All File Changes

v267_preview2 to v267_base (2012-05-08 to 2012-05-15) v267

• python/lib/README
  • lines changed 1, context: html, text, full: html, text
    Updated files to state the new name of the library, didn't modify examples as that would be too hard to update with constant reorganization. Redmine #7029.
• python/lib/setup.py
  • lines changed 1, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
• python/lib/ucscGb/__init__.py
  • lines changed 0, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
• python/lib/ucscGb/cv.py
  • lines changed 453, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
  • lines changed 453, context: html, text, full: html, text
    First step in python lib reogranization. Redmine #7029.
• python/lib/ucscGb/encode.py
  • lines changed 115, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
  • lines changed 115, context: html, text, full: html, text
    First step in python lib reogranization. Redmine #7029.
• python/lib/ucscGb/encode/__init__.py
  • lines changed 0, context: html, text, full: html, text
    First step in python lib reogranization. Redmine #7029.
• python/lib/ucscGb/encode/cv.py
  • lines changed 453, context: html, text, full: html, text
    First step in python lib reogranization. Redmine #7029.
  • lines changed 3, context: html, text, full: html, text
    Changing calls to modules. Redmine #7029.
  • lines changed 6, context: html, text, full: html, text
    updated calling for split of ra.py into raFile.py and raStanza.py. Also updated calls for ucscGb from ucscgenomics. Redmine #7029.
• python/lib/ucscGb/encode/encodeUtils.py
  • lines changed 115, context: html, text, full: html, text
    First step in python lib reogranization. Redmine #7029.
  • lines changed 0, context: html, text, full: html, text
    Changing calls to modules. Redmine #7029.
  • lines changed 13, context: html, text, full: html, text
    fixed ucscGb and some of the more important scripts using it since they broke during the move to the new library structure
• python/lib/ucscGb/encode/mdb.py
  • lines changed 182, context: html, text, full: html, text
    First step in python lib reogranization. Redmine #7029.
  • lines changed 3, context: html, text, full: html, text
    Changing calls to modules. Redmine #7029.
  • lines changed 7, context: html, text, full: html, text
    updated calling for split of ra.py into raFile.py and raStanza.py. Also updated calls for ucscGb from ucscgenomics. Redmine #7029.
  • lines changed 15, context: html, text, full: html, text
    fixed ucscGb and some of the more important scripts using it since they broke during the move to the new library structure
• python/lib/ucscGb/encode/mkChangeNotes.py
  • lines changed 727, context: html, text, full: html, text
    First step in python lib reogranization. Redmine #7029.
  • lines changed 3, context: html, text, full: html, text
    Changing calls to modules. Redmine #7029.
  • lines changed 4, context: html, text, full: html, text
    updated calling for split of ra.py into raFile.py and raStanza.py. Also updated calls for ucscGb from ucscgenomics. Redmine #7029.
• python/lib/ucscGb/encode/styles.py
  • lines changed 38, context: html, text, full: html, text
    First step in python lib reogranization. Redmine #7029.
• python/lib/ucscGb/encode/test/test_cv
  • lines changed 96, context: html, text, full: html, text
    Moved cv tests and update library calls. Redmine #7029.
  • lines changed 1, context: html, text, full: html, text
    updated calling for split of ra.py into raFile.py and raStanza.py. Also updated calls for ucscGb from ucscgenomics. Redmine #7029.
• python/lib/ucscGb/encode/test/test_cv_input/Antibody/BlankKey.ra
  • lines changed 25, context: html, text, full: html, text
    Moved cv tests and update library calls. Redmine #7029.
• python/lib/ucscGb/encode/test/test_cv_input/Antibody/ExtraKey.ra
  • lines changed 26, context: html, text, full: html, text
    Moved cv tests and update library calls. Redmine #7029.
• python/lib/ucscGb/encode/test/test_cv_input/Antibody/MissingKey.ra
  • lines changed 24, context: html, text, full: html, text
    Moved cv tests and update library calls. Redmine #7029.
• python/lib/ucscGb/encode/test/test_cv_input/Antibody/NonmatchKey.ra
  • lines changed 34, context: html, text, full: html, text
    Moved cv tests and update library calls. Redmine #7029.
• python/lib/ucscGb/encode/test/test_cv_input/Antibody/ValidStanza.ra
  • lines changed 45, context: html, text, full: html, text
    Moved cv tests and update library calls. Redmine #7029.
• python/lib/ucscGb/encode/test/test_cv_input/CellLine/BlankKey.ra
  • lines changed 42, context: html, text, full: html, text
    Moved cv tests and update library calls. Redmine #7029.
• python/lib/ucscGb/encode/test/test_cv_input/CellLine/ExtraKey.ra
  • lines changed 43, context: html, text, full: html, text
    Moved cv tests and update library calls. Redmine #7029.
• python/lib/ucscGb/encode/test/test_cv_input/CellLine/MissingKey.ra
  • lines changed 41, context: html, text, full: html, text
    Moved cv tests and update library calls. Redmine #7029.
• python/lib/ucscGb/encode/test/test_cv_input/CellLine/NonmatchKey.ra
  • lines changed 42, context: html, text, full: html, text
    Moved cv tests and update library calls. Redmine #7029.
• python/lib/ucscGb/encode/test/test_cv_input/CellLine/ValidStanza.ra
  • lines changed 42, context: html, text, full: html, text
    Moved cv tests and update library calls. Redmine #7029.
• python/lib/ucscGb/encode/test/test_cv_input/Mouse/BlankKey.ra
  • lines changed 37, context: html, text, full: html, text
    Moved cv tests and update library calls. Redmine #7029.
• python/lib/ucscGb/encode/test/test_cv_input/Mouse/ExtraKey.ra
  • lines changed 38, context: html, text, full: html, text
    Moved cv tests and update library calls. Redmine #7029.
• python/lib/ucscGb/encode/test/test_cv_input/Mouse/MissingKey.ra
  • lines changed 36, context: html, text, full: html, text
    Moved cv tests and update library calls. Redmine #7029.
• python/lib/ucscGb/encode/test/test_cv_input/Mouse/NonmatchKey.ra
  • lines changed 46, context: html, text, full: html, text
    Moved cv tests and update library calls. Redmine #7029.
• python/lib/ucscGb/encode/test/test_cv_input/Mouse/ValidStanza.ra
  • lines changed 46, context: html, text, full: html, text
    Moved cv tests and update library calls. Redmine #7029.
• python/lib/ucscGb/encode/track.py
  • lines changed 458, context: html, text, full: html, text
    First step in python lib reogranization. Redmine #7029.
  • lines changed 10, context: html, text, full: html, text
    Changing calls to modules. Redmine #7029.
  • lines changed 2, context: html, text, full: html, text
    updated calling for split of ra.py into raFile.py and raStanza.py. Also updated calls for ucscGb from ucscgenomics. Redmine #7029.
  • lines changed 18, context: html, text, full: html, text
    fixed ucscGb and some of the more important scripts using it since they broke during the move to the new library structure
  • lines changed 40, context: html, text, full: html, text
    added more release object support to tracks, and fixed cvValidate for new libs
• python/lib/ucscGb/externalData/__init__.py
  • lines changed 0, context: html, text, full: html, text
    First step in python lib reogranization. Redmine #7029.
• python/lib/ucscGb/externalData/geo/__init__.py
  • lines changed 0, context: html, text, full: html, text
    First step in python lib reogranization. Redmine #7029.
• python/lib/ucscGb/externalData/geo/soft.py
  • lines changed 392, context: html, text, full: html, text
    First step in python lib reogranization. Redmine #7029.
  • lines changed 1, context: html, text, full: html, text
    Fixed call to library. Redmine #7029.
  • lines changed 1, context: html, text, full: html, text
    updated calling for split of ra.py into raFile.py and raStanza.py. Also updated calls for ucscGb from ucscgenomics. Redmine #7029.
• python/lib/ucscGb/externalData/geo/submission.py
  • lines changed 96, context: html, text, full: html, text
    First step in python lib reogranization. Redmine #7029.
  • lines changed 4, context: html, text, full: html, text
    fixed ucscGb and some of the more important scripts using it since they broke during the move to the new library structure
• python/lib/ucscGb/externalData/geo/test/test_soft
  • lines changed 10, context: html, text, full: html, text
    Moved soft tests and update library calls. Redmine #7029
• python/lib/ucscGb/gbData/__init__.py
  • lines changed 0, context: html, text, full: html, text
    First step in python lib reogranization. Redmine #7029.
• python/lib/ucscGb/gbData/ordereddict.py
  • lines changed 67, context: html, text, full: html, text
    First step in python lib reogranization. Redmine #7029.
• python/lib/ucscGb/gbData/ra.py
  • lines changed 613, context: html, text, full: html, text
    First step in python lib reogranization. Redmine #7029.
  • lines changed 2, context: html, text, full: html, text
    Fixed call to library and modules. Redmine #7029.
  • lines changed 613, context: html, text, full: html, text
    Split ra.py into raStanza.py and raFile.py. Redmine #7029.
• python/lib/ucscGb/gbData/ra/__init__.py
  • lines changed 0, context: html, text, full: html, text
    Split ra.py into raStanza.py and raFile.py. Redmine #7029.
