All File Changes
v253_base to v254_preview (2011-06-28 to 2011-07-05) v254
- python/ucscgenomics/cvValidate/README
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forgot to include a few files
- python/ucscgenomics/cvValidate/cvValidate
- lines changed 30, context: html, text, full: html, text
updated directory structure to fit library design goal. modify PYTHONPATH to now point at python/ucscgenomics/lib instead of python/ucscgenomics/rafile
- python/ucscgenomics/lib/__init__.py
- lines changed 0, context: html, text, full: html, text
updated directory structure to fit library design goal. modify PYTHONPATH to now point at python/ucscgenomics/lib instead of python/ucscgenomics/rafile
- python/ucscgenomics/lib/cvfile/CvFile.py
- lines changed 568, context: html, text, full: html, text
updated directory structure to fit library design goal. modify PYTHONPATH to now point at python/ucscgenomics/lib instead of python/ucscgenomics/rafile
- python/ucscgenomics/lib/cvfile/__init__.py
- lines changed 0, context: html, text, full: html, text
updated directory structure to fit library design goal. modify PYTHONPATH to now point at python/ucscgenomics/lib instead of python/ucscgenomics/rafile
- python/ucscgenomics/lib/cvfile/unittest/input/Antibody/BlankKey.ra
- lines changed 25, context: html, text, full: html, text
updated directory structure to fit library design goal. modify PYTHONPATH to now point at python/ucscgenomics/lib instead of python/ucscgenomics/rafile
- python/ucscgenomics/lib/cvfile/unittest/input/Antibody/ExtraKey.ra
- lines changed 26, context: html, text, full: html, text
updated directory structure to fit library design goal. modify PYTHONPATH to now point at python/ucscgenomics/lib instead of python/ucscgenomics/rafile
- python/ucscgenomics/lib/cvfile/unittest/input/Antibody/MissingKey.ra
- lines changed 24, context: html, text, full: html, text
updated directory structure to fit library design goal. modify PYTHONPATH to now point at python/ucscgenomics/lib instead of python/ucscgenomics/rafile
- python/ucscgenomics/lib/cvfile/unittest/input/Antibody/NonmatchKey.ra
- lines changed 25, context: html, text, full: html, text
updated directory structure to fit library design goal. modify PYTHONPATH to now point at python/ucscgenomics/lib instead of python/ucscgenomics/rafile
- python/ucscgenomics/lib/cvfile/unittest/input/Antibody/ValidStanza.ra
- lines changed 36, context: html, text, full: html, text
updated directory structure to fit library design goal. modify PYTHONPATH to now point at python/ucscgenomics/lib instead of python/ucscgenomics/rafile
- python/ucscgenomics/lib/cvfile/unittest/input/CellLine/BlankKey.ra
- lines changed 34, context: html, text, full: html, text
updated directory structure to fit library design goal. modify PYTHONPATH to now point at python/ucscgenomics/lib instead of python/ucscgenomics/rafile
- python/ucscgenomics/lib/cvfile/unittest/input/CellLine/ExtraKey.ra
- lines changed 35, context: html, text, full: html, text
updated directory structure to fit library design goal. modify PYTHONPATH to now point at python/ucscgenomics/lib instead of python/ucscgenomics/rafile
- python/ucscgenomics/lib/cvfile/unittest/input/CellLine/MissingKey.ra
- lines changed 33, context: html, text, full: html, text
updated directory structure to fit library design goal. modify PYTHONPATH to now point at python/ucscgenomics/lib instead of python/ucscgenomics/rafile
- python/ucscgenomics/lib/cvfile/unittest/input/CellLine/NonmatchKey.ra
- lines changed 34, context: html, text, full: html, text
updated directory structure to fit library design goal. modify PYTHONPATH to now point at python/ucscgenomics/lib instead of python/ucscgenomics/rafile
- python/ucscgenomics/lib/cvfile/unittest/input/CellLine/ValidStanza.ra
- lines changed 33, context: html, text, full: html, text
updated directory structure to fit library design goal. modify PYTHONPATH to now point at python/ucscgenomics/lib instead of python/ucscgenomics/rafile
- python/ucscgenomics/lib/cvfile/unittest/input/Mouse/BlankKey.ra
- lines changed 37, context: html, text, full: html, text
updated directory structure to fit library design goal. modify PYTHONPATH to now point at python/ucscgenomics/lib instead of python/ucscgenomics/rafile
- python/ucscgenomics/lib/cvfile/unittest/input/Mouse/ExtraKey.ra
- lines changed 38, context: html, text, full: html, text
updated directory structure to fit library design goal. modify PYTHONPATH to now point at python/ucscgenomics/lib instead of python/ucscgenomics/rafile
- python/ucscgenomics/lib/cvfile/unittest/input/Mouse/MissingKey.ra
- lines changed 36, context: html, text, full: html, text
updated directory structure to fit library design goal. modify PYTHONPATH to now point at python/ucscgenomics/lib instead of python/ucscgenomics/rafile
- python/ucscgenomics/lib/cvfile/unittest/input/Mouse/NonmatchKey.ra
- lines changed 37, context: html, text, full: html, text
updated directory structure to fit library design goal. modify PYTHONPATH to now point at python/ucscgenomics/lib instead of python/ucscgenomics/rafile
- python/ucscgenomics/lib/cvfile/unittest/input/Mouse/ValidStanza.ra
- lines changed 37, context: html, text, full: html, text
updated directory structure to fit library design goal. modify PYTHONPATH to now point at python/ucscgenomics/lib instead of python/ucscgenomics/rafile
- python/ucscgenomics/lib/cvfile/unittest/testCvFile
- lines changed 95, context: html, text, full: html, text
updated directory structure to fit library design goal. modify PYTHONPATH to now point at python/ucscgenomics/lib instead of python/ucscgenomics/rafile
- python/ucscgenomics/lib/ordereddict/OrderedDict.py
- lines changed 57, context: html, text, full: html, text
updated directory structure to fit library design goal. modify PYTHONPATH to now point at python/ucscgenomics/lib instead of python/ucscgenomics/rafile
