All File Changes
v254_preview to v254_preview2 (2011-07-05 to 2011-07-12) v254
- python/lib/ucscgenomics/__init__.py
- lines changed 0, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/lib/ucscgenomics/cvfile/CvFile.py
- lines changed 579, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/lib/ucscgenomics/cvfile/__init__.py
- lines changed 0, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/lib/ucscgenomics/cvfile/unittest/input/Antibody/BlankKey.ra
- lines changed 25, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/lib/ucscgenomics/cvfile/unittest/input/Antibody/ExtraKey.ra
- lines changed 26, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/lib/ucscgenomics/cvfile/unittest/input/Antibody/MissingKey.ra
- lines changed 24, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/lib/ucscgenomics/cvfile/unittest/input/Antibody/NonmatchKey.ra
- lines changed 25, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/lib/ucscgenomics/cvfile/unittest/input/Antibody/ValidStanza.ra
- lines changed 36, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/lib/ucscgenomics/cvfile/unittest/input/CellLine/BlankKey.ra
- lines changed 34, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/lib/ucscgenomics/cvfile/unittest/input/CellLine/ExtraKey.ra
- lines changed 35, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/lib/ucscgenomics/cvfile/unittest/input/CellLine/MissingKey.ra
- lines changed 33, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/lib/ucscgenomics/cvfile/unittest/input/CellLine/NonmatchKey.ra
- lines changed 34, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/lib/ucscgenomics/cvfile/unittest/input/CellLine/ValidStanza.ra
- lines changed 33, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/lib/ucscgenomics/cvfile/unittest/input/Mouse/BlankKey.ra
- lines changed 37, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/lib/ucscgenomics/cvfile/unittest/input/Mouse/ExtraKey.ra
- lines changed 38, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/lib/ucscgenomics/cvfile/unittest/input/Mouse/MissingKey.ra
- lines changed 36, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/lib/ucscgenomics/cvfile/unittest/input/Mouse/NonmatchKey.ra
- lines changed 37, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/lib/ucscgenomics/cvfile/unittest/input/Mouse/ValidStanza.ra
- lines changed 37, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/lib/ucscgenomics/cvfile/unittest/testCvFile
- lines changed 95, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/lib/ucscgenomics/ordereddict/OrderedDict.py
- lines changed 58, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/lib/ucscgenomics/ordereddict/__init__.py
- lines changed 0, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/lib/ucscgenomics/rafile/RaFile.py
- lines changed 183, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/lib/ucscgenomics/rafile/__init__.py
- lines changed 0, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/lib/ucscgenomics/rafile/unittest/testRaFile.py
- lines changed 205, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/lib/ucscgenomics/rafile/unittest/testoutput/BasicDiff.out
- lines changed 27, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/lib/ucscgenomics/rafile/unittest/testoutput/CommentsDiff.out
- lines changed 31, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/lib/ucscgenomics/rafile/unittest/testoutput/DeleteItem.out
- lines changed 39, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/lib/ucscgenomics/rafile/unittest/testoutput/ExtraneousWhitespace.out
- lines changed 70, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/lib/ucscgenomics/rafile/unittest/testoutput/GetItem.out
- lines changed 13, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/lib/ucscgenomics/rafile/unittest/testoutput/InlineCommentsDiff.out
- lines changed 27, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/lib/ucscgenomics/rafile/unittest/testoutput/IterEntryItems.out
- lines changed 27, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/lib/ucscgenomics/rafile/unittest/testoutput/IterEntryKeys.out
- lines changed 27, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/lib/ucscgenomics/rafile/unittest/testoutput/IterEntryValues.out
- lines changed 27, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/lib/ucscgenomics/rafile/unittest/testoutput/IterItems.out
- lines changed 19, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/lib/ucscgenomics/rafile/unittest/testoutput/IterKeys.out
- lines changed 11, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/lib/ucscgenomics/rafile/unittest/testoutput/IterValues.out
- lines changed 41, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/lib/ucscgenomics/rafile/unittest/tests/BasicDiff.ra
- lines changed 12, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/lib/ucscgenomics/rafile/unittest/tests/CommentsDiff.ra
- lines changed 14, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/lib/ucscgenomics/rafile/unittest/tests/DeleteItem.ra
- lines changed 18, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/lib/ucscgenomics/rafile/unittest/tests/DuplicateKeys.ra
- lines changed 8, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/lib/ucscgenomics/rafile/unittest/tests/FunctionalityCheck.ra
- lines changed 23, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/lib/ucscgenomics/rafile/unittest/tests/GetItem.ra
- lines changed 5, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/lib/ucscgenomics/rafile/unittest/tests/InlineCommentsDiff.ra
- lines changed 12, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/lib/ucscgenomics/rafile/unittest/tests/IterEntryItems.ra
- lines changed 12, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/lib/ucscgenomics/rafile/unittest/tests/IterEntryKeys.ra
- lines changed 12, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/lib/ucscgenomics/rafile/unittest/tests/IterEntryValues.ra
- lines changed 12, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/lib/ucscgenomics/rafile/unittest/tests/IterItems.ra
- lines changed 8, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/lib/ucscgenomics/rafile/unittest/tests/IterKeys.ra
- lines changed 4, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/lib/ucscgenomics/rafile/unittest/tests/IterValues.ra
