Commits for mmaddren

v254_preview to v254_preview2 (2011-07-05 to 2011-07-12) v254

• removed protocols from the cv directory and put them in the correct spot on htdocsExtras
  • src/hg/makeDb/trackDb/cv/alpha/CD34+Mobilized_Stam_protocol.pdf - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
  • src/hg/makeDb/trackDb/cv/alpha/HBVP_Stam_protocol.pdf - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
  • src/hg/makeDb/trackDb/cv/alpha/HBVSMC_Stam_protocol.pdf - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
  • src/hg/makeDb/trackDb/cv/alpha/HMVECdAd_Stam_protocol.pdf - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
  • src/hg/makeDb/trackDb/cv/alpha/HPAEC_Stam_protocol.pdf - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
  • src/hg/makeDb/trackDb/cv/alpha/NHBE_Stam_protocol.pdf - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
• restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
  • python/lib/ucscgenomics/__init__.py - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
  • python/lib/ucscgenomics/cvfile/CvFile.py - lines changed 579, context: html, text, full: html, text
  • python/lib/ucscgenomics/cvfile/__init__.py - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
  • python/lib/ucscgenomics/cvfile/unittest/input/Antibody/BlankKey.ra - lines changed 25, context: html, text, full: html, text
  • python/lib/ucscgenomics/cvfile/unittest/input/Antibody/ExtraKey.ra - lines changed 26, context: html, text, full: html, text
  • python/lib/ucscgenomics/cvfile/unittest/input/Antibody/MissingKey.ra - lines changed 24, context: html, text, full: html, text
  • python/lib/ucscgenomics/cvfile/unittest/input/Antibody/NonmatchKey.ra - lines changed 25, context: html, text, full: html, text
  • python/lib/ucscgenomics/cvfile/unittest/input/Antibody/ValidStanza.ra - lines changed 36, context: html, text, full: html, text
  • python/lib/ucscgenomics/cvfile/unittest/input/CellLine/BlankKey.ra - lines changed 34, context: html, text, full: html, text
  • python/lib/ucscgenomics/cvfile/unittest/input/CellLine/ExtraKey.ra - lines changed 35, context: html, text, full: html, text
  • python/lib/ucscgenomics/cvfile/unittest/input/CellLine/MissingKey.ra - lines changed 33, context: html, text, full: html, text
  • python/lib/ucscgenomics/cvfile/unittest/input/CellLine/NonmatchKey.ra - lines changed 34, context: html, text, full: html, text
  • python/lib/ucscgenomics/cvfile/unittest/input/CellLine/ValidStanza.ra - lines changed 33, context: html, text, full: html, text
  • python/lib/ucscgenomics/cvfile/unittest/input/Mouse/BlankKey.ra - lines changed 37, context: html, text, full: html, text
  • python/lib/ucscgenomics/cvfile/unittest/input/Mouse/ExtraKey.ra - lines changed 38, context: html, text, full: html, text
  • python/lib/ucscgenomics/cvfile/unittest/input/Mouse/MissingKey.ra - lines changed 36, context: html, text, full: html, text
  • python/lib/ucscgenomics/cvfile/unittest/input/Mouse/NonmatchKey.ra - lines changed 37, context: html, text, full: html, text
  • python/lib/ucscgenomics/cvfile/unittest/input/Mouse/ValidStanza.ra - lines changed 37, context: html, text, full: html, text
  • python/lib/ucscgenomics/cvfile/unittest/testCvFile - lines changed 95, context: html, text, full: html, text
  • python/lib/ucscgenomics/ordereddict/OrderedDict.py - lines changed 58, context: html, text, full: html, text
  • python/lib/ucscgenomics/ordereddict/__init__.py - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
  • python/lib/ucscgenomics/rafile/RaFile.py - lines changed 183, context: html, text, full: html, text
  • python/lib/ucscgenomics/rafile/__init__.py - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
  • python/lib/ucscgenomics/rafile/unittest/testRaFile.py - lines changed 205, context: html, text, full: html, text