- python/ucscgenomics/lib/ordereddict/__init__.py
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updated directory structure to fit library design goal. modify PYTHONPATH to now point at python/ucscgenomics/lib instead of python/ucscgenomics/rafile
- python/ucscgenomics/lib/rafile/RaFile.py
- lines changed 183, context: html, text, full: html, text
updated directory structure to fit library design goal. modify PYTHONPATH to now point at python/ucscgenomics/lib instead of python/ucscgenomics/rafile
- python/ucscgenomics/lib/rafile/__init__.py
- lines changed 0, context: html, text, full: html, text
updated directory structure to fit library design goal. modify PYTHONPATH to now point at python/ucscgenomics/lib instead of python/ucscgenomics/rafile
- python/ucscgenomics/lib/rafile/unittest/testRaFile.py
- lines changed 205, context: html, text, full: html, text
updated directory structure to fit library design goal. modify PYTHONPATH to now point at python/ucscgenomics/lib instead of python/ucscgenomics/rafile
- python/ucscgenomics/lib/rafile/unittest/testoutput/BasicDiff.out
- lines changed 27, context: html, text, full: html, text
updated directory structure to fit library design goal. modify PYTHONPATH to now point at python/ucscgenomics/lib instead of python/ucscgenomics/rafile
- python/ucscgenomics/lib/rafile/unittest/testoutput/CommentsDiff.out
- lines changed 31, context: html, text, full: html, text
updated directory structure to fit library design goal. modify PYTHONPATH to now point at python/ucscgenomics/lib instead of python/ucscgenomics/rafile
- python/ucscgenomics/lib/rafile/unittest/testoutput/DeleteItem.out
- lines changed 39, context: html, text, full: html, text
updated directory structure to fit library design goal. modify PYTHONPATH to now point at python/ucscgenomics/lib instead of python/ucscgenomics/rafile
- python/ucscgenomics/lib/rafile/unittest/testoutput/ExtraneousWhitespace.out
- lines changed 70, context: html, text, full: html, text
updated directory structure to fit library design goal. modify PYTHONPATH to now point at python/ucscgenomics/lib instead of python/ucscgenomics/rafile
- python/ucscgenomics/lib/rafile/unittest/testoutput/GetItem.out
- lines changed 13, context: html, text, full: html, text
updated directory structure to fit library design goal. modify PYTHONPATH to now point at python/ucscgenomics/lib instead of python/ucscgenomics/rafile
- python/ucscgenomics/lib/rafile/unittest/testoutput/InlineCommentsDiff.out
- lines changed 27, context: html, text, full: html, text
updated directory structure to fit library design goal. modify PYTHONPATH to now point at python/ucscgenomics/lib instead of python/ucscgenomics/rafile
- python/ucscgenomics/lib/rafile/unittest/testoutput/IterEntryItems.out
- lines changed 27, context: html, text, full: html, text
updated directory structure to fit library design goal. modify PYTHONPATH to now point at python/ucscgenomics/lib instead of python/ucscgenomics/rafile
- python/ucscgenomics/lib/rafile/unittest/testoutput/IterEntryKeys.out
- lines changed 27, context: html, text, full: html, text
updated directory structure to fit library design goal. modify PYTHONPATH to now point at python/ucscgenomics/lib instead of python/ucscgenomics/rafile
- python/ucscgenomics/lib/rafile/unittest/testoutput/IterEntryValues.out
- lines changed 27, context: html, text, full: html, text
updated directory structure to fit library design goal. modify PYTHONPATH to now point at python/ucscgenomics/lib instead of python/ucscgenomics/rafile
- python/ucscgenomics/lib/rafile/unittest/testoutput/IterItems.out
- lines changed 19, context: html, text, full: html, text
updated directory structure to fit library design goal. modify PYTHONPATH to now point at python/ucscgenomics/lib instead of python/ucscgenomics/rafile
- python/ucscgenomics/lib/rafile/unittest/testoutput/IterKeys.out
- lines changed 11, context: html, text, full: html, text
updated directory structure to fit library design goal. modify PYTHONPATH to now point at python/ucscgenomics/lib instead of python/ucscgenomics/rafile
- python/ucscgenomics/lib/rafile/unittest/testoutput/IterValues.out
- lines changed 41, context: html, text, full: html, text
updated directory structure to fit library design goal. modify PYTHONPATH to now point at python/ucscgenomics/lib instead of python/ucscgenomics/rafile
- python/ucscgenomics/lib/rafile/unittest/tests/BasicDiff.ra
- lines changed 12, context: html, text, full: html, text
updated directory structure to fit library design goal. modify PYTHONPATH to now point at python/ucscgenomics/lib instead of python/ucscgenomics/rafile
- python/ucscgenomics/lib/rafile/unittest/tests/CommentsDiff.ra
- lines changed 14, context: html, text, full: html, text
updated directory structure to fit library design goal. modify PYTHONPATH to now point at python/ucscgenomics/lib instead of python/ucscgenomics/rafile
- python/ucscgenomics/lib/rafile/unittest/tests/DeleteItem.ra
- lines changed 18, context: html, text, full: html, text
updated directory structure to fit library design goal. modify PYTHONPATH to now point at python/ucscgenomics/lib instead of python/ucscgenomics/rafile
- python/ucscgenomics/lib/rafile/unittest/tests/DuplicateKeys.ra
- lines changed 8, context: html, text, full: html, text
updated directory structure to fit library design goal. modify PYTHONPATH to now point at python/ucscgenomics/lib instead of python/ucscgenomics/rafile
- python/ucscgenomics/lib/rafile/unittest/tests/FunctionalityCheck.ra
- lines changed 23, context: html, text, full: html, text
updated directory structure to fit library design goal. modify PYTHONPATH to now point at python/ucscgenomics/lib instead of python/ucscgenomics/rafile
- python/ucscgenomics/lib/rafile/unittest/tests/GetItem.ra
- lines changed 5, context: html, text, full: html, text