- lines changed 19, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/lib/ucscgenomics/rafile/unittest/tests/MisplacedKeys.ra
- lines changed 8, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/lib/ucscgenomics/rafile/unittest/tests/NonNewlineFile.ra
- lines changed 5, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/lib/ucscgenomics/softfile/SoftFile.py
- lines changed 390, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/lib/ucscgenomics/softfile/__init__.py
- lines changed 0, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/lib/ucscgenomics/softfile/unittest/testSoft
- lines changed 10, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/programs/cvValidate/README
- lines changed 1, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/programs/cvValidate/cvValidate
- lines changed 22, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/programs/mkGeoPkg/README
- lines changed 0, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/programs/mkGeoPkg/mkGeoPkg
- lines changed 419, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/style.txt
- lines changed 44, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/ucscgenomics/__init__.py
- lines changed 0, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/ucscgenomics/cvValidate/README
- lines changed 1, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/ucscgenomics/cvValidate/cvValidate
- lines changed 22, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/ucscgenomics/lib/__init__.py
- lines changed 0, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/ucscgenomics/lib/cvfile/CvFile.py
- lines changed 579, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/ucscgenomics/lib/cvfile/__init__.py
- lines changed 0, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/ucscgenomics/lib/cvfile/unittest/input/Antibody/BlankKey.ra
- lines changed 25, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/ucscgenomics/lib/cvfile/unittest/input/Antibody/ExtraKey.ra
- lines changed 26, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/ucscgenomics/lib/cvfile/unittest/input/Antibody/MissingKey.ra
- lines changed 24, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/ucscgenomics/lib/cvfile/unittest/input/Antibody/NonmatchKey.ra
- lines changed 25, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/ucscgenomics/lib/cvfile/unittest/input/Antibody/ValidStanza.ra
- lines changed 36, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/ucscgenomics/lib/cvfile/unittest/input/CellLine/BlankKey.ra
- lines changed 34, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/ucscgenomics/lib/cvfile/unittest/input/CellLine/ExtraKey.ra
- lines changed 35, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/ucscgenomics/lib/cvfile/unittest/input/CellLine/MissingKey.ra
- lines changed 33, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/ucscgenomics/lib/cvfile/unittest/input/CellLine/NonmatchKey.ra
- lines changed 34, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/ucscgenomics/lib/cvfile/unittest/input/CellLine/ValidStanza.ra
- lines changed 33, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/ucscgenomics/lib/cvfile/unittest/input/Mouse/BlankKey.ra
- lines changed 37, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/ucscgenomics/lib/cvfile/unittest/input/Mouse/ExtraKey.ra
- lines changed 38, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/ucscgenomics/lib/cvfile/unittest/input/Mouse/MissingKey.ra
- lines changed 36, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/ucscgenomics/lib/cvfile/unittest/input/Mouse/NonmatchKey.ra
- lines changed 37, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/ucscgenomics/lib/cvfile/unittest/input/Mouse/ValidStanza.ra
- lines changed 37, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/ucscgenomics/lib/cvfile/unittest/testCvFile
- lines changed 95, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/ucscgenomics/lib/ordereddict/OrderedDict.py
- lines changed 57, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/ucscgenomics/lib/ordereddict/__init__.py
- lines changed 0, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/ucscgenomics/lib/rafile/RaFile.py
- lines changed 183, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/ucscgenomics/lib/rafile/__init__.py
- lines changed 0, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/ucscgenomics/lib/rafile/unittest/testRaFile.py
- lines changed 205, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/ucscgenomics/lib/rafile/unittest/testoutput/BasicDiff.out
- lines changed 27, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/ucscgenomics/lib/rafile/unittest/testoutput/CommentsDiff.out
- lines changed 31, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/ucscgenomics/lib/rafile/unittest/testoutput/DeleteItem.out
- lines changed 39, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/ucscgenomics/lib/rafile/unittest/testoutput/ExtraneousWhitespace.out
- lines changed 70, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/ucscgenomics/lib/rafile/unittest/testoutput/GetItem.out
- lines changed 13, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/ucscgenomics/lib/rafile/unittest/testoutput/InlineCommentsDiff.out
- lines changed 27, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/ucscgenomics/lib/rafile/unittest/testoutput/IterEntryItems.out
- lines changed 27, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/ucscgenomics/lib/rafile/unittest/testoutput/IterEntryKeys.out
- lines changed 27, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/ucscgenomics/lib/rafile/unittest/testoutput/IterEntryValues.out
- lines changed 27, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/ucscgenomics/lib/rafile/unittest/testoutput/IterItems.out
- lines changed 19, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/ucscgenomics/lib/rafile/unittest/testoutput/IterKeys.out
- lines changed 11, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/ucscgenomics/lib/rafile/unittest/testoutput/IterValues.out
- lines changed 41, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/ucscgenomics/lib/rafile/unittest/tests/BasicDiff.ra
