out/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    fixed some issues with tester. no long need a copy of doEncodeValidate.pl in the directory
• src/hg/encode/encodeValidate/newtest/baddafs/noDataVersionComment/test.cfg
  • lines changed 1, context: html, text, full: html, text
    fixed some issues with tester. no long need a copy of doEncodeValidate.pl in the directory
• src/hg/encode/encodeValidate/newtest/config/pi.ra
  • lines changed 181, context: html, text, full: html, text
    removed pi.ra from teste config directory
• src/hg/encode/encodeValidate/newtest/doEncodeValidate.pl
  • lines changed 2409, context: html, text, full: html, text
    removed copy of doEncodeValidate
• src/hg/encode/encodeValidate/newtest/list
  • lines changed 18, context: html, text, full: html, text
    fixed some issues with tester. no long need a copy of doEncodeValidate.pl in the directory
  • lines changed 18, context: html, text, full: html, text
    fleshed out test some more
• src/hg/encode/encodeValidate/newtest/tester.pl
  • lines changed 19, context: html, text, full: html, text
    fixed some issues with tester. no long need a copy of doEncodeValidate.pl in the directory
• src/hg/encode/mkChangeNotes/makefile
  • lines changed 27, context: html, text, full: html, text
    changed mkChangeNotes test over to encodeMkChangeNotes and added README
• src/hg/encode/mkChangeNotes/mkChangeNotes
  • lines changed 61, context: html, text, full: html, text
    moved old version to .v09 and moved mkChangeNotes to encodeMkChangeNotes
• src/hg/encode/mkChangeNotes/tests/CurrentMkChangeNotes.py
  • lines changed 637, context: html, text, full: html, text
    changed mkChangeNotes test over to encodeMkChangeNotes and added README
• src/hg/encode/mkChangeNotes/tests/mkChangeTest
  • lines changed 83, context: html, text, full: html, text
    changed mkChangeNotes test over to encodeMkChangeNotes and added README
• src/hg/encode/mkChangeNotes/tests/testRunner
  • lines changed 61, context: html, text, full: html, text
    changed mkChangeNotes test over to encodeMkChangeNotes and added README
• src/hg/encode/qaRaDiff/makefile
  • lines changed 27, context: html, text, full: html, text
    added in qaRaDiff first draft
• src/hg/encode/qaRaDiff/qaRaDiff
  • lines changed 75, context: html, text, full: html, text
    added in qaRaDiff first draft
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra
  • lines changed 109, context: html, text, full: html, text
    revoked all the HEY1 entries, lab is not confident the antibody is binding to HEY1, looks like POL2 results
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
  • lines changed 1, context: html, text, full: html, text
    revoked all the HEY1 entries, lab is not confident the antibody is binding to HEY1, looks like POL2 results
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.new.ra
  • lines changed 8921, context: html, text, full: html, text
    revoked all the HEY1 entries, lab is not confident the antibody is binding to HEY1, looks like POL2 results
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.release2.ra
  • lines changed 8929, context: html, text, full: html, text
    revoked all the HEY1 entries, lab is not confident the antibody is binding to HEY1, looks like POL2 results
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.new.ra
  • lines changed 1, context: html, text, full: html, text
    changed visibility of hotspots to match the expected default behavior
• src/hg/utils/automation/Encode.pm
  • lines changed 21, context: html, text, full: html, text
    Revert "removed the need for labs.ra" This reverts commit 8dc382b443d003200c40eb60b1957d6bfcec5493.
  • lines changed 13, context: html, text, full: html, text
    Revert "removed the code for pi.ra" This reverts commit a8d2cd12a9005d8bb60f1c89c900ea5a76c145b6.
  • lines changed 3, context: html, text, full: html, text
    added comments to functions to be deprecated