updated directory structure to fit library design goal. modify PYTHONPATH to now point at python/ucscgenomics/lib instead of python/ucscgenomics/rafile
- python/ucscgenomics/lib/rafile/unittest/tests/InlineCommentsDiff.ra
- lines changed 12, context: html, text, full: html, text
updated directory structure to fit library design goal. modify PYTHONPATH to now point at python/ucscgenomics/lib instead of python/ucscgenomics/rafile
- python/ucscgenomics/lib/rafile/unittest/tests/IterEntryItems.ra
- lines changed 12, context: html, text, full: html, text
updated directory structure to fit library design goal. modify PYTHONPATH to now point at python/ucscgenomics/lib instead of python/ucscgenomics/rafile
- python/ucscgenomics/lib/rafile/unittest/tests/IterEntryKeys.ra
- lines changed 12, context: html, text, full: html, text
updated directory structure to fit library design goal. modify PYTHONPATH to now point at python/ucscgenomics/lib instead of python/ucscgenomics/rafile
- python/ucscgenomics/lib/rafile/unittest/tests/IterEntryValues.ra
- lines changed 12, context: html, text, full: html, text
updated directory structure to fit library design goal. modify PYTHONPATH to now point at python/ucscgenomics/lib instead of python/ucscgenomics/rafile
- python/ucscgenomics/lib/rafile/unittest/tests/IterItems.ra
- lines changed 8, context: html, text, full: html, text
updated directory structure to fit library design goal. modify PYTHONPATH to now point at python/ucscgenomics/lib instead of python/ucscgenomics/rafile
- python/ucscgenomics/lib/rafile/unittest/tests/IterKeys.ra
- lines changed 4, context: html, text, full: html, text
updated directory structure to fit library design goal. modify PYTHONPATH to now point at python/ucscgenomics/lib instead of python/ucscgenomics/rafile
- python/ucscgenomics/lib/rafile/unittest/tests/IterValues.ra
- lines changed 19, context: html, text, full: html, text
updated directory structure to fit library design goal. modify PYTHONPATH to now point at python/ucscgenomics/lib instead of python/ucscgenomics/rafile
- python/ucscgenomics/lib/rafile/unittest/tests/MisplacedKeys.ra
- lines changed 8, context: html, text, full: html, text
updated directory structure to fit library design goal. modify PYTHONPATH to now point at python/ucscgenomics/lib instead of python/ucscgenomics/rafile
- python/ucscgenomics/lib/rafile/unittest/tests/NonNewlineFile.ra
- lines changed 5, context: html, text, full: html, text
updated directory structure to fit library design goal. modify PYTHONPATH to now point at python/ucscgenomics/lib instead of python/ucscgenomics/rafile
- python/ucscgenomics/lib/softfile/SoftFile.py
- lines changed 299, context: html, text, full: html, text
updated directory structure to fit library design goal. modify PYTHONPATH to now point at python/ucscgenomics/lib instead of python/ucscgenomics/rafile
- python/ucscgenomics/lib/softfile/__init__.py
- lines changed 0, context: html, text, full: html, text
forgot to include a few files
- python/ucscgenomics/lib/softfile/unittest/testSoft
- lines changed 10, context: html, text, full: html, text
forgot to include a few files
- python/ucscgenomics/mkGeoPkg/README
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forgot to include a few files
- python/ucscgenomics/mkGeoPkg/mkGeoPkg
- lines changed 231, context: html, text, full: html, text
new version of mkGeoPkg
- python/ucscgenomics/rafile/OrderedDict.py
- lines changed 57, context: html, text, full: html, text
updated directory structure to fit library design goal. modify PYTHONPATH to now point at python/ucscgenomics/lib instead of python/ucscgenomics/rafile
- python/ucscgenomics/rafile/RaFile.py
- lines changed 183, context: html, text, full: html, text
updated directory structure to fit library design goal. modify PYTHONPATH to now point at python/ucscgenomics/lib instead of python/ucscgenomics/rafile
- python/ucscgenomics/rafile/__init__.py
- lines changed 0, context: html, text, full: html, text
updated directory structure to fit library design goal. modify PYTHONPATH to now point at python/ucscgenomics/lib instead of python/ucscgenomics/rafile
- python/ucscgenomics/rafile/cv/CvFile.py
- lines changed 568, context: html, text, full: html, text
updated directory structure to fit library design goal. modify PYTHONPATH to now point at python/ucscgenomics/lib instead of python/ucscgenomics/rafile
- python/ucscgenomics/rafile/cv/unittest/input/Antibody/BlankKey.ra
- lines changed 25, context: html, text, full: html, text
updated directory structure to fit library design goal. modify PYTHONPATH to now point at python/ucscgenomics/lib instead of python/ucscgenomics/rafile
- python/ucscgenomics/rafile/cv/unittest/input/Antibody/ExtraKey.ra
- lines changed 26, context: html, text, full: html, text
updated directory structure to fit library design goal. modify PYTHONPATH to now point at python/ucscgenomics/lib instead of python/ucscgenomics/rafile
- python/ucscgenomics/rafile/cv/unittest/input/Antibody/MissingKey.ra
- lines changed 24, context: html, text, full: html, text
updated directory structure to fit library design goal. modify PYTHONPATH to now point at python/ucscgenomics/lib instead of python/ucscgenomics/rafile
- python/ucscgenomics/rafile/cv/unittest/input/Antibody/NonmatchKey.ra
- lines changed 25, context: html, text, full: html, text
updated directory structure to fit library design goal. modify PYTHONPATH to now point at python/ucscgenomics/lib instead of python/ucscgenomics/rafile
- python/ucscgenomics/rafile/cv/unittest/input/Antibody/ValidStanza.ra
- lines changed 36, context: html, text, full: html, text
updated directory structure to fit library design goal. modify PYTHONPATH to now point at python/ucscgenomics/lib instead of python/ucscgenomics/rafile
- python/ucscgenomics/rafile/cv/unittest/input/CellLine/BlankKey.ra
- lines changed 34, context: html, text, full: html, text