- lines changed 12, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/ucscgenomics/lib/rafile/unittest/tests/CommentsDiff.ra
- lines changed 14, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/ucscgenomics/lib/rafile/unittest/tests/DeleteItem.ra
- lines changed 18, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/ucscgenomics/lib/rafile/unittest/tests/DuplicateKeys.ra
- lines changed 8, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/ucscgenomics/lib/rafile/unittest/tests/FunctionalityCheck.ra
- lines changed 23, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/ucscgenomics/lib/rafile/unittest/tests/GetItem.ra
- lines changed 5, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/ucscgenomics/lib/rafile/unittest/tests/InlineCommentsDiff.ra
- lines changed 12, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/ucscgenomics/lib/rafile/unittest/tests/IterEntryItems.ra
- lines changed 12, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/ucscgenomics/lib/rafile/unittest/tests/IterEntryKeys.ra
- lines changed 12, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/ucscgenomics/lib/rafile/unittest/tests/IterEntryValues.ra
- lines changed 12, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/ucscgenomics/lib/rafile/unittest/tests/IterItems.ra
- lines changed 8, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/ucscgenomics/lib/rafile/unittest/tests/IterKeys.ra
- lines changed 4, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/ucscgenomics/lib/rafile/unittest/tests/IterValues.ra
- lines changed 19, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/ucscgenomics/lib/rafile/unittest/tests/MisplacedKeys.ra
- lines changed 8, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/ucscgenomics/lib/rafile/unittest/tests/NonNewlineFile.ra
- lines changed 5, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/ucscgenomics/lib/softfile/SoftFile.py
- lines changed 390, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/ucscgenomics/lib/softfile/__init__.py
- lines changed 0, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/ucscgenomics/lib/softfile/unittest/testSoft
- lines changed 10, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/ucscgenomics/mkGeoPkg/README
- lines changed 0, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/ucscgenomics/mkGeoPkg/mkGeoPkg
- lines changed 231, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- python/ucscgenomics/style.txt
- lines changed 44, context: html, text, full: html, text
restructred directory again, updated mkGeoPkg, fixed a bug in OrderedDict, and removed extra __init__ file
- src/hg/encode/DAFs/2.0/uwMm9RnaSeq.daf
- lines changed 3, context: html, text, full: html, text
Updated the Views for to match cv.ra
- src/hg/encode/encodeReport/encodeReport.pl
- lines changed 10, context: html, text, full: html, text
Fixes to release date snarfing
- lines changed 42, context: html, text, full: html, text
1. More considered handling of submission ids and statuses -- use 'latest' pipeline status found associated with a submission id in the selected assembly. 2. Fix sorting of ID's (should be numeric)
- lines changed 4, context: html, text, full: html, text
Warn if no expvars in composite instead of just discarding
- lines changed 43, context: html, text, full: html, text
Fixes to handling of strain, age, treatment (treated specially in NHGRI reporting)
- lines changed 40, context: html, text, full: html, text
Add Lab_IDs column (#21) for showing labExpId metadata
- lines changed 17, context: html, text, full: html, text
1. Add -limit=string for debug 2. Bug fixes -- support for non-composites, missing database in projects table
- src/hg/encode/encodeValidate/doEncodeValidate.pl
- lines changed 95, context: html, text, full: html, text
made a new way of generating long labels in doEncodeValidate, it now generates long labels much closer to accepted convention. At least for human, sorry mouse.
- lines changed 13, context: html, text, full: html, text
added a function to make sure passed variables are at least defined, and a function to turn _ into spaces, and some comments
- src/hg/hgFileSearch/hgFileSearch.c
- lines changed 3, context: html, text, full: html, text
Moved all ddcl extension code into a ddcl object in ddcl.js. Reworked filterComp code to be more like filterTable code since IE was getting timeouts on HAIB TFBS.
- src/hg/hgHubConnect/hgHubConnect.c
- lines changed 1, context: html, text, full: html, text
Getting rid of compile warning on Ubuntu (format arg has to be a proper format string).
- lines changed 211, context: html, text, full: html, text
braney makes his first foray into Javascript. Hide yo' wives! #3271
- lines changed 1, context: html, text, full: html, text
Fix stricter-gcc warning: pass in a proper format string instead of a plain old char * variable.
- lines changed 32, context: html, text, full: html, text
stop using library routines which were hardcoding BGCOLOR.
- src/hg/hgTables/bigWig.c
- lines changed 26, context: html, text, full: html, text
MLQ #4463 (problem w/intersection):enabling intersection for bigWig uncovered a couple new bugs:
1. The secondary-table-fetching code didn't handle the bigWig case.
Fix: added bigWigIntervalsToBed and hooked it up in bitsForIntersectingTable.
2. The code for intersecting w/bigWig primary table had been written
but never tested, and the code for incompletely covered items from the
primary table was incorrect.
- src/hg/hgTables/hgTables.h
- lines changed 5, context: html, text, full: html, text
MLQ #4463 (problem w/intersection):enabling intersection for bigWig uncovered a couple new bugs:
1. The secondary-table-fetching code didn't handle the bigWig case.
Fix: added bigWigIntervalsToBed and hooked it up in bitsForIntersectingTable.
2. The code for intersecting w/bigWig primary table had been written
but never tested, and the code for incompletely covered items from the
primary table was incorrect.
- src/hg/hgTables/intersect.c
- lines changed 8, context: html, text, full: html, text
MLQ #4463 (problem w/intersection):enabling intersection for bigWig uncovered a couple new bugs:
1. The secondary-table-fetching code didn't handle the bigWig case.
Fix: added bigWigIntervalsToBed and hooked it up in bitsForIntersectingTable.