• python/lib/ucscGb/gbData/ra/raFile.py
  • lines changed 496, context: html, text, full: html, text
    Split ra.py into raStanza.py and raFile.py. Redmine #7029.
  • lines changed 3, context: html, text, full: html, text
    updated calling for split of ra.py into raFile.py and raStanza.py. Also updated calls for ucscGb from ucscgenomics. Redmine #7029.
• python/lib/ucscGb/gbData/ra/raStanza.py
  • lines changed 124, context: html, text, full: html, text
    Split ra.py into raStanza.py and raFile.py. Redmine #7029.
  • lines changed 2, context: html, text, full: html, text
    updated calling for split of ra.py into raFile.py and raStanza.py. Also updated calls for ucscGb from ucscgenomics. Redmine #7029.
• python/lib/ucscGb/gbData/ra/test/input/BasicDiff.ra
  • lines changed 12, context: html, text, full: html, text
    Split ra.py into raStanza.py and raFile.py. Redmine #7029.
• python/lib/ucscGb/gbData/ra/test/input/CommentsDiff.ra
  • lines changed 14, context: html, text, full: html, text
    Split ra.py into raStanza.py and raFile.py. Redmine #7029.
• python/lib/ucscGb/gbData/ra/test/input/DeleteItem.ra
  • lines changed 18, context: html, text, full: html, text
    Split ra.py into raStanza.py and raFile.py. Redmine #7029.
• python/lib/ucscGb/gbData/ra/test/input/DuplicateKeys.ra
  • lines changed 8, context: html, text, full: html, text
    Split ra.py into raStanza.py and raFile.py. Redmine #7029.
• python/lib/ucscGb/gbData/ra/test/input/FunctionalityCheck.ra
  • lines changed 23, context: html, text, full: html, text
    Split ra.py into raStanza.py and raFile.py. Redmine #7029.
• python/lib/ucscGb/gbData/ra/test/input/GetItem.ra
  • lines changed 5, context: html, text, full: html, text
    Split ra.py into raStanza.py and raFile.py. Redmine #7029.
• python/lib/ucscGb/gbData/ra/test/input/InlineCommentsDiff.ra
  • lines changed 12, context: html, text, full: html, text
    Split ra.py into raStanza.py and raFile.py. Redmine #7029.
• python/lib/ucscGb/gbData/ra/test/input/IterEntryItems.ra
  • lines changed 12, context: html, text, full: html, text
    Split ra.py into raStanza.py and raFile.py. Redmine #7029.
• python/lib/ucscGb/gbData/ra/test/input/IterEntryKeys.ra
  • lines changed 12, context: html, text, full: html, text
    Split ra.py into raStanza.py and raFile.py. Redmine #7029.
• python/lib/ucscGb/gbData/ra/test/input/IterEntryValues.ra
  • lines changed 12, context: html, text, full: html, text
    Split ra.py into raStanza.py and raFile.py. Redmine #7029.
• python/lib/ucscGb/gbData/ra/test/input/IterItems.ra
  • lines changed 8, context: html, text, full: html, text
    Split ra.py into raStanza.py and raFile.py. Redmine #7029.
• python/lib/ucscGb/gbData/ra/test/input/IterKeys.ra
  • lines changed 4, context: html, text, full: html, text
    Split ra.py into raStanza.py and raFile.py. Redmine #7029.
• python/lib/ucscGb/gbData/ra/test/input/IterValues.ra
  • lines changed 19, context: html, text, full: html, text
    Split ra.py into raStanza.py and raFile.py. Redmine #7029.
• python/lib/ucscGb/gbData/ra/test/input/MisplacedKeys.ra
  • lines changed 8, context: html, text, full: html, text
    Split ra.py into raStanza.py and raFile.py. Redmine #7029.
• python/lib/ucscGb/gbData/ra/test/input/NonNewlineFile.ra
  • lines changed 5, context: html, text, full: html, text
    Split ra.py into raStanza.py and raFile.py. Redmine #7029.
• python/lib/ucscGb/gbData/ra/test/test_ra
  • lines changed 188, context: html, text, full: html, text
    Split ra.py into raStanza.py and raFile.py. Redmine #7029.
  • lines changed 18, context: html, text, full: html, text
    updated calling for split of ra.py into raFile.py and raStanza.py. Also updated calls for ucscGb from ucscgenomics. Redmine #7029.
• python/lib/ucscGb/gbData/test/ra/input/BasicDiff.ra
  • lines changed 12, context: html, text, full: html, text
    Moved ra tests and update library calls. Redmine #7029.
  • lines changed 12, context: html, text, full: html, text
    Split ra.py into raStanza.py and raFile.py. Redmine #7029.
• python/lib/ucscGb/gbData/test/ra/input/CommentsDiff.ra
  • lines changed 14, context: html, text, full: html, text
    Moved ra tests and update library calls. Redmine #7029.
  • lines changed 14, context: html, text, full: html, text
    Split ra.py into raStanza.py and raFile.py. Redmine #7029.
• python/lib/ucscGb/gbData/test/ra/input/DeleteItem.ra
  • lines changed 18, context: html, text, full: html, text
    Moved ra tests and update library calls. Redmine #7029.
  • lines changed 18, context: html, text, full: html, text
    Split ra.py into raStanza.py and raFile.py. Redmine #7029.
• python/lib/ucscGb/gbData/test/ra/input/DuplicateKeys.ra
  • lines changed 8, context: html, text, full: html, text
    Moved ra tests and update library calls. Redmine #7029.
  • lines changed 8, context: html, text, full: html, text
    Split ra.py into raStanza.py and raFile.py. Redmine #7029.
• python/lib/ucscGb/gbData/test/ra/input/FunctionalityCheck.ra
  • lines changed 23, context: html, text, full: html, text
    Moved ra tests and update library calls. Redmine #7029.
  • lines changed 23, context: html, text, full: html, text
    Split ra.py into raStanza.py and raFile.py. Redmine #7029.
• python/lib/ucscGb/gbData/test/ra/input/GetItem.ra
  • lines changed 5, context: html, text, full: html, text
    Moved ra tests and update library calls. Redmine #7029.
  • lines changed 5, context: html, text, full: html, text
    Split ra.py into raStanza.py and raFile.py. Redmine #7029.
• python/lib/ucscGb/gbData/test/ra/input/InlineCommentsDiff.ra
  • lines changed 12, context: html, text, full: html, text
    Moved ra tests and update library calls. Redmine #7029.
  • lines changed 12, context: html, text, full: html, text
    Split ra.py into raStanza.py and raFile.py. Redmine #7029.
• python/lib/ucscGb/gbData/test/ra/input/IterEntryItems.ra
  • lines changed 12, context: html, text, full: html, text
    Moved ra tests and update library calls. Redmine #7029.
  • lines changed 12, context: html, text, full: html, text
    Split ra.py into raStanza.py and raFile.py. Redmine #7029.
• python/lib/ucscGb/gbData/test/ra/input/IterEntryKeys.ra
  • lines changed 12, context: html, text, full: html, text
    Moved ra tests and update library calls. Redmine #7029.
  • lines changed 12, context: html, text, full: html, text
    Split ra.py into raStanza.py and raFile.py. Redmine #7029.
• python/lib/ucscGb/gbData/test/ra/input/IterEntryValues.ra
  • lines changed 12, context: html, text, full: html, text
    Moved ra tests and update library calls. Redmine #7029.
  • lines changed 12, context: html, text, full: html, text
    Split ra.py into raStanza.py and raFile.py. Redmine #7029.
• python/lib/ucscGb/gbData/test/ra/input/IterItems.ra
  • lines changed 8, context: html, text, full: html, text
    Moved ra tests and update library calls. Redmine #7029.
  • lines changed 8, context: html, text, full: html, text
    Split ra.py into raStanza.py and raFile.py. Redmine #7029.
• python/lib/ucscGb/gbData/test/ra/input/IterKeys.ra
  • lines changed 4, context: html, text, full: html, text
    Moved ra tests and update library calls. Redmine #7029.
  • lines changed 4, context: html, text, full: html, text
    Split ra.py into raStanza.py and raFile.py. Redmine #7029.
• python/lib/ucscGb/gbData/test/ra/input/IterValues.ra
  • lines changed 19, context: html, text, full: html, text
    Moved ra tests and update library calls. Redmine #7029.
  • lines changed 19, context: html, text, full: html, text
    Split ra.py into raStanza.py and raFile.py. Redmine #7029.
• python/lib/ucscGb/gbData/test/ra/input/MisplacedKeys.ra
  • lines changed 8, context: html, text, full: html, text
    Moved ra tests and update library calls. Redmine #7029.
  • lines changed 8, context: html, text, full: html, text
    Split ra.py into raStanza.py and raFile.py. Redmine #7029.
• python/lib/ucscGb/gbData/test/ra/input/NonNewlineFile.ra
  • lines changed 5, context: html, text, full: html, text
    Moved ra tests and update library calls. Redmine #7029.
  • lines changed 5, context: html, text, full: html, text
    Split ra.py into raStanza.py and raFile.py. Redmine #7029.
• python/lib/ucscGb/gbData/test/ra/test_ra
  • lines changed 188, context: html, text, full: html, text
    Moved ra tests and update library calls. Redmine #7029.