updated directory structure to fit library design goal. modify PYTHONPATH to now point at python/ucscgenomics/lib instead of python/ucscgenomics/rafile
- python/ucscgenomics/rafile/cv/unittest/input/CellLine/ExtraKey.ra
- lines changed 35, context: html, text, full: html, text
updated directory structure to fit library design goal. modify PYTHONPATH to now point at python/ucscgenomics/lib instead of python/ucscgenomics/rafile
- python/ucscgenomics/rafile/cv/unittest/input/CellLine/MissingKey.ra
- lines changed 33, context: html, text, full: html, text
updated directory structure to fit library design goal. modify PYTHONPATH to now point at python/ucscgenomics/lib instead of python/ucscgenomics/rafile
- python/ucscgenomics/rafile/cv/unittest/input/CellLine/NonmatchKey.ra
- lines changed 34, context: html, text, full: html, text
updated directory structure to fit library design goal. modify PYTHONPATH to now point at python/ucscgenomics/lib instead of python/ucscgenomics/rafile
- python/ucscgenomics/rafile/cv/unittest/input/CellLine/ValidStanza.ra
- lines changed 33, context: html, text, full: html, text
updated directory structure to fit library design goal. modify PYTHONPATH to now point at python/ucscgenomics/lib instead of python/ucscgenomics/rafile
- python/ucscgenomics/rafile/cv/unittest/input/Mouse/BlankKey.ra
- lines changed 37, context: html, text, full: html, text
updated directory structure to fit library design goal. modify PYTHONPATH to now point at python/ucscgenomics/lib instead of python/ucscgenomics/rafile
- python/ucscgenomics/rafile/cv/unittest/input/Mouse/ExtraKey.ra
- lines changed 38, context: html, text, full: html, text
updated directory structure to fit library design goal. modify PYTHONPATH to now point at python/ucscgenomics/lib instead of python/ucscgenomics/rafile
- python/ucscgenomics/rafile/cv/unittest/input/Mouse/MissingKey.ra
- lines changed 36, context: html, text, full: html, text
updated directory structure to fit library design goal. modify PYTHONPATH to now point at python/ucscgenomics/lib instead of python/ucscgenomics/rafile
- python/ucscgenomics/rafile/cv/unittest/input/Mouse/NonmatchKey.ra
- lines changed 37, context: html, text, full: html, text
updated directory structure to fit library design goal. modify PYTHONPATH to now point at python/ucscgenomics/lib instead of python/ucscgenomics/rafile
- python/ucscgenomics/rafile/cv/unittest/input/Mouse/ValidStanza.ra
- lines changed 37, context: html, text, full: html, text
updated directory structure to fit library design goal. modify PYTHONPATH to now point at python/ucscgenomics/lib instead of python/ucscgenomics/rafile
- python/ucscgenomics/rafile/cv/unittest/testCvFile
- lines changed 95, context: html, text, full: html, text
updated directory structure to fit library design goal. modify PYTHONPATH to now point at python/ucscgenomics/lib instead of python/ucscgenomics/rafile
- python/ucscgenomics/rafile/cv/validate
- lines changed 30, context: html, text, full: html, text
updated directory structure to fit library design goal. modify PYTHONPATH to now point at python/ucscgenomics/lib instead of python/ucscgenomics/rafile
- python/ucscgenomics/rafile/unittest/testRaFile.py
- lines changed 205, context: html, text, full: html, text
updated directory structure to fit library design goal. modify PYTHONPATH to now point at python/ucscgenomics/lib instead of python/ucscgenomics/rafile
- python/ucscgenomics/rafile/unittest/testoutput/BasicDiff.out
- lines changed 27, context: html, text, full: html, text
updated directory structure to fit library design goal. modify PYTHONPATH to now point at python/ucscgenomics/lib instead of python/ucscgenomics/rafile
- python/ucscgenomics/rafile/unittest/testoutput/CommentsDiff.out
- lines changed 31, context: html, text, full: html, text
updated directory structure to fit library design goal. modify PYTHONPATH to now point at python/ucscgenomics/lib instead of python/ucscgenomics/rafile
- python/ucscgenomics/rafile/unittest/testoutput/DeleteItem.out
- lines changed 39, context: html, text, full: html, text
updated directory structure to fit library design goal. modify PYTHONPATH to now point at python/ucscgenomics/lib instead of python/ucscgenomics/rafile
- python/ucscgenomics/rafile/unittest/testoutput/ExtraneousWhitespace.out
- lines changed 70, context: html, text, full: html, text
updated directory structure to fit library design goal. modify PYTHONPATH to now point at python/ucscgenomics/lib instead of python/ucscgenomics/rafile
- python/ucscgenomics/rafile/unittest/testoutput/GetItem.out
- lines changed 13, context: html, text, full: html, text
updated directory structure to fit library design goal. modify PYTHONPATH to now point at python/ucscgenomics/lib instead of python/ucscgenomics/rafile
- python/ucscgenomics/rafile/unittest/testoutput/InlineCommentsDiff.out
- lines changed 27, context: html, text, full: html, text
updated directory structure to fit library design goal. modify PYTHONPATH to now point at python/ucscgenomics/lib instead of python/ucscgenomics/rafile
- python/ucscgenomics/rafile/unittest/testoutput/IterEntryItems.out
- lines changed 27, context: html, text, full: html, text
updated directory structure to fit library design goal. modify PYTHONPATH to now point at python/ucscgenomics/lib instead of python/ucscgenomics/rafile
- python/ucscgenomics/rafile/unittest/testoutput/IterEntryKeys.out
- lines changed 27, context: html, text, full: html, text
updated directory structure to fit library design goal. modify PYTHONPATH to now point at python/ucscgenomics/lib instead of python/ucscgenomics/rafile
- python/ucscgenomics/rafile/unittest/testoutput/IterEntryValues.out
- lines changed 27, context: html, text, full: html, text
updated directory structure to fit library design goal. modify PYTHONPATH to now point at python/ucscgenomics/lib instead of python/ucscgenomics/rafile
- python/ucscgenomics/rafile/unittest/testoutput/IterItems.out