2. The code for intersecting w/bigWig primary table had been written
but never tested, and the code for incompletely covered items from the
primary table was incorrect.
- src/hg/hgTables/mainPage.c
- lines changed 1, context: html, text, full: html, text
fix typo on import tracks form
- src/hg/hgTracks/bedTrack.c
- lines changed 11, context: html, text, full: html, text
Bug #4263 (track items not being drawn in hgTracks when zoomed way in):Building on Fan's fix for integer overflow in bedPlusLabelDrawAt's x1
calculation, I changed the x1 and x2 calculations to use pre-clipped
chromosome coordinates so that they're using reasonably small inputs.
The ISCA Retrospective track (bedDrawSimpleAt) had the same problem
with long items and large scale factor causing integer overflow, so I
applied the same fix there. hgTracks code still has ~50 places that
use the same round((double)(... method, but it takes extreme conditions
to cause integer overflow so I'll leave those alone for now.
- src/hg/hgTracks/hgTracks.c
- lines changed 6, context: html, text, full: html, text
Moved all ddcl extension code into a ddcl object in ddcl.js. Reworked filterComp code to be more like filterTable code since IE was getting timeouts on HAIB TFBS.
- lines changed 2, context: html, text, full: html, text
make sure all the track hubs are after all the normal tracks
- lines changed 20, context: html, text, full: html, text
move javascript globals from hiddens to an object
- lines changed 6, context: html, text, full: html, text
Fix for redmine 2763. Return to browser from ps/pdf page now works.
- lines changed 35, context: html, text, full: html, text
put hub track groups up top with user tracks.
- src/hg/hgTracks/mainMain.c
- lines changed 2, context: html, text, full: html, text
remove obsolete vars from excludeVars
- src/hg/hgTracks/searchTracks.c
- lines changed 3, context: html, text, full: html, text
Moved all ddcl extension code into a ddcl object in ddcl.js. Reworked filterComp code to be more like filterTable code since IE was getting timeouts on HAIB TFBS.
- src/hg/hgTracks/simpleTracks.c
- lines changed 8, context: html, text, full: html, text
Corrected a subtle error introduced by adding gene symbol filter for OMIM Genes.
- lines changed 5, context: html, text, full: html, text
Fixed a bug in bedPlusLabelDrawAt() when zone to a few bases level.
- lines changed 11, context: html, text, full: html, text
Bug #4263 (track items not being drawn in hgTracks when zoomed way in):Building on Fan's fix for integer overflow in bedPlusLabelDrawAt's x1
calculation, I changed the x1 and x2 calculations to use pre-clipped
chromosome coordinates so that they're using reasonably small inputs.
The ISCA Retrospective track (bedDrawSimpleAt) had the same problem
with long items and large scale factor causing integer overflow, so I
applied the same fix there. hgTracks code still has ~50 places that
use the same round((double)(... method, but it takes extreme conditions
to cause integer overflow so I'll leave those alone for now.
- lines changed 2, context: html, text, full: html, text
change some table names to correlate with reality #4502
- lines changed 5, context: html, text, full: html, text
Bug #4263 (track items not being drawn in hgTracks when zoomed way in):fixing same integer overflow problem, for RGD tracks -- thanks Brooke for
catching those.
- src/hg/hgc/hgc.c
- src/hg/htdocs/ENCODE/transfragBed6CshlDescription.html
- lines changed 252, context: html, text, full: html, text
Spelling error in the name
- src/hg/htdocs/ENCODE/transfragBed6CshlDiscription.html
- lines changed 252, context: html, text, full: html, text
Spelling error in the name
- src/hg/htdocs/goldenPath/help/customTrackText.html
- lines changed 1, context: html, text, full: html, text
Should have been fixed long ago.
- src/hg/htdocs/images/Macropus_eugenii.jpg
- lines changed 0, context: html, text, full: html, text
Added wallaby picture: Macropus_eugenii.jpg
- src/hg/htdocs/style/hgHubConnect.css
- lines changed 29, context: html, text, full: html, text
braney makes his first foray into Javascript. Hide yo' wives! #3271
- src/hg/htdocs/style/makefile
- lines changed 3, context: html, text, full: html, text
braney makes his first foray into Javascript. Hide yo' wives! #3271
- src/hg/inc/bamFile.h
- lines changed 94, context: html, text, full: html, text
Separated BAM code into that which must compile into jkhgap.a (and be linked with mysql), and that which can go into jkweb.a (most of it). Older BAM open, fetch, and exists functions call the new ones with the UDC fuse root parameter set to the hg.conf setting. It is not yet clear to me if the UdcFuseRoot parameter can be set to NULL and used in a general way.
- src/hg/inc/jsHelper.h
- lines changed 16, context: html, text, full: html, text
add jsPrintHash and related routines
- src/hg/js/ddcl.js
- lines changed 329, context: html, text, full: html, text
Moved all ddcl extension code into a ddcl object in ddcl.js. Reworked filterComp code to be more like filterTable code since IE was getting timeouts on HAIB TFBS.
- src/hg/js/hgHubConnect.js
- lines changed 14, context: html, text, full: html, text
braney makes his first foray into Javascript. Hide yo' wives! #3271
- src/hg/js/hgTracks.js
- lines changed 4, context: html, text, full: html, text
Moved all ddcl extension code into a ddcl object in ddcl.js. Reworked filterComp code to be more like filterTable code since IE was getting timeouts on HAIB TFBS.