  • lines changed 188, context: html, text, full: html, text
    Split ra.py into raStanza.py and raFile.py. Redmine #7029.
• python/lib/ucscGb/gbData/ucscUtils.py
  • lines changed 152, context: html, text, full: html, text
    First step in python lib reogranization. Redmine #7029.
• python/lib/ucscGb/geo.py
  • lines changed 96, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
  • lines changed 96, context: html, text, full: html, text
    First step in python lib reogranization. Redmine #7029.
• python/lib/ucscGb/mdb.py
  • lines changed 182, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
  • lines changed 182, context: html, text, full: html, text
    First step in python lib reogranization. Redmine #7029.
• python/lib/ucscGb/mkChangeNotes.py
  • lines changed 727, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
  • lines changed 727, context: html, text, full: html, text
    First step in python lib reogranization. Redmine #7029.
• python/lib/ucscGb/ordereddict.py
  • lines changed 67, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
  • lines changed 67, context: html, text, full: html, text
    First step in python lib reogranization. Redmine #7029.
• python/lib/ucscGb/qa/__init__.py
  • lines changed 0, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
• python/lib/ucscGb/qa/encode/__init__.py
  • lines changed 0, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
• python/lib/ucscGb/qa/encode/tableCheck.py
  • lines changed 317, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
  • lines changed 1, context: html, text, full: html, text
    updated calling for split of ra.py into raFile.py and raStanza.py. Also updated calls for ucscGb from ucscgenomics. Redmine #7029.
• python/lib/ucscGb/qa/qaUtils.py
  • lines changed 52, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
  • lines changed 28, context: html, text, full: html, text
    Moved two functions from qaUtils to qaGbTracks, and got rid of a duplicated function from qaUtils.
• python/lib/ucscGb/qa/tables/__init__.py
  • lines changed 0, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
• python/lib/ucscGb/qa/tables/factory.py
  • lines changed 50, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
  • lines changed 5, context: html, text, full: html, text
    updated calling for split of ra.py into raFile.py and raStanza.py. Also updated calls for ucscGb from ucscgenomics. Redmine #7029.
• python/lib/ucscGb/qa/tables/genePredQa.py
  • lines changed 23, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
  • lines changed 2, context: html, text, full: html, text
    updated calling for split of ra.py into raFile.py and raStanza.py. Also updated calls for ucscGb from ucscgenomics. Redmine #7029.
• python/lib/ucscGb/qa/tables/pointerQa.py
  • lines changed 10, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
  • lines changed 1, context: html, text, full: html, text
    updated calling for split of ra.py into raFile.py and raStanza.py. Also updated calls for ucscGb from ucscgenomics. Redmine #7029.
  • lines changed 1, context: html, text, full: html, text
    Removed unused argument from validate(). Thanks, Greg.
  • lines changed 9, context: html, text, full: html, text
    Made PointerQa into a PositionalQa object instead of a generic TableQa object so that the check for label lengths can be done. Made validate and statistics methods mostly call TableQa methods plus the PositionalQa checkLabelLengths method. Also moved label length limits into a global variable.
  • lines changed 1, context: html, text, full: html, text
    Removed check for table descriptions from PointerQa types. See redmine #7896.
• python/lib/ucscGb/qa/tables/positionalQa.py
  • lines changed 94, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
  • lines changed 2, context: html, text, full: html, text
    updated calling for split of ra.py into raFile.py and raStanza.py. Also updated calls for ucscGb from ucscgenomics. Redmine #7029.
  • lines changed 5, context: html, text, full: html, text
    Made getAttributeForTrack function check for the table setting in addition to the track setting, and made the getLabels function strip the on or off setting for parents so that they can be used to find more labels.
  • lines changed 6, context: html, text, full: html, text
    Made PointerQa into a PositionalQa object instead of a generic TableQa object so that the check for label lengths can be done. Made validate and statistics methods mostly call TableQa methods plus the PositionalQa checkLabelLengths method. Also moved label length limits into a global variable.
  • lines changed 26, context: html, text, full: html, text
    Made search for parent track labels look for deprecated subTrack setting in addition to parent setting; made it so that 'view' labels are not checked.
  • lines changed 24, context: html, text, full: html, text
    Excluded Genbank tables from positionalTblCheck. Also removed spaces from label printing.
• python/lib/ucscGb/qa/tables/pslQa.py
  • lines changed 24, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
  • lines changed 2, context: html, text, full: html, text
    updated calling for split of ra.py into raFile.py and raStanza.py. Also updated calls for ucscGb from ucscgenomics. Redmine #7029.
• python/lib/ucscGb/qa/tables/reporter.py
  • lines changed 67, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
• python/lib/ucscGb/qa/tables/summary.py
  • lines changed 39, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
• python/lib/ucscGb/qa/tables/tableQa.py
  • lines changed 69, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
  • lines changed 2, context: html, text, full: html, text
    updated calling for split of ra.py into raFile.py and raStanza.py. Also updated calls for ucscGb from ucscgenomics. Redmine #7029.
  • lines changed 4, context: html, text, full: html, text
    Removed check for table descriptions from PointerQa types. See redmine #7896.
• python/lib/ucscGb/ra.py
  • lines changed 613, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
  • lines changed 613, context: html, text, full: html, text
    First step in python lib reogranization. Redmine #7029.
• python/lib/ucscGb/soft.py
  • lines changed 392, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
  • lines changed 392, context: html, text, full: html, text
    First step in python lib reogranization. Redmine #7029.
• python/lib/ucscGb/styles.py
  • lines changed 38, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
  • lines changed 38, context: html, text, full: html, text
    First step in python lib reogranization. Redmine #7029.
• python/lib/ucscGb/test/ra/input/BasicDiff.ra
  • lines changed 12, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
  • lines changed 12, context: html, text, full: html, text
    Moved ra tests and update library calls. Redmine #7029.
• python/lib/ucscGb/test/ra/input/CommentsDiff.ra
  • lines changed 14, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
  • lines changed 14, context: html, text, full: html, text
    Moved ra tests and update library calls. Redmine #7029.
• python/lib/ucscGb/test/ra/input/DeleteItem.ra
  • lines changed 18, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
  • lines changed 18, context: html, text, full: html, text
    Moved ra tests and update library calls. Redmine #7029.
• python/lib/ucscGb/test/ra/input/DuplicateKeys.ra
  • lines changed 8, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
  • lines changed 8, context: html, text, full: html, text
    Moved ra tests and update library calls. Redmine #7029.
• python/lib/ucscGb/test/ra/input/FunctionalityCheck.ra
  • lines changed 23, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
  • lines changed 23, context: html, text, full: html, text
    Moved ra tests and update library calls. Redmine #7029.
• python/lib/ucscGb/test/ra/input/GetItem.ra
  • lines changed 5, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
  • lines changed 5, context: html, text, full: html, text
    Moved ra tests and update library calls. Redmine #7029.
• python/lib/ucscGb/test/ra/input/InlineCommentsDiff.ra
  • lines changed 12, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
  • lines changed 12, context: html, text, full: html, text
    Moved ra tests and update library calls. Redmine #7029.
• python/lib/ucscGb/test/ra/input/IterEntryItems.ra
  • lines changed 12, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
  • lines changed 12, context: html, text, full: html, text
    Moved ra tests and update library calls. Redmine #7029.
• python/lib/ucscGb/test/ra/input/IterEntryKeys.ra
  • lines changed 12, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
  • lines changed 12, context: html, text, full: html, text
    Moved ra tests and update library calls. Redmine #7029.
• python/lib/ucscGb/test/ra/input/IterEntryValues.ra
  • lines changed 12, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
  • lines changed 12, context: html, text, full: html, text
    Moved ra tests and update library calls. Redmine #7029.
• python/lib/ucscGb/test/ra/input/IterItems.ra
  • lines changed 8, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
  • lines changed 8, context: html, text, full: html, text
    Moved ra tests and update library calls. Redmine #7029.
• python/lib/ucscGb/test/ra/input/IterKeys.ra
  • lines changed 4, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
  • lines changed 4, context: html, text, full: html, text
    Moved ra tests and update library calls. Redmine #7029.
• python/lib/ucscGb/test/ra/input/IterValues.ra
  • lines changed 19, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
  • lines changed 19, context: html, text, full: html, text
    Moved ra tests and update library calls. Redmine #7029.
• python/lib/ucscGb/test/ra/input/MisplacedKeys.ra
  • lines changed 8, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
  • lines changed 8, context: html, text, full: html, text
    Moved ra tests and update library calls. Redmine #7029.
• python/lib/ucscGb/test/ra/input/NonNewlineFile.ra
  • lines changed 5, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
  • lines changed 5, context: html, text, full: html, text
    Moved ra tests and update library calls. Redmine #7029.
• python/lib/ucscGb/test/ra/test_ra
  • lines changed 188, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
  • lines changed 188, context: html, text, full: html, text
    Moved ra tests and update library calls. Redmine #7029.
• python/lib/ucscGb/test/test_cv
  • lines changed 94, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
  • lines changed 94, context: html, text, full: html, text
    Moved cv tests and update library calls. Redmine #7029.
• python/lib/ucscGb/test/test_cv_input/Antibody/BlankKey.ra
  • lines changed 25, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
  • lines changed 25, context: html, text, full: html, text
    Moved cv tests and update library calls. Redmine #7029.