- lines changed 19, context: html, text, full: html, text
updated directory structure to fit library design goal. modify PYTHONPATH to now point at python/ucscgenomics/lib instead of python/ucscgenomics/rafile
- python/ucscgenomics/rafile/unittest/testoutput/IterKeys.out
- lines changed 11, context: html, text, full: html, text
updated directory structure to fit library design goal. modify PYTHONPATH to now point at python/ucscgenomics/lib instead of python/ucscgenomics/rafile
- python/ucscgenomics/rafile/unittest/testoutput/IterValues.out
- lines changed 41, context: html, text, full: html, text
updated directory structure to fit library design goal. modify PYTHONPATH to now point at python/ucscgenomics/lib instead of python/ucscgenomics/rafile
- python/ucscgenomics/rafile/unittest/tests/.IterKeysExpected.ra.swp
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updated directory structure to fit library design goal. modify PYTHONPATH to now point at python/ucscgenomics/lib instead of python/ucscgenomics/rafile
- python/ucscgenomics/rafile/unittest/tests/BasicDiff.ra
- lines changed 12, context: html, text, full: html, text
updated directory structure to fit library design goal. modify PYTHONPATH to now point at python/ucscgenomics/lib instead of python/ucscgenomics/rafile
- python/ucscgenomics/rafile/unittest/tests/CommentsDiff.ra
- lines changed 14, context: html, text, full: html, text
updated directory structure to fit library design goal. modify PYTHONPATH to now point at python/ucscgenomics/lib instead of python/ucscgenomics/rafile
- python/ucscgenomics/rafile/unittest/tests/DeleteItem.ra
- lines changed 18, context: html, text, full: html, text
updated directory structure to fit library design goal. modify PYTHONPATH to now point at python/ucscgenomics/lib instead of python/ucscgenomics/rafile
- python/ucscgenomics/rafile/unittest/tests/DuplicateKeys.ra
- lines changed 8, context: html, text, full: html, text
updated directory structure to fit library design goal. modify PYTHONPATH to now point at python/ucscgenomics/lib instead of python/ucscgenomics/rafile
- python/ucscgenomics/rafile/unittest/tests/FunctionalityCheck.ra
- lines changed 23, context: html, text, full: html, text
updated directory structure to fit library design goal. modify PYTHONPATH to now point at python/ucscgenomics/lib instead of python/ucscgenomics/rafile
- python/ucscgenomics/rafile/unittest/tests/GetItem.ra
- lines changed 5, context: html, text, full: html, text
updated directory structure to fit library design goal. modify PYTHONPATH to now point at python/ucscgenomics/lib instead of python/ucscgenomics/rafile
- python/ucscgenomics/rafile/unittest/tests/InlineCommentsDiff.ra
- lines changed 12, context: html, text, full: html, text
updated directory structure to fit library design goal. modify PYTHONPATH to now point at python/ucscgenomics/lib instead of python/ucscgenomics/rafile
- python/ucscgenomics/rafile/unittest/tests/IterEntryItems.ra
- lines changed 12, context: html, text, full: html, text
updated directory structure to fit library design goal. modify PYTHONPATH to now point at python/ucscgenomics/lib instead of python/ucscgenomics/rafile
- python/ucscgenomics/rafile/unittest/tests/IterEntryKeys.ra
- lines changed 12, context: html, text, full: html, text
updated directory structure to fit library design goal. modify PYTHONPATH to now point at python/ucscgenomics/lib instead of python/ucscgenomics/rafile
- python/ucscgenomics/rafile/unittest/tests/IterEntryValues.ra
- lines changed 12, context: html, text, full: html, text
updated directory structure to fit library design goal. modify PYTHONPATH to now point at python/ucscgenomics/lib instead of python/ucscgenomics/rafile
- python/ucscgenomics/rafile/unittest/tests/IterItems.ra
- lines changed 8, context: html, text, full: html, text
updated directory structure to fit library design goal. modify PYTHONPATH to now point at python/ucscgenomics/lib instead of python/ucscgenomics/rafile
- python/ucscgenomics/rafile/unittest/tests/IterKeys.ra
- lines changed 4, context: html, text, full: html, text
updated directory structure to fit library design goal. modify PYTHONPATH to now point at python/ucscgenomics/lib instead of python/ucscgenomics/rafile
- python/ucscgenomics/rafile/unittest/tests/IterValues.ra
- lines changed 19, context: html, text, full: html, text
updated directory structure to fit library design goal. modify PYTHONPATH to now point at python/ucscgenomics/lib instead of python/ucscgenomics/rafile
- python/ucscgenomics/rafile/unittest/tests/MisplacedKeys.ra
- lines changed 8, context: html, text, full: html, text
updated directory structure to fit library design goal. modify PYTHONPATH to now point at python/ucscgenomics/lib instead of python/ucscgenomics/rafile
- python/ucscgenomics/rafile/unittest/tests/NonNewlineFile.ra
- lines changed 5, context: html, text, full: html, text
updated directory structure to fit library design goal. modify PYTHONPATH to now point at python/ucscgenomics/lib instead of python/ucscgenomics/rafile
- python/ucscgenomics/softfile/SoftFile.py
- lines changed 299, context: html, text, full: html, text
Working soft file. mkGeoPkg is 1 step above pseudocode
- lines changed 299, context: html, text, full: html, text
new version of mkGeoPkg
- python/ucscgenomics/softfile/mkGeoPkg
- lines changed 23, context: html, text, full: html, text
Working soft file. mkGeoPkg is 1 step above pseudocode
- python/ucscgenomics/softfile/testSoft
- lines changed 10, context: html, text, full: html, text
Working soft file. mkGeoPkg is 1 step above pseudocode
- src/hg/encode/DAFs/2.0/haibMethyl450.daf
- lines changed 40, context: html, text, full: html, text
New Daf for new data type
- src/hg/encode/DAFs/2.0/uwMm9DnaseSeq.daf
- lines changed 3, context: html, text, full: html, text
Updated View Raw Signal -> Signal as request by lab.