  • python/lib/ucscgenomics/rafile/unittest/testoutput/BasicDiff.out - lines changed 27, context: html, text, full: html, text
  • python/lib/ucscgenomics/rafile/unittest/testoutput/CommentsDiff.out - lines changed 31, context: html, text, full: html, text
  • python/lib/ucscgenomics/rafile/unittest/testoutput/DeleteItem.out - lines changed 39, context: html, text, full: html, text
  • python/lib/ucscgenomics/rafile/unittest/testoutput/ExtraneousWhitespace.out - lines changed 70, context: html, text, full: html, text
  • python/lib/ucscgenomics/rafile/unittest/testoutput/GetItem.out - lines changed 13, context: html, text, full: html, text
  • python/lib/ucscgenomics/rafile/unittest/testoutput/InlineCommentsDiff.out - lines changed 27, context: html, text, full: html, text
  • python/lib/ucscgenomics/rafile/unittest/testoutput/IterEntryItems.out - lines changed 27, context: html, text, full: html, text
  • python/lib/ucscgenomics/rafile/unittest/testoutput/IterEntryKeys.out - lines changed 27, context: html, text, full: html, text
  • python/lib/ucscgenomics/rafile/unittest/testoutput/IterEntryValues.out - lines changed 27, context: html, text, full: html, text
  • python/lib/ucscgenomics/rafile/unittest/testoutput/IterItems.out - lines changed 19, context: html, text, full: html, text
  • python/lib/ucscgenomics/rafile/unittest/testoutput/IterKeys.out - lines changed 11, context: html, text, full: html, text
  • python/lib/ucscgenomics/rafile/unittest/testoutput/IterValues.out - lines changed 41, context: html, text, full: html, text
  • python/lib/ucscgenomics/rafile/unittest/tests/BasicDiff.ra - lines changed 12, context: html, text, full: html, text
  • python/lib/ucscgenomics/rafile/unittest/tests/CommentsDiff.ra - lines changed 14, context: html, text, full: html, text
  • python/lib/ucscgenomics/rafile/unittest/tests/DeleteItem.ra - lines changed 18, context: html, text, full: html, text
  • python/lib/ucscgenomics/rafile/unittest/tests/DuplicateKeys.ra - lines changed 8, context: html, text, full: html, text
  • python/lib/ucscgenomics/rafile/unittest/tests/FunctionalityCheck.ra - lines changed 23, context: html, text, full: html, text
  • python/lib/ucscgenomics/rafile/unittest/tests/GetItem.ra - lines changed 5, context: html, text, full: html, text
  • python/lib/ucscgenomics/rafile/unittest/tests/InlineCommentsDiff.ra - lines changed 12, context: html, text, full: html, text
  • python/lib/ucscgenomics/rafile/unittest/tests/IterEntryItems.ra - lines changed 12, context: html, text, full: html, text
  • python/lib/ucscgenomics/rafile/unittest/tests/IterEntryKeys.ra - lines changed 12, context: html, text, full: html, text
  • python/lib/ucscgenomics/rafile/unittest/tests/IterEntryValues.ra - lines changed 12, context: html, text, full: html, text
  • python/lib/ucscgenomics/rafile/unittest/tests/IterItems.ra - lines changed 8, context: html, text, full: html, text
  • python/lib/ucscgenomics/rafile/unittest/tests/IterKeys.ra - lines changed 4, context: html, text, full: html, text
  • python/lib/ucscgenomics/rafile/unittest/tests/IterValues.ra - lines changed 19, context: html, text, full: html, text
  • python/lib/ucscgenomics/rafile/unittest/tests/MisplacedKeys.ra - lines changed 8, context: html, text, full: html, text
  • python/lib/ucscgenomics/rafile/unittest/tests/NonNewlineFile.ra - lines changed 5, context: html, text, full: html, text
  • python/lib/ucscgenomics/softfile/SoftFile.py - lines changed 390, context: html, text, full: html, text
  • python/lib/ucscgenomics/softfile/__init__.py - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
  • python/lib/ucscgenomics/softfile/unittest/testSoft - lines changed 10, context: html, text, full: html, text
  • python/programs/cvValidate/README - lines changed 1, context: html, text, full: html, text