• python/lib/ucscGb/test/test_cv_input/Antibody/ExtraKey.ra
  • lines changed 26, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
  • lines changed 26, context: html, text, full: html, text
    Moved cv tests and update library calls. Redmine #7029.
• python/lib/ucscGb/test/test_cv_input/Antibody/MissingKey.ra
  • lines changed 24, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
  • lines changed 24, context: html, text, full: html, text
    Moved cv tests and update library calls. Redmine #7029.
• python/lib/ucscGb/test/test_cv_input/Antibody/NonmatchKey.ra
  • lines changed 34, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
  • lines changed 34, context: html, text, full: html, text
    Moved cv tests and update library calls. Redmine #7029.
• python/lib/ucscGb/test/test_cv_input/Antibody/ValidStanza.ra
  • lines changed 45, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
  • lines changed 45, context: html, text, full: html, text
    Moved cv tests and update library calls. Redmine #7029.
• python/lib/ucscGb/test/test_cv_input/CellLine/BlankKey.ra
  • lines changed 42, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
  • lines changed 42, context: html, text, full: html, text
    Moved cv tests and update library calls. Redmine #7029.
• python/lib/ucscGb/test/test_cv_input/CellLine/ExtraKey.ra
  • lines changed 43, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
  • lines changed 43, context: html, text, full: html, text
    Moved cv tests and update library calls. Redmine #7029.
• python/lib/ucscGb/test/test_cv_input/CellLine/MissingKey.ra
  • lines changed 41, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
  • lines changed 41, context: html, text, full: html, text
    Moved cv tests and update library calls. Redmine #7029.
• python/lib/ucscGb/test/test_cv_input/CellLine/NonmatchKey.ra
  • lines changed 42, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
  • lines changed 42, context: html, text, full: html, text
    Moved cv tests and update library calls. Redmine #7029.
• python/lib/ucscGb/test/test_cv_input/CellLine/ValidStanza.ra
  • lines changed 42, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
  • lines changed 42, context: html, text, full: html, text
    Moved cv tests and update library calls. Redmine #7029.
• python/lib/ucscGb/test/test_cv_input/Mouse/BlankKey.ra
  • lines changed 37, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
  • lines changed 37, context: html, text, full: html, text
    Moved cv tests and update library calls. Redmine #7029.
• python/lib/ucscGb/test/test_cv_input/Mouse/ExtraKey.ra
  • lines changed 38, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
  • lines changed 38, context: html, text, full: html, text
    Moved cv tests and update library calls. Redmine #7029.
• python/lib/ucscGb/test/test_cv_input/Mouse/MissingKey.ra
  • lines changed 36, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
  • lines changed 36, context: html, text, full: html, text
    Moved cv tests and update library calls. Redmine #7029.
• python/lib/ucscGb/test/test_cv_input/Mouse/NonmatchKey.ra
  • lines changed 46, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
  • lines changed 46, context: html, text, full: html, text
    Moved cv tests and update library calls. Redmine #7029.
• python/lib/ucscGb/test/test_cv_input/Mouse/ValidStanza.ra
  • lines changed 46, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
  • lines changed 46, context: html, text, full: html, text
    Moved cv tests and update library calls. Redmine #7029.
• python/lib/ucscGb/test/test_soft
  • lines changed 10, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
  • lines changed 10, context: html, text, full: html, text
    Moved soft tests and update library calls. Redmine #7029
• python/lib/ucscGb/track.py
  • lines changed 458, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
  • lines changed 458, context: html, text, full: html, text
    First step in python lib reogranization. Redmine #7029.
• python/lib/ucscGb/ucscUtils.py
  • lines changed 152, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
  • lines changed 152, context: html, text, full: html, text
    First step in python lib reogranization. Redmine #7029.
• python/lib/ucscgenomics/__init__.py
  • lines changed 0, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
• python/lib/ucscgenomics/cv.py
  • lines changed 453, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
• python/lib/ucscgenomics/encode.py
  • lines changed 115, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
• python/lib/ucscgenomics/geo.py
  • lines changed 96, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
• python/lib/ucscgenomics/mdb.py
  • lines changed 182, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
• python/lib/ucscgenomics/mkChangeNotes.py
  • lines changed 727, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
• python/lib/ucscgenomics/ordereddict.py
  • lines changed 67, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
• python/lib/ucscgenomics/qa/__init__.py
  • lines changed 0, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
• python/lib/ucscgenomics/qa/encode/__init__.py
  • lines changed 0, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
• python/lib/ucscgenomics/qa/encode/tableCheck.py
  • lines changed 317, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
• python/lib/ucscgenomics/qa/qaUtils.py
  • lines changed 52, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
• python/lib/ucscgenomics/qa/tables/__init__.py
  • lines changed 0, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
• python/lib/ucscgenomics/qa/tables/factory.py
  • lines changed 50, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
• python/lib/ucscgenomics/qa/tables/genePredQa.py
  • lines changed 1, context: html, text, full: html, text
    Removed __ from __recordPassOrError() and got rid of calls to its name-mangled string, per Mark.
  • lines changed 23, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
• python/lib/ucscgenomics/qa/tables/pointerQa.py
  • lines changed 10, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
• python/lib/ucscgenomics/qa/tables/positionalQa.py
  • lines changed 4, context: html, text, full: html, text
    Removed __ from __recordPassOrError() and got rid of calls to its name-mangled string, per Mark.
  • lines changed 3, context: html, text, full: html, text
    Put in a special case for Chain/Net shortlabels, which are longer than the current shortLabel limit of 17 chars but are an exception to the rule.
  • lines changed 94, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
• python/lib/ucscgenomics/qa/tables/pslQa.py
  • lines changed 1, context: html, text, full: html, text
    Removed __ from __recordPassOrError() and got rid of calls to its name-mangled string, per Mark.
  • lines changed 24, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
• python/lib/ucscgenomics/qa/tables/reporter.py
  • lines changed 67, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
• python/lib/ucscgenomics/qa/tables/summary.py
  • lines changed 39, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
• python/lib/ucscgenomics/qa/tables/tableQa.py
  • lines changed 5, context: html, text, full: html, text
    Removed __ from __recordPassOrError() and got rid of calls to its name-mangled string, per Mark.
  • lines changed 2, context: html, text, full: html, text
    Added trackDb and hgFindSpec to pattern of exceptions for table name underscore check.
  • lines changed 69, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
• python/lib/ucscgenomics/ra.py
  • lines changed 613, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
• python/lib/ucscgenomics/soft.py
  • lines changed 392, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
• python/lib/ucscgenomics/styles.py
  • lines changed 38, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
• python/lib/ucscgenomics/test/ra/input/BasicDiff.ra
  • lines changed 12, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
• python/lib/ucscgenomics/test/ra/input/CommentsDiff.ra
  • lines changed 14, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
• python/lib/ucscgenomics/test/ra/input/DeleteItem.ra
  • lines changed 18, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
• python/lib/ucscgenomics/test/ra/input/DuplicateKeys.ra
  • lines changed 8, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
• python/lib/ucscgenomics/test/ra/input/FunctionalityCheck.ra
  • lines changed 23, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
• python/lib/ucscgenomics/test/ra/input/GetItem.ra
  • lines changed 5, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
• python/lib/ucscgenomics/test/ra/input/InlineCommentsDiff.ra
  • lines changed 12, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
• python/lib/ucscgenomics/test/ra/input/IterEntryItems.ra
  • lines changed 12, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
• python/lib/ucscgenomics/test/ra/input/IterEntryKeys.ra
  • lines changed 12, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
• python/lib/ucscgenomics/test/ra/input/IterEntryValues.ra
  • lines changed 12, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
• python/lib/ucscgenomics/test/ra/input/IterItems.ra
  • lines changed 8, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
• python/lib/ucscgenomics/test/ra/input/IterKeys.ra
  • lines changed 4, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
• python/lib/ucscgenomics/test/ra/input/IterValues.ra
  • lines changed 19, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
• python/lib/ucscgenomics/test/ra/input/MisplacedKeys.ra
  • lines changed 8, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
• python/lib/ucscgenomics/test/ra/input/NonNewlineFile.ra
  • lines changed 5, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
• python/lib/ucscgenomics/test/ra/test_ra
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    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
• python/lib/ucscgenomics/test/test_cv
  • lines changed 94, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
• python/lib/ucscgenomics/test/test_cv_input/Antibody/BlankKey.ra
  • lines changed 25, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
• python/lib/ucscgenomics/test/test_cv_input/Antibody/ExtraKey.ra
  • lines changed 26, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
• python/lib/ucscgenomics/test/test_cv_input/Antibody/MissingKey.ra
  • lines changed 24, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
• python/lib/ucscgenomics/test/test_cv_input/Antibody/NonmatchKey.ra
  • lines changed 34, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
• python/lib/ucscgenomics/test/test_cv_input/Antibody/ValidStanza.ra
  • lines changed 45, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
• python/lib/ucscgenomics/test/test_cv_input/CellLine/BlankKey.ra
  • lines changed 42, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
• python/lib/ucscgenomics/test/test_cv_input/CellLine/ExtraKey.ra
  • lines changed 43, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
• python/lib/ucscgenomics/test/test_cv_input/CellLine/MissingKey.ra
  • lines changed 41, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
• python/lib/ucscgenomics/test/test_cv_input/CellLine/NonmatchKey.ra
  • lines changed 42, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
• python/lib/ucscgenomics/test/test_cv_input/CellLine/ValidStanza.ra
  • lines changed 42, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
• python/lib/ucscgenomics/test/test_cv_input/Mouse/BlankKey.ra
  • lines changed 37, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
• python/lib/ucscgenomics/test/test_cv_input/Mouse/ExtraKey.ra
  • lines changed 38, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
• python/lib/ucscgenomics/test/test_cv_input/Mouse/MissingKey.ra
  • lines changed 36, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
• python/lib/ucscgenomics/test/test_cv_input/Mouse/NonmatchKey.ra
  • lines changed 46, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
• python/lib/ucscgenomics/test/test_cv_input/Mouse/ValidStanza.ra
  • lines changed 46, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
• python/lib/ucscgenomics/test/test_soft
  • lines changed 10, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
• python/lib/ucscgenomics/track.py
  • lines changed 458, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
• python/lib/ucscgenomics/ucscUtils.py
  • lines changed 152, context: html, text, full: html, text
    Renamed library from ucscgenomics to ucscGb. Redmine #7029.