- lines changed 52, context: html, text, full: html, text
move javascript globals from hiddens to an object
- src/hg/js/hui.js
- lines changed 3, context: html, text, full: html, text
Major performance improvements for IE javascript. parent() and add() both dragged the JSript engine to it's knees. Debug code is being checked in but not called.
- lines changed 297, context: html, text, full: html, text
Moved all ddcl extension code into a ddcl object in ddcl.js. Reworked filterComp code to be more like filterTable code since IE was getting timeouts on HAIB TFBS.
- lines changed 1, context: html, text, full: html, text
Since IE is so slow on giant composites, limited filterBox invalid options being grayed to only occur when there are a limited number of subtracks checked (<300) or files (<300).
- src/hg/js/makefile
- lines changed 1, context: html, text, full: html, text
Moved all ddcl extension code into a ddcl object in ddcl.js. Reworked filterComp code to be more like filterTable code since IE was getting timeouts on HAIB TFBS.
- lines changed 8, context: html, text, full: html, text
braney makes his first foray into Javascript. Hide yo' wives! #3271
- src/hg/js/utils.js
- lines changed 277, context: html, text, full: html, text
Major performance improvements for IE javascript. parent() and add() both dragged the JSript engine to it's knees. Debug code is being checked in but not called.
- lines changed 9, context: html, text, full: html, text
IE was creating 2 rows instead of 1 when the plus button was pressed in trackSearch.
- lines changed 383, context: html, text, full: html, text
Moved all ddcl extension code into a ddcl object in ddcl.js. Reworked filterComp code to be more like filterTable code since IE was getting timeouts on HAIB TFBS.
- lines changed 12, context: html, text, full: html, text
Since IE is so slow on giant composites, limited filterBox invalid options being grayed to only occur when there are a limited number of subtracks checked (<300) or files (<300).
- src/hg/lib/bamFile.c
- lines changed 644, context: html, text, full: html, text
Separated BAM code into that which must compile into jkhgap.a (and be linked with mysql), and that which can go into jkweb.a (most of it). Older BAM open, fetch, and exists functions call the new ones with the UDC fuse root parameter set to the hg.conf setting. It is not yet clear to me if the UdcFuseRoot parameter can be set to NULL and used in a general way.
- src/hg/lib/fileUi.c
- lines changed 1, context: html, text, full: html, text
Major performance improvements for IE javascript. parent() and add() both dragged the JSript engine to it's knees. Debug code is being checked in but not called.
- lines changed 2, context: html, text, full: html, text
Moved all ddcl extension code into a ddcl object in ddcl.js. Reworked filterComp code to be more like filterTable code since IE was getting timeouts on HAIB TFBS.
- src/hg/lib/hui.c
- lines changed 13, context: html, text, full: html, text
Moved all ddcl extension code into a ddcl object in ddcl.js. Reworked filterComp code to be more like filterTable code since IE was getting timeouts on HAIB TFBS.
- src/hg/lib/jsHelper.c
- lines changed 50, context: html, text, full: html, text
add jsPrintHash and related routines
- src/hg/makeDb/doc/encodeDccHg18/wgEncodeHudsonalphaChipSeq.release3.notes
- lines changed 768, context: html, text, full: html, text
Added notes file for release of track for third time. Redmine #825.
- lines changed 5, context: html, text, full: html, text
Removed replicate 2 of lab=HudsonAlpha dataType=ChipSeq cell=K562 antibody=Input treatment=None protocol=PCR2x, as this is not linked as a control for any experiment. Redmine #70, note 29 and Redmine #825, note 20. This was forgotten in commit edcf0a7a003f2e14a299793df2fedd55d70932b0.
- lines changed 45, context: html, text, full: html, text
Added Deprecated Tables that are Signals.
- src/hg/makeDb/doc/encodeDccHg19/wgEncodeHaibTfbs.release1.notes
- lines changed 1680, context: html, text, full: html, text
Updated release notes to accuratley reflect files only for release 1.
- src/hg/makeDb/doc/encodeDccHg19/wgEncodeSydhHistone.release2.notes
- lines changed 395, context: html, text, full: html, text
added sydh histone release2 notes
- src/hg/makeDb/doc/encodeDccMm9/wgEncodeSydhTfbs.release2.notes
- lines changed 393, context: html, text, full: html, text
Updated release notes to refelect the correct number of dropped gbdb files and deprecated tables.
- src/hg/makeDb/doc/hg19.txt
- lines changed 265, context: html, text, full: html, text
working on fosEnds and starting patch5
- src/hg/makeDb/doc/hg19Patch5.txt
- lines changed 629, context: html, text, full: html, text
initial tracks on hg19Patch5 browser
- src/hg/makeDb/doc/melGal1.txt
- src/hg/makeDb/doc/proteins/090821.txt
- src/hg/makeDb/genbank/etc/genbank.conf
- lines changed 2, context: html, text, full: html, text
take out some commented out data #4502
- src/hg/makeDb/schema/all.joiner
- lines changed 6, context: html, text, full: html, text
Starting to add enttries for RGD Genes.