- src/hg/encode/antibodyWikiParser.py
- lines changed 2, context: html, text, full: html, text
Added a script for scraping the cell type wiki table, producing CV stanzas and downloading approved cell protocol documents
- src/hg/encode/cellTypeParser.py
- lines changed 195, context: html, text, full: html, text
Added a script for scraping the cell type wiki table, producing CV stanzas and downloading approved cell protocol documents
- src/hg/encode/encodeMkChangeNotes/encodeMkChangeNotes
- lines changed 2, context: html, text, full: html, text
Removed accidentental changes by Morgan restored commit 4ee524db8c5e8f8d510ad5b53fd057b827ceaa3d. Also forced gbdb_path into string since it can return type None and can't be printed as type None.
- lines changed 4, context: html, text, full: html, text
Fixed logic error in Krish's script that placed unchanged bai and removed bai files in new files list.
- src/hg/encode/encodeReport/encodeReport.pl
- lines changed 86, context: html, text, full: html, text
Some preliminary exp ID fishing. This version in use Apr 13 - late June
- lines changed 97, context: html, text, full: html, text
Use experiment-defining variables from MDB and experiment table
- lines changed 38, context: html, text, full: html, text
Go to extreme lengths to locate release date
- lines changed 4, context: html, text, full: html, text
Exclude objects in composites w/o expVars. Including them added spurious Caltech submissions from the ENCODE Reg track
- src/hg/encode/encodeValidate/config/fields.ra
- lines changed 6, context: html, text, full: html, text
Adding obtainedBy, not sure why validate does not work without it
- src/hg/hgFileSearch/hgFileSearch.c
- lines changed 6, context: html, text, full: html, text
Big checkin of jquery 1.5.1, jquery-ui 1.8 and ui-dropdownchecklist 1.3. Needs more testing and CSS work. DDCL is working on FF, Chrome and IE. Both Chrome and IE support required tiny changes to the DDCL wigit code. DDCL may still have problems with IE. Other jquery wigits have been tested at a cursory level and work fine. Ajax calls may need an extrat dataType: html param. Dialog (popup) needs CSS tuning.
- src/hg/hgGateway/hgGateway.c
- lines changed 4, context: html, text, full: html, text
Big checkin of jquery 1.5.1, jquery-ui 1.8 and ui-dropdownchecklist 1.3. Needs more testing and CSS work. DDCL is working on FF, Chrome and IE. Both Chrome and IE support required tiny changes to the DDCL wigit code. DDCL may still have problems with IE. Other jquery wigits have been tested at a cursory level and work fine. Ajax calls may need an extrat dataType: html param. Dialog (popup) needs CSS tuning.
- lines changed 2, context: html, text, full: html, text
Fixed redmine 2813 note 23. The gene autocomplete dialog overflowed the page and had bad css.
- src/hg/hgLiftOver/hgLiftOver.c
- lines changed 2, context: html, text, full: html, text
added <ul> tags around the <li>'s in the data formats section bc it a.) is required in html, and b.) was not showing correctly in FF on Linux because of this omission.
- src/hg/hgTables/intersect.c
- lines changed 1, context: html, text, full: html, text
MLQ #4463 (Problem with intersection in the table browser):an undefined Javascript variable was preventing drop-down menu changes from
triggering submission of hiddenForm. The primary table's inversion checkbox
is not drawn when the primary table is bigWig, so the onChange javascript
needs to omit that variable when primary table is bigWig.
- lines changed 4, context: html, text, full: html, text
MLQ #4463 (problem w/intersection): another bug: canIntersect() wasreturning false for bigWig, so clicking submit on the intersection
page had no effect. Added clauses for bigWig and bigBed.
- src/hg/hgTables/mainPage.c
- lines changed 8, context: html, text, full: html, text
Adding parallel-fetch loading of remote bigDataUrl tracks using pthreads
- src/hg/hgTrackUi/hgTrackUi.c
- lines changed 5, context: html, text, full: html, text
Big checkin of jquery 1.5.1, jquery-ui 1.8 and ui-dropdownchecklist 1.3. Needs more testing and CSS work. DDCL is working on FF, Chrome and IE. Both Chrome and IE support required tiny changes to the DDCL wigit code. DDCL may still have problems with IE. Other jquery wigits have been tested at a cursory level and work fine. Ajax calls may need an extrat dataType: html param. Dialog (popup) needs CSS tuning.