  • python/programs/cvValidate/cvValidate - lines changed 22, context: html, text, full: html, text
  • python/programs/mkGeoPkg/README - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
  • python/programs/mkGeoPkg/mkGeoPkg - lines changed 419, context: html, text, full: html, text
  • python/style.txt - lines changed 44, context: html, text, full: html, text
  • python/ucscgenomics/__init__.py - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
  • python/ucscgenomics/cvValidate/README - lines changed 1, context: html, text, full: html, text
  • python/ucscgenomics/cvValidate/cvValidate - lines changed 22, context: html, text, full: html, text
  • python/ucscgenomics/lib/__init__.py - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
  • python/ucscgenomics/lib/cvfile/CvFile.py - lines changed 579, context: html, text, full: html, text
  • python/ucscgenomics/lib/cvfile/__init__.py - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
  • python/ucscgenomics/lib/cvfile/unittest/input/Antibody/BlankKey.ra - lines changed 25, context: html, text, full: html, text
  • python/ucscgenomics/lib/cvfile/unittest/input/Antibody/ExtraKey.ra - lines changed 26, context: html, text, full: html, text
  • python/ucscgenomics/lib/cvfile/unittest/input/Antibody/MissingKey.ra - lines changed 24, context: html, text, full: html, text
  • python/ucscgenomics/lib/cvfile/unittest/input/Antibody/NonmatchKey.ra - lines changed 25, context: html, text, full: html, text
  • python/ucscgenomics/lib/cvfile/unittest/input/Antibody/ValidStanza.ra - lines changed 36, context: html, text, full: html, text
  • python/ucscgenomics/lib/cvfile/unittest/input/CellLine/BlankKey.ra - lines changed 34, context: html, text, full: html, text
  • python/ucscgenomics/lib/cvfile/unittest/input/CellLine/ExtraKey.ra - lines changed 35, context: html, text, full: html, text
  • python/ucscgenomics/lib/cvfile/unittest/input/CellLine/MissingKey.ra - lines changed 33, context: html, text, full: html, text
  • python/ucscgenomics/lib/cvfile/unittest/input/CellLine/NonmatchKey.ra - lines changed 34, context: html, text, full: html, text
  • python/ucscgenomics/lib/cvfile/unittest/input/CellLine/ValidStanza.ra - lines changed 33, context: html, text, full: html, text
  • python/ucscgenomics/lib/cvfile/unittest/input/Mouse/BlankKey.ra - lines changed 37, context: html, text, full: html, text
  • python/ucscgenomics/lib/cvfile/unittest/input/Mouse/ExtraKey.ra - lines changed 38, context: html, text, full: html, text
  • python/ucscgenomics/lib/cvfile/unittest/input/Mouse/MissingKey.ra - lines changed 36, context: html, text, full: html, text
  • python/ucscgenomics/lib/cvfile/unittest/input/Mouse/NonmatchKey.ra - lines changed 37, context: html, text, full: html, text
  • python/ucscgenomics/lib/cvfile/unittest/input/Mouse/ValidStanza.ra - lines changed 37, context: html, text, full: html, text
  • python/ucscgenomics/lib/cvfile/unittest/testCvFile - lines changed 95, context: html, text, full: html, text
  • python/ucscgenomics/lib/ordereddict/OrderedDict.py - lines changed 57, context: html, text, full: html, text
  • python/ucscgenomics/lib/ordereddict/__init__.py - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
  • python/ucscgenomics/lib/rafile/RaFile.py - lines changed 183, context: html, text, full: html, text
  • python/ucscgenomics/lib/rafile/__init__.py - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
  • python/ucscgenomics/lib/rafile/unittest/testRaFile.py - lines changed 205, context: html, text, full: html, text
  • python/ucscgenomics/lib/rafile/unittest/testoutput/BasicDiff.out - lines changed 27, context: html, text, full: html, text
  • python/ucscgenomics/lib/rafile/unittest/testoutput/CommentsDiff.out - lines changed 31, context: html, text, full: html, text