- lines changed 2, context: html, text, full: html, text
Added two tables to the ignored list; one for mm9 and one for hg19; this is for pushQ 5661, the tables are allHg19RS_BW allMm9RS_BW
- src/hg/makeDb/trackDb/cv/alpha/CD34+Mobilized_Stam_protocol.pdf
- lines changed 0, context: html, text, full: html, text
removed protocols from the cv directory and put them in the correct spot on htdocsExtras
- src/hg/makeDb/trackDb/cv/alpha/HBVP_Stam_protocol.pdf
- lines changed 0, context: html, text, full: html, text
removed protocols from the cv directory and put them in the correct spot on htdocsExtras
- src/hg/makeDb/trackDb/cv/alpha/HBVSMC_Stam_protocol.pdf
- lines changed 0, context: html, text, full: html, text
removed protocols from the cv directory and put them in the correct spot on htdocsExtras
- src/hg/makeDb/trackDb/cv/alpha/HMVECdAd_Stam_protocol.pdf
- lines changed 0, context: html, text, full: html, text
removed protocols from the cv directory and put them in the correct spot on htdocsExtras
- src/hg/makeDb/trackDb/cv/alpha/HPAEC_Stam_protocol.pdf
- lines changed 0, context: html, text, full: html, text
removed protocols from the cv directory and put them in the correct spot on htdocsExtras
- src/hg/makeDb/trackDb/cv/alpha/NHBE_Stam_protocol.pdf
- lines changed 0, context: html, text, full: html, text
removed protocols from the cv directory and put them in the correct spot on htdocsExtras
- src/hg/makeDb/trackDb/cv/alpha/cv.ra
- lines changed 10, context: html, text, full: html, text
Added more descriptions of views
- lines changed 5, context: html, text, full: html, text
Preliminary defnition for new control RevXLinkChromatin.
- lines changed 9, context: html, text, full: html, text
Made changes according to ticket 4498
- lines changed 1, context: html, text, full: html, text
Changing a description for ticket 4498
- lines changed 1, context: html, text, full: html, text
Added new definition for RevXlinkChromatin provided by Flo and Preti. Redmine #4527.
- lines changed 60, context: html, text, full: html, text
Commenting out the BJ terms until resolved ticket #4536
- lines changed 12, context: html, text, full: html, text
Added 2 extra views that are on a Mouse track. Redmine #3608.
- src/hg/makeDb/trackDb/cv/beta/cv.ra
- lines changed 324, context: html, text, full: html, text
The changes for the cv this week can be put into 6 basica categories: PROTOCOL All the protocols have been given a standardized naming format of Lab:LabsProtocolName_protocol.pdf. VANESSA REQEUSTS Changes from the revious code review RESEARCHED ADDITIONS Jeff added many vendorNames and lineages KATE REQUESTS Many datatypes and labs were altered to be constent with NHGRI TYPOS Minor changes that hardly show in the diff PROVISIONALS Larger changes or additions to cell lines and views that are still being debated, my understanding is that we mark them with PROVISIONAL so that you can still push and the outside world will see them as provisional.
- src/hg/makeDb/trackDb/cv/public/cv.ra
- lines changed 1283, context: html, text, full: html, text
copying the beta cv.ra to public redmine#4498
- src/hg/makeDb/trackDb/drosophila/bdtnpDnase.html
- lines changed 19, context: html, text, full: html, text
Track #671 (BDTNP): updated BDTNP DNase references, requested by Mark Biggin.
- lines changed 17, context: html, text, full: html, text
Track #671 (BDTNP): oops, fixing a couple things caught by Brooke.
- src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeHudsonalphaChipSeq.ra
- lines changed 91, context: html, text, full: html, text
Updated antibody=Input to antibody=RevXlinkChromatin. Also update the subGroups to remove any control's in antibody and only have zRXLCH. Redmine #4527.
- lines changed 48, context: html, text, full: html, text
Removed replicate 2 of lab=HudsonAlpha dataType=ChipSeq cell=K562 antibody=Input treatment=None protocol=PCR2x, as this is not linked as a control for any experiment. Redmine #70, note 29 and Redmine #825, note 20. This was forgotten in commit edcf0a7a003f2e14a299793df2fedd55d70932b0.
- lines changed 715, context: html, text, full: html, text
Added expId's and dccAccessions. Redmine #825, note 25.
- lines changed 715, context: html, text, full: html, text
Removed dccAccessions added by mistake in commit ea5881c6f148e2a4bfafc533a63d6240a3ef330e. Redmine #825, note 25.
- src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaChipSeq.new.html
- lines changed 191, context: html, text, full: html, text
Added new html file to explain the change of antibody=Input to RevXlinkChromatin. Redmine #4527, #825.
- src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaChipSeq.new.ra
- lines changed 29, context: html, text, full: html, text
Updated antibody=Input to antibody=RevXlinkChromatin. Also update the subGroups to remove any control's in antibody and only have zRXLCH. Redmine #4527.
- lines changed 1, context: html, text, full: html, text
Added new html file to explain the change of antibody=Input to RevXlinkChromatin. Redmine #4527, #825.
- lines changed 8, context: html, text, full: html, text
Removed replicate 2 of lab=HudsonAlpha dataType=ChipSeq cell=K562 antibody=Input treatment=None protocol=PCR2x, as this is not linked as a control for any experiment. Redmine #70, note 29 and Redmine #825, note 20. This was forgotten in commit edcf0a7a003f2e14a299793df2fedd55d70932b0.