• python/programs/cvValidate/cvValidate
  • lines changed 1, context: html, text, full: html, text
    added more release object support to tracks, and fixed cvValidate for new libs
• python/programs/mkGeoPkg/mkGeoPkg
  • lines changed 36, context: html, text, full: html, text
    fixed ucscGb and some of the more important scripts using it since they broke during the move to the new library structure
• python/programs/trackInfo/trackInfo
  • lines changed 3, context: html, text, full: html, text
    fixed ucscGb and some of the more important scripts using it since they broke during the move to the new library structure
• python/programs/viewTrack/viewTrack
  • lines changed 8, context: html, text, full: html, text
    fixed ucscGb and some of the more important scripts using it since they broke during the move to the new library structure
• python/style.txt
  • lines changed 6, context: html, text, full: html, text
    Updated files to state the new name of the library, didn't modify examples as that would be too hard to update with constant reorganization. Redmine #7029.
• python/virtual.txt
  • lines changed 2, context: html, text, full: html, text
    Updated files to state the new name of the library, didn't modify examples as that would be too hard to update with constant reorganization. Redmine #7029.
• src/hg/encode/DAFs/3.0/mm9/wgEncodePsuDnase.daf
  • lines changed 63, context: html, text, full: html, text
    First version of DAF for DNase data. Redmine #109.
• src/hg/encode/DAFs/3.0/mm9/wgEncodeSydhRnaSeq.daf
  • lines changed 3, context: html, text, full: html, text
    Fixed DAF for Stanford and fixed code to load documents as type was changed from doc to document.
• src/hg/encode/antibodyWikiParser/antibodyWikiParser.py
  • lines changed 1, context: html, text, full: html, text
    Updated scripts to accomadate the new library organization. Redmine #7029.
• src/hg/encode/cellTypeParser/cellTypeParser.py
  • lines changed 1, context: html, text, full: html, text
    Updated scripts to accomadate the new library organization. Redmine #7029.
• src/hg/encode/cvValidate/README
  • lines changed 1, context: html, text, full: html, text
    Removed README file.
• src/hg/encode/cvValidate/cvValidate
  • lines changed 31, context: html, text, full: html, text
    Removing redudant code. This was supposed to be moved from python/programs in October but someone existed in both places. These versions haven't been updated since the attempted move.
• src/hg/encode/encodeLoad/doEncodeLoad.pl
  • lines changed 1, context: html, text, full: html, text
    Fixed DAF for Stanford and fixed code to load documents as type was changed from doc to document.
• src/hg/encode/metaCheck/metaCheck.c
  • lines changed 14, context: html, text, full: html, text
    added in functionality to correctly use the releaseNum variable for downloadDir. also made it so that downloadDir is explicit in the path to downloadDir
• src/hg/encode/mkGeoPkg/mkGeoPkg
  • lines changed 707, context: html, text, full: html, text
    Removing redudant code. This was supposed to be moved from python/programs in October but someone existed in both places. These versions haven't been updated since the attempted move.
• src/hg/encode/trackInfo/trackInfo
  • lines changed 182, context: html, text, full: html, text
    Removing redudant code. This was supposed to be moved from python/programs in October but someone existed in both places. These versions haven't been updated since the attempted move.
• src/hg/hgLogin/hgLogin.c
  • lines changed 1004, context: html, text, full: html, text
    Change coding style in hgLogin and hgSession to confirm to kent'style standard.
  • lines changed 25, context: html, text, full: html, text
    Finalized the activation email.
  • lines changed 10, context: html, text, full: html, text
    Finalized send new password email test.
• src/hg/hgLogin/hgLogin.h
  • lines changed 62, context: html, text, full: html, text
    Change coding style in hgLogin and hgSession to confirm to kent'style standard.
• src/hg/hgSession/hgSession.c
  • lines changed 10, context: html, text, full: html, text
    Change coding style in hgLogin and hgSession to confirm to kent'style standard.
• src/hg/hgTracks/config.c
  • lines changed 4, context: html, text, full: html, text
    add some missing td's and tr's to fix formatting problems when browser.theme is disabled (#7867)
• src/hg/hgTracks/hgTracks.c
  • lines changed 15, context: html, text, full: html, text
    Adding support for IUPAC nucleotide ambiguity codes to 'short match' track. Made iupac.c library module.
  • lines changed 2, context: html, text, full: html, text
    fix cruft that was causing an empty "Ensembl" in blue bar for fr2 (pointed out by greg); menuBar => printMenuBar to fix name collision with some new code
• src/hg/hgTracks/menu.c
  • lines changed 3, context: html, text, full: html, text
    fix cruft that was causing an empty "Ensembl" in blue bar for fr2 (pointed out by greg); menuBar => printMenuBar to fix name collision with some new code
• src/hg/hgTracks/multiWig.c
  • lines changed 10, context: html, text, full: html, text
    add alwaysZero support to multiWig (#7851)
• src/hg/hgc/hgc.c
  • lines changed 22, context: html, text, full: html, text
    Added facility (itemDetailsHtml) for having a table containing HTML fragments to display on generic BED, genePred, and PSL tables. This provides an easy way for mirror sites to create specialized details pages without modifying the C code.
• src/hg/htdocs/ENCODE/dataMatrix/encodeChipMatrixHuman.html
  • lines changed 3, context: html, text, full: html, text
    Correct js syntax
• src/hg/htdocs/ENCODE/dataMatrix/encodeChipMatrixMouse.html
  • lines changed 9, context: html, text, full: html, text
    Add top menu bar items for Mouse experiment matrix
  • lines changed 3, context: html, text, full: html, text
    Correct js syntax
• src/hg/htdocs/ENCODE/dataMatrix/encodeDataMatrixHuman.html
  • lines changed 3, context: html, text, full: html, text
    Correct js syntax
• src/hg/htdocs/ENCODE/dataMatrix/encodeDataMatrixMouse.html
  • lines changed 8, context: html, text, full: html, text
    Add top menu bar items for Mouse experiment matrix
  • lines changed 3, context: html, text, full: html, text
    Generalize experiment matrix to handle mouse
  • lines changed 3, context: html, text, full: html, text
    Correct js syntax
• src/hg/htdocs/ENCODE/dataMatrix/encodeDataSummaryHuman.html
  • lines changed 3, context: html, text, full: html, text
    Correct js syntax
• src/hg/htdocs/ENCODE/dataMatrix/encodeDataSummaryMouse.html
  • lines changed 13, context: html, text, full: html, text
    Update for new var names
  • lines changed 3, context: html, text, full: html, text
    Add top menu bar items for Mouse experiment matrix
  • lines changed 3, context: html, text, full: html, text
    Correct js syntax
• src/hg/htdocs/ENCODE/dataSummary.html
  • lines changed 84, context: html, text, full: html, text
    changing the Experiment List pages (dataSummary.html and dataSummaryMouse.html) to the new ENCODE styling, redmine #7797
• src/hg/htdocs/ENCODE/dataSummaryMouse.html
  • lines changed 83, context: html, text, full: html, text
    changing the Experiment List pages (dataSummary.html and dataSummaryMouse.html) to the new ENCODE styling, redmine #7797
• src/hg/htdocs/ENCODE/downloadsMouse.html
  • lines changed 5, context: html, text, full: html, text
    adding Caltech RNA-seq to mouse downloads, redmine #4156
• src/hg/htdocs/ENCODE/index.html
  • lines changed 1, context: html, text, full: html, text
    changing mouse 'Experiment Summary' to 'Experiment List' for consistency with human, redmine #7797
  • lines changed 9, context: html, text, full: html, text
    Update tools section to reflect new link titles for data summaries, and now that mouse data is released, it doesn't need a special mention of preview browser and plans pages
  • lines changed 3, context: html, text, full: html, text
    Add links for Mouse experiment summary
• src/hg/htdocs/ENCODE/search.html
  • lines changed 10, context: html, text, full: html, text
    per Vanessa's code review, making this page more valid by adding quotes around _blank and by changing & in urls to %26, redmine #7887
• src/hg/htdocs/FAQ/FAQblat.html
  • lines changed 8, context: html, text, full: html, text
    Prompted by user question, updated description of minimum guaranteed match length, adding information about the way to calculate it for minMatch=1 which is the default for protein
  • lines changed 9, context: html, text, full: html, text
    Made some formatting changes (redmine #7911)
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 37, context: html, text, full: html, text
    Added announcement about OpenHelix webinars to home page and archives.