  • python/ucscgenomics/lib/rafile/unittest/testoutput/DeleteItem.out - lines changed 39, context: html, text, full: html, text
  • python/ucscgenomics/lib/rafile/unittest/testoutput/ExtraneousWhitespace.out - lines changed 70, context: html, text, full: html, text
  • python/ucscgenomics/lib/rafile/unittest/testoutput/GetItem.out - lines changed 13, context: html, text, full: html, text
  • python/ucscgenomics/lib/rafile/unittest/testoutput/InlineCommentsDiff.out - lines changed 27, context: html, text, full: html, text
  • python/ucscgenomics/lib/rafile/unittest/testoutput/IterEntryItems.out - lines changed 27, context: html, text, full: html, text
  • python/ucscgenomics/lib/rafile/unittest/testoutput/IterEntryKeys.out - lines changed 27, context: html, text, full: html, text
  • python/ucscgenomics/lib/rafile/unittest/testoutput/IterEntryValues.out - lines changed 27, context: html, text, full: html, text
  • python/ucscgenomics/lib/rafile/unittest/testoutput/IterItems.out - lines changed 19, context: html, text, full: html, text
  • python/ucscgenomics/lib/rafile/unittest/testoutput/IterKeys.out - lines changed 11, context: html, text, full: html, text
  • python/ucscgenomics/lib/rafile/unittest/testoutput/IterValues.out - lines changed 41, context: html, text, full: html, text
  • python/ucscgenomics/lib/rafile/unittest/tests/BasicDiff.ra - lines changed 12, context: html, text, full: html, text
  • python/ucscgenomics/lib/rafile/unittest/tests/CommentsDiff.ra - lines changed 14, context: html, text, full: html, text
  • python/ucscgenomics/lib/rafile/unittest/tests/DeleteItem.ra - lines changed 18, context: html, text, full: html, text
  • python/ucscgenomics/lib/rafile/unittest/tests/DuplicateKeys.ra - lines changed 8, context: html, text, full: html, text
  • python/ucscgenomics/lib/rafile/unittest/tests/FunctionalityCheck.ra - lines changed 23, context: html, text, full: html, text
  • python/ucscgenomics/lib/rafile/unittest/tests/GetItem.ra - lines changed 5, context: html, text, full: html, text
  • python/ucscgenomics/lib/rafile/unittest/tests/InlineCommentsDiff.ra - lines changed 12, context: html, text, full: html, text
  • python/ucscgenomics/lib/rafile/unittest/tests/IterEntryItems.ra - lines changed 12, context: html, text, full: html, text
  • python/ucscgenomics/lib/rafile/unittest/tests/IterEntryKeys.ra - lines changed 12, context: html, text, full: html, text
  • python/ucscgenomics/lib/rafile/unittest/tests/IterEntryValues.ra - lines changed 12, context: html, text, full: html, text
  • python/ucscgenomics/lib/rafile/unittest/tests/IterItems.ra - lines changed 8, context: html, text, full: html, text
  • python/ucscgenomics/lib/rafile/unittest/tests/IterKeys.ra - lines changed 4, context: html, text, full: html, text
  • python/ucscgenomics/lib/rafile/unittest/tests/IterValues.ra - lines changed 19, context: html, text, full: html, text
  • python/ucscgenomics/lib/rafile/unittest/tests/MisplacedKeys.ra - lines changed 8, context: html, text, full: html, text
  • python/ucscgenomics/lib/rafile/unittest/tests/NonNewlineFile.ra - lines changed 5, context: html, text, full: html, text
  • python/ucscgenomics/lib/softfile/SoftFile.py - lines changed 390, context: html, text, full: html, text
  • python/ucscgenomics/lib/softfile/__init__.py - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
  • python/ucscgenomics/lib/softfile/unittest/testSoft - lines changed 10, context: html, text, full: html, text
  • python/ucscgenomics/mkGeoPkg/README - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
  • python/ucscgenomics/mkGeoPkg/mkGeoPkg - lines changed 231, context: html, text, full: html, text
  • python/ucscgenomics/style.txt - lines changed 44, context: html, text, full: html, text
• Merge branch 'master' into mmaddren_pythondev
• Merge branch 'mmaddren_pythondev'