- lines changed 4, context: html, text, full: html, text
Add links (just dummy for now) to preview browser in trackUI
- lines changed 3, context: html, text, full: html, text
Activate preview browser links on track UI
- lines changed 5, context: html, text, full: html, text
Changes after review by Katrina -- remove ENCODE top link on trackUi, instead link to image, etc.
- lines changed 1, context: html, text, full: html, text
Cosmetics on ENCODE track UI
- lines changed 1, context: html, text, full: html, text
Got tired of waiting for Kate to fix this path. Don't want people blaming this on the jquery upgrade
- src/hg/hgTracks/bamTrack.c
- lines changed 48, context: html, text, full: html, text
Adding parallel-fetch loading of remote bigDataUrl tracks using pthreads
- src/hg/hgTracks/bedTrack.c
- lines changed 23, context: html, text, full: html, text
Adding parallel-fetch loading of remote bigDataUrl tracks using pthreads
- src/hg/hgTracks/bigBedTrack.c
- lines changed 49, context: html, text, full: html, text
Adding parallel-fetch loading of remote bigDataUrl tracks using pthreads
- src/hg/hgTracks/bigWigTrack.c
- lines changed 27, context: html, text, full: html, text
Adding parallel-fetch loading of remote bigDataUrl tracks using pthreads
- src/hg/hgTracks/chainTrack.c
- src/hg/hgTracks/container.c
- lines changed 1, context: html, text, full: html, text
Adding parallel-fetch loading of remote bigDataUrl tracks using pthreads
- src/hg/hgTracks/encode.c
- lines changed 2, context: html, text, full: html, text
move some defines into one central location in hgTracks.h
- src/hg/hgTracks/hgTracks.c
- lines changed 15, context: html, text, full: html, text
Big checkin of jquery 1.5.1, jquery-ui 1.8 and ui-dropdownchecklist 1.3. Needs more testing and CSS work. DDCL is working on FF, Chrome and IE. Both Chrome and IE support required tiny changes to the DDCL wigit code. DDCL may still have problems with IE. Other jquery wigits have been tested at a cursory level and work fine. Ajax calls may need an extrat dataType: html param. Dialog (popup) needs CSS tuning.
- lines changed 3, context: html, text, full: html, text
Fixed redmine 2813 note 23. The gene autocomplete dialog overflowed the page and had bad css.
- lines changed 224, context: html, text, full: html, text
Adding parallel-fetch loading of remote bigDataUrl tracks using pthreads
- src/hg/hgTracks/hgTracks.h
- lines changed 4, context: html, text, full: html, text
move some defines into one central location in hgTracks.h
- lines changed 3, context: html, text, full: html, text
Adding parallel-fetch loading of remote bigDataUrl tracks using pthreads
- src/hg/hgTracks/searchTracks.c
- lines changed 6, context: html, text, full: html, text
Big checkin of jquery 1.5.1, jquery-ui 1.8 and ui-dropdownchecklist 1.3. Needs more testing and CSS work. DDCL is working on FF, Chrome and IE. Both Chrome and IE support required tiny changes to the DDCL wigit code. DDCL may still have problems with IE. Other jquery wigits have been tested at a cursory level and work fine. Ajax calls may need an extrat dataType: html param. Dialog (popup) needs CSS tuning.
- src/hg/hgTracks/simpleTracks.c
- lines changed 1, context: html, text, full: html, text
move some defines into one central location in hgTracks.h
- lines changed 2, context: html, text, full: html, text
fix filtering for Gencode tracks (#2608)
- lines changed 12, context: html, text, full: html, text
While working on VCF, caught a couple little bugs in pgSnpTextRight:
1. When restoring the clipping rectangle after snapping a label to the
left, pgSnpTextRight thought it was using the track y offset -- but
the DrawAt routine only gets the item y, not track y. So when an item
on row N had a label that snapped left, the restored clipping
rectangle clips out any subsequent items on rows 0..N-1. The top
row(s) looks suspiciously empty, as if the packer hadn't fully
utilized the row, but it's only that those items are made invisible.
The fix was to get the real y clipping coords before clipping for
left text, so they could be restored correctly.
2. The text width was subtracted twice from the item pixel start before
the comparison with insideX (by the caller, and inside pgSnpTextRight).
Thus snapLeft was triggered too easily, causing overwriting of left
labels when items in the same row were close to each other and to the
left edge. Fix: the caller doesn't subtract (width + 2); pgSnpTextRight
uses textX, not x1, when drawing text.
- lines changed 3, context: html, text, full: html, text
Adding parallel-fetch loading of remote bigDataUrl tracks using pthreads
- src/hg/hgTracks/snakeTrack.c
- src/hg/hgTracks/vcfTrack.c
- lines changed 25, context: html, text, full: html, text
Feature #986 (VCF): When converting VCF to pgSnp for display, abbreviate long alleles.
- lines changed 33, context: html, text, full: html, text
Adding parallel-fetch loading of remote bigDataUrl tracks using pthreads
- src/hg/hgTracks/wigTrack.c
- lines changed 3, context: html, text, full: html, text
move some defines into one central location in hgTracks.h
- src/hg/hgc/bamClick.c
- lines changed 1, context: html, text, full: html, text
Use new tag bamSkipPrintQualScore to skip printing quality score in bam item details page
- src/hg/hgc/gencodeClick.c
- lines changed 41, context: html, text, full: html, text
include transcript and sequence positions and browser links in details page
- src/hg/hgc/vcfClick.c
- lines changed 3, context: html, text, full: html, text
Feature #986 (VCF): keys can have <>'s, so html encode them for display.