• src/hg/htdocs/goldenPath/pubs.html
  • lines changed 26, context: html, text, full: html, text
    added two refs and cleaned up some whitespace at the end of some lines
• src/hg/htdocs/images/Canis_lupus_familiaris.jpg
  • lines changed 0, context: html, text, full: html, text
    dog also has this scientific name
• src/hg/htdocs/inc/encodeProject.topbar.html
  • lines changed 8, context: html, text, full: html, text
    Add top menu bar items for Mouse experiment matrix
• src/hg/htdocs/indexNews.html
  • lines changed 43, context: html, text, full: html, text
    Added announcement about OpenHelix webinars to home page and archives.
• src/hg/htdocs/style/makefile
  • lines changed 2, context: html, text, full: html, text
    commit some files that max forgot to commit (#7867)
• src/hg/htdocs/style/theme-modern.css
  • lines changed 1, context: html, text, full: html, text
    commit some files that max forgot to commit (#7867)
• src/hg/inc/hgLoginLink.h
  • lines changed 32, context: html, text, full: html, text
    Retire hgLoginLink.c and hgLoginLink.h, reuse wikiLink.c and .h instead.
  • lines changed 32, context: html, text, full: html, text
    Retire hgLoginLink.c and .h, use wikiLink.c and .h instead.
• src/hg/inc/itemDetailsHtml.h
  • lines changed 62, context: html, text, full: html, text
    Added facility (itemDetailsHtml) for having a table containing HTML fragments to display on generic BED, genePred, and PSL tables. This provides an easy way for mirror sites to create specialized details pages without modifying the C code.
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    New version number v267
• src/hg/inc/web.h
  • lines changed 3, context: html, text, full: html, text
    adding lazarus keepalive call to prevent apoptosis from terminating a legitimately busy long-running process
• src/hg/js/encodeChipMatrix.js
  • lines changed 13, context: html, text, full: html, text
    Generalize experiment matrix to handle mouse
• src/hg/js/encodeDataMatrix.js
  • lines changed 18, context: html, text, full: html, text
    Generalize experiment matrix to handle mouse
• src/hg/js/encodeDataSummary.js
  • lines changed 2, context: html, text, full: html, text
    Generalize experiment matrix to handle mouse
• src/hg/js/encodeMatrix.js
  • lines changed 25, context: html, text, full: html, text
    Generalize experiment matrix to handle mouse
• src/hg/js/encodeProject.js
  • lines changed 51, context: html, text, full: html, text
    Generalize experiment matrix to handle mouse
• src/hg/js/hgTracks.js
  • lines changed 1, context: html, text, full: html, text
    fix "hgTracks is undefined" error that was occurring when using the PDF Output page
• src/hg/lib/cart.c
  • lines changed 28, context: html, text, full: html, text
    fix problem in setThemeFromCart (assumed order of style, background didn't match what was in hg.conf (#7867)
  • lines changed 1, context: html, text, full: html, text
    add a missing cloneString
  • lines changed 6, context: html, text, full: html, text
    Adding comment to some bad HTML generation that is near ubiquitous - in cartWebStart to remind us to test what happens when we take it out.
• src/hg/lib/hgLoginLink.c
  • lines changed 108, context: html, text, full: html, text
    Retire hgLoginLink.c and hgLoginLink.h, reuse wikiLink.c and .h instead.
  • lines changed 108, context: html, text, full: html, text
    Retire hgLoginLink.c and .h, use wikiLink.c and .h instead.
• src/hg/lib/itemDetailsHtml.as
  • lines changed 6, context: html, text, full: html, text
    Added facility (itemDetailsHtml) for having a table containing HTML fragments to display on generic BED, genePred, and PSL tables. This provides an easy way for mirror sites to create specialized details pages without modifying the C code.
  • lines changed 1, context: html, text, full: html, text
    use blobs rather than varchar for html details, add to valid tags
• src/hg/lib/itemDetailsHtml.c
  • lines changed 123, context: html, text, full: html, text
    Added facility (itemDetailsHtml) for having a table containing HTML fragments to display on generic BED, genePred, and PSL tables. This provides an easy way for mirror sites to create specialized details pages without modifying the C code.
• src/hg/lib/itemDetailsHtml.sql
  • lines changed 12, context: html, text, full: html, text
    Added facility (itemDetailsHtml) for having a table containing HTML fragments to display on generic BED, genePred, and PSL tables. This provides an easy way for mirror sites to create specialized details pages without modifying the C code.
  • lines changed 2, context: html, text, full: html, text
    use blobs rather than varchar for html details, add to valid tags
• src/hg/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    Added facility (itemDetailsHtml) for having a table containing HTML fragments to display on generic BED, genePred, and PSL tables. This provides an easy way for mirror sites to create specialized details pages without modifying the C code.
• src/hg/lib/web.c
  • lines changed 14, context: html, text, full: html, text
    adding lazarus keepalive call to prevent apoptosis from terminating a legitimately busy long-running process
• src/hg/makeDb/doc/chrPic1.txt
  • lines changed 91, context: html, text, full: html, text
    completed genbank run
• src/hg/makeDb/doc/dasNov3.txt
  • lines changed 84, context: html, text, full: html, text
    done with genbank run
• src/hg/makeDb/doc/dipOrd1.txt
  • lines changed 6, context: html, text, full: html, text
    done with genbank run
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeGisChiaPet.release1.notes
  • lines changed 4, context: html, text, full: html, text
    Adding in README
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeSydhTfbs.release2.notes
  • lines changed 8, context: html, text, full: html, text
    Forgot to add the README.txt file. Redmine #4486.
• src/hg/makeDb/doc/felCat5.txt
  • lines changed 89, context: html, text, full: html, text
    done with genbank run
• src/hg/makeDb/doc/galGal4.txt
  • lines changed 88, context: html, text, full: html, text
    done with genbank run
• src/hg/makeDb/doc/hetGla2.txt
  • lines changed 85, context: html, text, full: html, text
    done with genbank run
• src/hg/makeDb/doc/hg19.txt
  • lines changed 41, context: html, text, full: html, text
    lifting HapMap recombination maps from hg18
• src/hg/makeDb/doc/latCha1.txt
  • lines changed 90, context: html, text, full: html, text
    done with genbank run
• src/hg/makeDb/doc/mm10.txt
  • lines changed 5, context: html, text, full: html, text
    opps, add note to mm8 when it belonged in mm10
  • lines changed 21, context: html, text, full: html, text
    liftover to mm9
• src/hg/makeDb/doc/mm8.txt
  • lines changed 5, context: html, text, full: html, text
    documented add orfeome tracks for mouse
  • lines changed 5, context: html, text, full: html, text
    opps, add note to mm8 when it belonged in mm10
• src/hg/makeDb/doc/mm9.txt
  • lines changed 6, context: html, text, full: html, text
    documented add orfeome tracks for mouse
• src/hg/makeDb/doc/nomLeu2.txt
  • lines changed 85, context: html, text, full: html, text
    done with genbank run
• src/hg/makeDb/doc/otoGar3.txt
  • lines changed 94, context: html, text, full: html, text
    done with genbank run
• src/hg/makeDb/doc/rn5.txt
  • lines changed 87, context: html, text, full: html, text
    genbank done
  • lines changed 7, context: html, text, full: html, text
    download files constructed, ready for documentation
• src/hg/makeDb/doc/saiBol1.txt
  • lines changed 90, context: html, text, full: html, text
    done with genbank run
• src/hg/makeDb/doc/susScr3.txt
  • lines changed 94, context: html, text, full: html, text
    done with genbank run
• src/hg/makeDb/genbank/etc/align.dbs
  • lines changed 1, context: html, text, full: html, text
    Added rn5.
  • lines changed 1, context: html, text, full: html, text
    Added galGal4.
  • lines changed 1, context: html, text, full: html, text
    Added felCat5.
  • lines changed 1, context: html, text, full: html, text
    Added susScr3.
  • lines changed 1, context: html, text, full: html, text
    Added chrPic1.
  • lines changed 1, context: html, text, full: html, text
    Added dasNov3.
  • lines changed 1, context: html, text, full: html, text
    Added dipOrd1.
  • lines changed 1, context: html, text, full: html, text
    Added hetGla2.
  • lines changed 1, context: html, text, full: html, text
    Added otoGar3.
  • lines changed 1, context: html, text, full: html, text
    Added nomLeu2.
  • lines changed 1, context: html, text, full: html, text
    Added saiBol1.
  • lines changed 1, context: html, text, full: html, text
    Added latCha1.