- src/hg/makeDb/trackDb/human/hg19/allHg19RS_BW.html
- lines changed 95, context: html, text, full: html, text
cleaned up html, added hard line breaks at 100 characters.
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra
- lines changed 1536, context: html, text, full: html, text
Adding readType and seqPlatform
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlShortRnaSeq.ra
- lines changed 437, context: html, text, full: html, text
Adding readType and seqPlatform
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra
- lines changed 7327, context: html, text, full: html, text
Updated antibody=Input to antibody=RevXlinkChromatin. Also update the subGroups to remove any control's in antibody and only have zRXLCH. Renamed files that used Control to Rxlch in file name. Updated name changes to .new.ra for release 2 updates. Redmine #4527
- lines changed 154, context: html, text, full: html, text
Error: Last commit didn't include the following. Updated antibody=Input to antibody=RevXlinkChromatin. Redmine #4527.
- lines changed 2, context: html, text, full: html, text
Fixed invalide date 2008-12-117 to 2008-12-11. Redmine #4393. Note 55.
- lines changed 7, context: html, text, full: html, text
Added dccAccession and expId's for release 1. Redmine #70 note 35.
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra
- lines changed 105, context: html, text, full: html, text
changed short labels, other minor corrections, and changed incorrect controls
- lines changed 834, context: html, text, full: html, text
changed hek293 and hepg2 from b to original, also cleaned up some tags in trackDb
- lines changed 42, context: html, text, full: html, text
removed all traces of hepg2b and hek293b
- src/hg/makeDb/trackDb/human/hg19/metaDb/beta/makefile
- lines changed 1, context: html, text, full: html, text
Staging Gencode Genes V7, redmine# 2608
- src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeGencodeV7.ra
- lines changed 246, context: html, text, full: html, text
Staging Gencode Genes V7, redmine# 2608
- src/hg/makeDb/trackDb/human/hg19/metaDb/public/makefile
- lines changed 1, context: html, text, full: html, text
releasing GENCODE Genes V7, redmine #2608
- src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeGencodeV7.ra
- lines changed 246, context: html, text, full: html, text
releasing GENCODE Genes V7, redmine #2608
- src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
- lines changed 1, context: html, text, full: html, text
Staging Gencode Genes V7, redmine# 2608
- lines changed 1, context: html, text, full: html, text
releasing GENCODE Genes V7, redmine #2608
- src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.html
- lines changed 1, context: html, text, full: html, text
Fixed the typo for Discription to Description
- src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.new.html
- lines changed 3, context: html, text, full: html, text
Fixed the typo for Discription to Description
- src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV7.html
- lines changed 7, context: html, text, full: html, text
Changed Release Notes to Description, changed the location of the PI link to be consistent with the rest of the chart, changed the gencode email to be sanitized
- lines changed 11, context: html, text, full: html, text
fixed typos, redmine# 2608
- lines changed 1, context: html, text, full: html, text
added a period, redmine# 2608
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibGenotype.html
- lines changed 13, context: html, text, full: html, text
fixed some html errors redmine #1708
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibShRnaSeq.html
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.html
- lines changed 5, context: html, text, full: html, text
cleaned up short labels and html for haib tfbs
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.new.ra
- lines changed 155, context: html, text, full: html, text
Updated antibody=Input to antibody=RevXlinkChromatin. Also update the subGroups to remove any control's in antibody and only have zRXLCH. Renamed files that used Control to Rxlch in file name. Updated name changes to .new.ra for release 2 updates. Redmine #4527
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.ra
- lines changed 155, context: html, text, full: html, text
Updated antibody=Input to antibody=RevXlinkChromatin. Also update the subGroups to remove any control's in antibody and only have zRXLCH. Renamed files that used Control to Rxlch in file name. Updated name changes to .new.ra for release 2 updates. Redmine #4527
- lines changed 563, context: html, text, full: html, text
cleaned up short labels and html for haib tfbs
- src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.new.ra
- lines changed 191, context: html, text, full: html, text
changed short labels, other minor corrections, and changed incorrect controls
- lines changed 48, context: html, text, full: html, text
fixed some short label stuff, propagated the name changes to the .new.ra, merged the hek293b and hepg2b into the originals
- src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.ra
- lines changed 16, context: html, text, full: html, text
changed short labels, other minor corrections, and changed incorrect controls
- lines changed 182, context: html, text, full: html, text
fixed some short label stuff, propagated the name changes to the .new.ra, merged the hek293b and hepg2b into the originals
- lines changed 298, context: html, text, full: html, text
changed hek293 and hepg2 from b to original, also cleaned up some tags in trackDb
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.new.ra
- lines changed 1, context: html, text, full: html, text
missing semicolon in cell name
- src/hg/makeDb/trackDb/human/hg19Patch5/description.html
- lines changed 129, context: html, text, full: html, text
initial files from makeGenomeDb.pl
- src/hg/makeDb/trackDb/human/hg19Patch5/gap.html
- lines changed 64, context: html, text, full: html, text
initial files from makeGenomeDb.pl
- src/hg/makeDb/trackDb/human/hg19Patch5/gold.html
- lines changed 23, context: html, text, full: html, text
initial files from makeGenomeDb.pl
- src/hg/makeDb/trackDb/human/hg19Patch5/trackDb.ra
- lines changed 7, context: html, text, full: html, text
initial files from makeGenomeDb.pl
- lines changed 31, context: html, text, full: html, text
adding the additional tracks
- src/hg/makeDb/trackDb/human/polyA.html
- lines changed 1, context: html, text, full: html, text
MLQ #4385 Fixed broken url link to PolyA_DB web site.