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 17, context: html, text, full: html, text
    adding eriEur1 European hedgehog
  • lines changed 17, context: html, text, full: html, text
    adding gadMor1 Atlantic cod
  • lines changed 17, context: html, text, full: html, text
    adding latCha1 Coelacanth
  • lines changed 17, context: html, text, full: html, text
    adding melUnd1 budgerigar
  • lines changed 17, context: html, text, full: html, text
    adding micMur1 mouse lemur
  • lines changed 17, context: html, text, full: html, text
    adding ochPri2 pika
  • lines changed 17, context: html, text, full: html, text
    adding oreNil2 Nile tilapia
  • lines changed 17, context: html, text, full: html, text
    adding proCap1 Rock hyrax
  • lines changed 17, context: html, text, full: html, text
    adding pteVam1 megabat
  • lines changed 17, context: html, text, full: html, text
    adding saiBol1 squirrel monkey
  • lines changed 17, context: html, text, full: html, text
    adding sorAra1 common shrew
  • lines changed 17, context: html, text, full: html, text
    adding speTri2 13-lined ground squirrel
  • lines changed 17, context: html, text, full: html, text
    adding tarSyr1 tarsier
  • lines changed 17, context: html, text, full: html, text
    adding tupBel1 tree shrew
  • lines changed 18, context: html, text, full: html, text
    adding vicPac1 alpaca
• src/hg/makeDb/genbank/etc/hgwdev.dbs
  • lines changed 1, context: html, text, full: html, text
    Added rn5.
  • lines changed 1, context: html, text, full: html, text
    Added galGal4.
  • lines changed 1, context: html, text, full: html, text
    Added felCat5.
  • lines changed 1, context: html, text, full: html, text
    Added susScr3.
  • lines changed 1, context: html, text, full: html, text
    Added chrPic1.
  • lines changed 1, context: html, text, full: html, text
    Added dasNov3.
  • lines changed 1, context: html, text, full: html, text
    Added dipOrd1.
  • lines changed 1, context: html, text, full: html, text
    Added hetGla2.
  • lines changed 1, context: html, text, full: html, text
    Added otoGar3.
  • lines changed 1, context: html, text, full: html, text
    Added nomLeu2.
  • lines changed 1, context: html, text, full: html, text
    Added saiBol1.
  • lines changed 1, context: html, text, full: html, text
    Added latCha1.
• src/hg/makeDb/genbank/etc/ignore.idx
  • lines changed 5, context: html, text, full: html, text
    some organism changes to ignore
• src/hg/makeDb/genbank/etc/rr.dbs
  • lines changed 1, context: html, text, full: html, text
    added naked mole-rat assembly
  • lines changed 1, context: html, text, full: html, text
    Added fr3 to list, staged on RR.
• src/hg/makeDb/genbank/src/lib/gbGenome.c
  • lines changed 31, context: html, text, full: html, text
    adding: otoGar turTru eriEur gadMor latCha melUnd micMur ochPri oreNil proCap pteVam saiBol sorAra speTri tarSyr tupBel vicPac
  • lines changed 1, context: html, text, full: html, text
    additional name for Saimiri boliviensis
  • lines changed 1, context: html, text, full: html, text
    speTri AKA Ictidomys tridecemlineatus
• src/hg/makeDb/schema/all.joiner
  • lines changed 16, context: html, text, full: html, text
    add ignore tables for the ones in decodeRmap
  • lines changed 15, context: html, text, full: html, text
    Per Hiram's instructions, added the hg18/hg19 deCODE Recomb tables into the hg-ignored section (redmine #3303)
  • lines changed 16, context: html, text, full: html, text
    Hiram also added entries for deCODE Recomb, but he added them to the hg19 section. They need to be ignored for both hg18 and hg19. Removed Hiram's entries and left my previous entries in the overall hg section (redmine #3303).
  • lines changed 2, context: html, text, full: html, text
    adding rn5 and chain net Mm10 definitions
  • lines changed 22, context: html, text, full: html, text
    adding assemblies: canFam3,chrPic1,dasNov3,felCat5,gadMor1,galGal4,hetGla2,latCha1,melUnd1,nomLeu2,oreNil2,otoGar3,panTro4,papHam1,saiBol1,speTri2,susScr3,triMan1,turTru2
  • lines changed 46, context: html, text, full: html, text
    fixup missing tables in the new databases just added
  • lines changed 9, context: html, text, full: html, text
    clean up all errors on the new assemblies recently added
• src/hg/makeDb/trackDb/README
  • lines changed 10, context: html, text, full: html, text
    Added facility (itemDetailsHtml) for having a table containing HTML fragments to display on generic BED, genePred, and PSL tables. This provides an easy way for mirror sites to create specialized details pages without modifying the C code.
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 1, context: html, text, full: html, text
    Fixed GingerasGingeras in protocol
  • lines changed 1, context: html, text, full: html, text
    Fixed :: in protocol
  • lines changed 1, context: html, text, full: html, text
    Fixed Primer files for 5C data to be Supplemental data and not in the normal downloads directory. Removed dccAccession, deprecated view and added objStatus. Redmine #7245.
  • lines changed 1, context: html, text, full: html, text
    Fixed spelling of missing causing broken link.
• src/hg/makeDb/trackDb/cv/beta/cv.ra
  • lines changed 152, context: html, text, full: html, text
    Copying alpha cv to beta
• src/hg/makeDb/trackDb/cv/public/cv.ra
  • lines changed 194, context: html, text, full: html, text
    Moved over approved stanzas from beta/cv.ra. Redmine #7872.
• src/hg/makeDb/trackDb/dog/canFam3/description.html
  • lines changed 106, context: html, text, full: html, text
    new style minimalist content
• src/hg/makeDb/trackDb/fugu/fr3/cons8way.html
  • lines changed 7, context: html, text, full: html, text
    Fixed border display of tables
  • lines changed 2, context: html, text, full: html, text
    A couple minor grammar tweaks
  • lines changed 196, context: html, text, full: html, text
    HTML cleanup. Lowercased tags, added quotes around attributes where missing. Deleted redendant align attributes (those elements align left anyway).
  • lines changed 2, context: html, text, full: html, text
    Spelled out Phylogenetic Hidden Markov Model
  • lines changed 1, context: html, text, full: html, text
    Removed unneeded period.
• src/hg/makeDb/trackDb/fugu/fr3/trackDb.chainNet.ra
  • lines changed 3, context: html, text, full: html, text
    Added an override for Medaka min chain score.
• src/hg/makeDb/trackDb/fugu/fr3/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    Added an override for Medaka min chain score.
• src/hg/makeDb/trackDb/human/decode.rmap.ra
  • lines changed 8, context: html, text, full: html, text
    Edited short labels to be <= 17 characters and to ensure consistency (redmine #3303)
• src/hg/makeDb/trackDb/human/decodeRmap.html
  • lines changed 58, context: html, text, full: html, text
    Made corrections to html code, fixed line spacing, fixed references and made minor grammatical corrections (redmine #3303)
  • lines changed 14, context: html, text, full: html, text
    Corrected order of articles in References section (redmine #3303)
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra
  • lines changed 27, context: html, text, full: html, text
    added in missing experiment
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlShortRnaSeq.ra
  • lines changed 423, context: html, text, full: html, text
    added in expIds and accessions where known
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhHistone.ra
  • lines changed 134, context: html, text, full: html, text
    Added MCF7 input data that was initially on hg18. Redmine #7510.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUmassDekker5C.ra
  • lines changed 5, context: html, text, full: html, text
    Fixed Primer files for 5C data to be Supplemental data and not in the normal downloads directory. Removed dccAccession, deprecated view and added objStatus. Redmine #7245.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUw5C.ra
  • lines changed 5, context: html, text, full: html, text
    Fixed Primer files for 5C data to be Supplemental data and not in the normal downloads directory. Removed dccAccession, deprecated view and added objStatus. Redmine #7245.
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/makefile
  • lines changed 1, context: html, text, full: html, text
    Staging ChIA-PET (Release 1) on beta, redmine# 1664
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeBroadHistone.ra
  • lines changed 2742, context: html, text, full: html, text
    releasing update to metadata to remove data unrestricted from published items; also pushes out some metadata for next release, but ok because no stanzas dropped, redmine#7515
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeGisChiaPet.ra
  • lines changed 1647, context: html, text, full: html, text
    Staging ChIA-PET (Release 1) on beta, redmine# 1664
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeUmassDekker5C.ra
  • lines changed 5, context: html, text, full: html, text
    staging patch for UmassDekker5C & Uw5C on beta, remdine# 7245
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeUw5C.ra
  • lines changed 5, context: html, text, full: html, text
    staging patch for UmassDekker5C & Uw5C on beta, remdine# 7245
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeBroadHistone.ra
  • lines changed 2742, context: html, text, full: html, text
    releasing update to metadata to remove data unrestricted from published items; also pushes out some metadata for next release, but ok because no stanzas dropped, redmine#7515
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeSydhTfbs.ra
  • lines changed 11224, context: html, text, full: html, text
    Releasing SYDH TFBS (Release 2), redmine# 4486
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
  • lines changed 1, context: html, text, full: html, text
    Added release 2 to alpha, was forgotten to be moved over whent he patch went public.
  • lines changed 14, context: html, text, full: html, text
    Incorporating the GENCODE Super Track
  • lines changed 6, context: html, text, full: html, text
    Fixed Primer files for 5C data to be Supplemental data and not in the normal downloads directory. Removed dccAccession, deprecated view and added objStatus. Redmine #7245.
  • lines changed 2, context: html, text, full: html, text
    Releasing SYDH TFBS (Release 2), redmine# 4486
  • lines changed 1, context: html, text, full: html, text
    Staging ChIA-PET (Release 1) on beta, redmine# 1664
  • lines changed 4, context: html, text, full: html, text
    staging patch for UmassDekker5C & Uw5C on beta, remdine# 7245
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.release2.html
  • lines changed 5, context: html, text, full: html, text
    Cleaning up a few links and the views descriptions
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.release2.ra
  • lines changed 8, context: html, text, full: html, text
    added in missing experiment
  • lines changed 2, context: html, text, full: html, text
    setting defaults to avoid greyed out checkboxes
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeSuper.html
  • lines changed 162, context: html, text, full: html, text
    Description for GENCODE super track.
  • lines changed 1, context: html, text, full: html, text
    Minor edit to text.
  • lines changed 26, context: html, text, full: html, text
    Incorporating the GENCODE Super Track
  • lines changed 75, context: html, text, full: html, text
    Changing the pubmeds into references
  • lines changed 17, context: html, text, full: html, text
    Expanded supertrack description.
  • lines changed 53, context: html, text, full: html, text
    Changing the references section and updating all Gencode to GENCODE
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV10.release2.ra
  • lines changed 224, context: html, text, full: html, text
    Incorporating the GENCODE Super Track
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV11.release2.ra
  • lines changed 224, context: html, text, full: html, text
    Incorporating the GENCODE Super Track
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV3.html
  • lines changed 5, context: html, text, full: html, text
    Changing the references section and updating all Gencode to GENCODE
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV3.ra
  • lines changed 2, context: html, text, full: html, text
    Incorporating the GENCODE Super Track
  • lines changed 1, context: html, text, full: html, text
    Fixing typo in GENCODE/ENCODE
  • lines changed 6, context: html, text, full: html, text
    Changing the references section and updating all Gencode to GENCODE
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV4.html
  • lines changed 5, context: html, text, full: html, text
    Changing the references section and updating all Gencode to GENCODE
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV4.ra
  • lines changed 2, context: html, text, full: html, text
    Incorporating the GENCODE Super Track
  • lines changed 1, context: html, text, full: html, text
    Fixing typo in GENCODE/ENCODE
  • lines changed 4, context: html, text, full: html, text
    Changing the references section and updating all Gencode to GENCODE
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV5.ra
  • lines changed 2, context: html, text, full: html, text
    Incorporating the GENCODE Super Track
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV6.ra
  • lines changed 1, context: html, text, full: html, text
    Incorporating the GENCODE Super Track
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV7.release2.ra
  • lines changed 189, context: html, text, full: html, text
    Incorporating the GENCODE Super Track
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV9.ra
  • lines changed 1, context: html, text, full: html, text
    Incorporating the GENCODE Super Track
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGisChiaPet.html
  • lines changed 36, context: html, text, full: html, text
    Rewriting sections for clarity
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSuper.release2.ra
  • lines changed 78, context: html, text, full: html, text
    Incorporating the GENCODE Super Track
  • lines changed 1, context: html, text, full: html, text
    Changeing long label to read more clearly when Tracks is appended
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhHistone.release3.ra
  • lines changed 7, context: html, text, full: html, text
    Added MCF7 input data that was initially on hg18. Redmine #7510.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.release2.html
  • lines changed 1, context: html, text, full: html, text
    Replaced broken link for Peggy Farnham. Redmine #4486.
  • lines changed 2, context: html, text, full: html, text
    fixed a broken link for SYDH TFBS (Release 2), redmine# 4486 note# 50
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUmassDekker5C.patch.html
  • lines changed 212, context: html, text, full: html, text
    Fixed Primer files for 5C data to be Supplemental data and not in the normal downloads directory. Removed dccAccession, deprecated view and added objStatus. Redmine #7245.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUmassDekker5C.patch.ra
  • lines changed 59, context: html, text, full: html, text
    Fixed Primer files for 5C data to be Supplemental data and not in the normal downloads directory. Removed dccAccession, deprecated view and added objStatus. Redmine #7245.
  • lines changed 1, context: html, text, full: html, text
    Spelled html file correctly.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUw5C.patch2.html
  • lines changed 139, context: html, text, full: html, text
    Fixed Primer files for 5C data to be Supplemental data and not in the normal downloads directory. Removed dccAccession, deprecated view and added objStatus. Redmine #7245.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUw5C.patch2.ra
  • lines changed 13, context: html, text, full: html, text
    Fixed Primer files for 5C data to be Supplemental data and not in the normal downloads directory. Removed dccAccession, deprecated view and added objStatus. Redmine #7245.
• src/hg/makeDb/trackDb/moleRat/hetGla1/description.html
  • lines changed 1, context: html, text, full: html, text
    fixed a typo
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeCaltechRnaSeq.ra
  • lines changed 61, context: html, text, full: html, text
    Added rnaExtract that was missing from metaDb to allow for GEO submissions.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhRnaSeq.ra
  • lines changed 670, context: html, text, full: html, text
    Added all of the experiments for this track. Revoked old data sets due to new methods. Redmine #829.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeUwRnaSeq.ra
  • lines changed 11, context: html, text, full: html, text
    Moved replicate 3's and 4's to attic, as per decission with lab. Redmine #4469.
  • lines changed 11, context: html, text, full: html, text
    Fixed spelling of attic found by cron job.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/wgEncodePsuHistone.ra
  • lines changed 102, context: html, text, full: html, text
    dropping date unrestricted for some experiments because they were published on already and so are now unrestricted, redmine #7515
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/public/wgEncodePsuHistone.ra
  • lines changed 102, context: html, text, full: html, text
    dropping date unrestricted for some experiments because they were published on already and so are now unrestricted, redmine #7515
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrRnaSeq.release2.html
  • lines changed 1, context: html, text, full: html, text
    changing <DD> tag to the proper </DD> tag and adding quotes around _blank, left all caps because all the html tags in the whole doc are all caps, redmine #7887
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuRnaSeq.html
  • lines changed 176, context: html, text, full: html, text
    Added track description. Redmine #107.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhRnaSeq.ra
  • lines changed 116, context: html, text, full: html, text
    Added all of the experiments for this track. Revoked old data sets due to new methods. Redmine #829.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwRnaSeq.ra
  • lines changed 64, context: html, text, full: html, text
    Moved replicate 3's and 4's to attic, as per decission with lab. Redmine #4469.
  • lines changed 3, context: html, text, full: html, text
    Updated display settings. Redmine #4469.
• src/hg/makeDb/trackDb/orfeomeMrna.html
  • lines changed 27, context: html, text, full: html, text
    Made some minor corrections (redmine #11)
• src/hg/makeDb/trackDb/pubs.html
  • lines changed 36, context: html, text, full: html, text
    Fixed References section and made various other corrections
• src/hg/makeDb/trackDb/rat/rn5/description.html
  • lines changed 106, context: html, text, full: html, text
    new style minimalist content
• src/hg/makeDb/trackDb/tagTypes.tab
  • lines changed 1, context: html, text, full: html, text
    use blobs rather than varchar for html details, add to valid tags
• src/hg/utils/automation/doBlastzChainNet.pl
  • lines changed 2, context: html, text, full: html, text
    default smallClusterHub is encodek, memk is gone
• src/hg/utils/automation/doWindowMasker.pl
  • lines changed 1, context: html, text, full: html, text
    name of doLoad step script is actually doLoad
• src/inc/iupac.h
  • lines changed 42, context: html, text, full: html, text
    Adding support for IUPAC nucleotide ambiguity codes to 'short match' track. Made iupac.c library module.
• src/lib/iupac.c
  • lines changed 213, context: html, text, full: html, text
    Adding support for IUPAC nucleotide ambiguity codes to 'short match' track. Made iupac.c library module.
• src/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    Adding support for IUPAC nucleotide ambiguity codes to 'short match' track. Made iupac.c library module.
• src/lib/sqlList.c
  • lines changed 3, context: html, text, full: html, text
    fixing some bugs turned up by testing
• src/lib/sqlNum.c
  • lines changed 2, context: html, text, full: html, text
    fixing some bugs turned up by testing
  • lines changed 11, context: html, text, full: html, text
    with Jims blessing adding check to not return empty input as 0 but to errabort like the other data types do
• src/product/README.trackDb
  • lines changed 1, context: html, text, full: html, text
    correct reference to trackDb/README file
• src/utils/htmlCheck/htmlCheck.c
  • lines changed 2, context: html, text, full: html, text
    Making it do a GET rather than a HEAD call when checking links, to avoid 405 errors on some sites.
• src/utils/qa/qaGbTracks
  • lines changed 18, context: html, text, full: html, text
    Changed and reordered help comment wording a little and added option to use the name of a single table at the command line rather than supply a list of tables.
  • lines changed 5, context: html, text, full: html, text
    Changed ucscgenomics to ucscGb in import statements to match reorganization.
  • lines changed 12, context: html, text, full: html, text
    Moved two functions from qaUtils to qaGbTracks, and got rid of a duplicated function from qaUtils.
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 3, context: html, text, full: html, text
    v267 final build

• lines changed: 48941
• files changed: 539