- src/hg/makeDb/trackDb/human/trackDb.ra
- src/hg/makeDb/trackDb/makefile
- lines changed 1, context: html, text, full: html, text
adding hg19Patch5 to the build
- src/hg/makeDb/trackDb/mouse/mm9/allMm9RS_BW.html
- lines changed 95, context: html, text, full: html, text
cleaned up html, added hard line breaks at 100 characters.
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodePsuTfbs.ra
- lines changed 3, context: html, text, full: html, text
Updated spelling of train to strain in metaDb.
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhHistone.ra
- lines changed 55, context: html, text, full: html, text
Added expId's and dccAccession's.
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhRnaSeq.ra
- lines changed 13, context: html, text, full: html, text
Added age and strain information that were missing for the MEL cell line.
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhTfbs.ra
- lines changed 517, context: html, text, full: html, text
Added dccAccession and expId's.
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeUwRnaSeq.ra
- lines changed 47, context: html, text, full: html, text
Updated the Views for to match cv.ra
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/makefile
- lines changed 1, context: html, text, full: html, text
staging LICR TFBS on beta, redmine# 101
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/wgEncodeLicrTfbs.ra
- lines changed 5445, context: html, text, full: html, text
staging LICR TFBS on beta, redmine# 101
- src/hg/makeDb/trackDb/mouse/mm9/trackDb.wgEncode.ra
- lines changed 1, context: html, text, full: html, text
staging LICR TFBS on beta, redmine# 101
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhHistone.ra
- lines changed 11, context: html, text, full: html, text
Updated Long labels to all be under 80 characters.
- lines changed 18, context: html, text, full: html, text
Fixed long and short labels on the recomendation of Kate. Redmine #97. Note 17.
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhTfbs.new.html
- lines changed 171, context: html, text, full: html, text
Added new html for relese 2 that descirbes resubmitted data and newly added data.
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhTfbs.newR2.ra
- lines changed 5, context: html, text, full: html, text
Added more descriptive long label for the second p300 antibody.
- lines changed 1, context: html, text, full: html, text
Added new html for relese 2 that descirbes resubmitted data and newly added data.
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwRnaSeq.ra
- lines changed 49, context: html, text, full: html, text
Updated the Views for to match cv.ra
- src/hg/makeDb/trackDb/turkey/melGal1/trackDb.ra
- src/hg/makeDb/trackDb/wallaby/macEug2/description.html
- lines changed 6, context: html, text, full: html, text
Added wallaby picture: Macropus_eugenii.jpg
- src/hg/utils/makeTableList/makeTableList.c
- lines changed 12, context: html, text, full: html, text
make changes suggested by markd in his code review
- src/hg/visiGene/hgVisiGene/hgVisiGene.c
- lines changed 1, context: html, text, full: html, text
minor fix for visiGene download link when errors occur
- src/inc/bamUdc.h
- lines changed 132, context: html, text, full: html, text
Separated BAM code into that which must compile into jkhgap.a (and be linked with mysql), and that which can go into jkweb.a (most of it). Older BAM open, fetch, and exists functions call the new ones with the UDC fuse root parameter set to the hg.conf setting. It is not yet clear to me if the UdcFuseRoot parameter can be set to NULL and used in a general way.
- src/inc/errabort.h
- src/lib/bamUdc.c
- lines changed 686, context: html, text, full: html, text
Separated BAM code into that which must compile into jkhgap.a (and be linked with mysql), and that which can go into jkweb.a (most of it). Older BAM open, fetch, and exists functions call the new ones with the UDC fuse root parameter set to the hg.conf setting. It is not yet clear to me if the UdcFuseRoot parameter can be set to NULL and used in a general way.
- lines changed 8, context: html, text, full: html, text
changed the errAbort back to a warning. Also fixing (hopefully fixing) problem loading the index of local BAM files. with remote BAM files a chdir to a trash dir is made where the index is automatically downloaded however if the index is local, then the chdir is actually moving away from the index file and it cannot load correctly. so I check if the file is a URL or not first.
- lines changed 4, context: html, text, full: html, text
compile-error fixed: unused var
- src/lib/errabort.c
- src/lib/log.c
- src/lib/makefile
- lines changed 1, context: html, text, full: html, text
Separated BAM code into that which must compile into jkhgap.a (and be linked with mysql), and that which can go into jkweb.a (most of it). Older BAM open, fetch, and exists functions call the new ones with the UDC fuse root parameter set to the hg.conf setting. It is not yet clear to me if the UdcFuseRoot parameter can be set to NULL and used in a general way.
- src/lib/portimpl.c
- lines changed 1, context: html, text, full: html, text
Removed comment that had become incorrect.
- src/utils/qa/weeklybld/buildEnv.csh
- lines changed: 37546
- files changed: 287