- src/hg/htdocs/ENCODE/contacts.html
- src/hg/htdocs/ENCODE/dataPlansMouse.html
- lines changed 1, context: html, text, full: html, text
Fix to use correct blue bar (not the special one for the Data Policy page)
- src/hg/htdocs/ENCODE/dataStandards.html
- lines changed 14, context: html, text, full: html, text
Add RNA-seq doc to standards page
- src/hg/htdocs/ENCODE/dataSummary.html
- lines changed 1, context: html, text, full: html, text
Fix to use correct blue bar (not the special one for the Data Policy page)
- src/hg/htdocs/ENCODE/dataSummaryMouse.html
- lines changed 1, context: html, text, full: html, text
Fix to use correct blue bar (not the special one for the Data Policy page)
- src/hg/htdocs/ENCODE/downloads.html
- lines changed 2, context: html, text, full: html, text
Fix to use correct blue bar (not the special one for the Data Policy page)
- src/hg/htdocs/ENCODE/downloadsMouse.html
- lines changed 8, context: html, text, full: html, text
Fix to use correct blue bar (not the special one for the Data Policy page)
- lines changed 7, context: html, text, full: html, text
added UW DNase, redmine# 191
- src/hg/htdocs/ENCODE/index.html
- lines changed 1, context: html, text, full: html, text
Changes after review by Katrina -- remove ENCODE top link on trackUi, instead link to image, etc.
- src/hg/htdocs/ENCODE/search.html
- lines changed 1, context: html, text, full: html, text
Fix to use correct blue bar (not the special one for the Data Policy page)
- src/hg/htdocs/goldenPath/help/vcf.html
- lines changed 180, context: html, text, full: html, text
Feature #986 (VCF+tabix support): basic custom-track how-to page.Lots of broken links -- still need to generate example files and to
write a configuration help page (hgVcfTrackHelp.html).
- src/hg/htdocs/images/Myotis_lucifugus.jpg
- lines changed 0, context: html, text, full: html, text
Finished description.html for myoLuc2
- src/hg/htdocs/inc/encode.topbar.html
- lines changed 4, context: html, text, full: html, text
Add Preview browser link to top blue bar for ENCODE static pages
- src/hg/htdocs/style/jquery-ui.css
- lines changed 384, context: html, text, full: html, text
Big checkin of jquery 1.5.1, jquery-ui 1.8 and ui-dropdownchecklist 1.3. Needs more testing and CSS work. DDCL is working on FF, Chrome and IE. Both Chrome and IE support required tiny changes to the DDCL wigit code. DDCL may still have problems with IE. Other jquery wigits have been tested at a cursory level and work fine. Ajax calls may need an extrat dataType: html param. Dialog (popup) needs CSS tuning.
- lines changed 5, context: html, text, full: html, text
Fixed redmine 2813 note 23. The gene autocomplete dialog overflowed the page and had bad css.
- lines changed 2, context: html, text, full: html, text
Minor adjustments to autocomplete list and DDCL selectory box
- src/hg/htdocs/style/ui.dropdownchecklist.css
- lines changed 59, context: html, text, full: html, text
Big checkin of jquery 1.5.1, jquery-ui 1.8 and ui-dropdownchecklist 1.3. Needs more testing and CSS work. DDCL is working on FF, Chrome and IE. Both Chrome and IE support required tiny changes to the DDCL wigit code. DDCL may still have problems with IE. Other jquery wigits have been tested at a cursory level and work fine. Ajax calls may need an extrat dataType: html param. Dialog (popup) needs CSS tuning.
- lines changed 1, context: html, text, full: html, text
Minor adjustments to autocomplete list and DDCL selectory box
- lines changed 0, context: html, text, full: html, text
Undos'ed this file which came from the DDCL people with CRLFs
- src/hg/inc/hCommon.h
- lines changed 3, context: html, text, full: html, text
Adding parallel-fetch loading of remote bigDataUrl tracks using pthreads
- src/hg/inc/hvGfx.h
- lines changed 13, context: html, text, full: html, text
While working on VCF, caught a couple little bugs in pgSnpTextRight:
1. When restoring the clipping rectangle after snapping a label to the
left, pgSnpTextRight thought it was using the track y offset -- but
the DrawAt routine only gets the item y, not track y. So when an item
on row N had a label that snapped left, the restored clipping
rectangle clips out any subsequent items on rows 0..N-1. The top
row(s) looks suspiciously empty, as if the packer hadn't fully
utilized the row, but it's only that those items are made invisible.
The fix was to get the real y clipping coords before clipping for
left text, so they could be restored correctly.
2. The text width was subtracted twice from the item pixel start before
the comparison with insideX (by the caller, and inside pgSnpTextRight).
Thus snapLeft was triggered too easily, causing overwriting of left
labels when items in the same row were close to each other and to the
left edge. Fix: the caller doesn't subtract (width + 2); pgSnpTextRight
uses textX, not x1, when drawing text.
- src/hg/inc/jsHelper.h
- lines changed 1, context: html, text, full: html, text
This define definitely needs to be on, and checked in to this branch, as I just spent 1/2 an hour trying to figure out why the branch wasn't building properly.
- src/hg/js/hgGateway.js
- lines changed 12, context: html, text, full: html, text
Fixed redmine 2813 note 23. The gene autocomplete dialog overflowed the page and had bad css.
- src/hg/js/hgTracks.js
- lines changed 26, context: html, text, full: html, text
Big checkin of jquery 1.5.1, jquery-ui 1.8 and ui-dropdownchecklist 1.3. Needs more testing and CSS work. DDCL is working on FF, Chrome and IE. Both Chrome and IE support required tiny changes to the DDCL wigit code. DDCL may still have problems with IE. Other jquery wigits have been tested at a cursory level and work fine. Ajax calls may need an extrat dataType: html param. Dialog (popup) needs CSS tuning.
- lines changed 12, context: html, text, full: html, text
Fixed redmine 2813 note 23. The gene autocomplete dialog overflowed the page and had bad css.
- src/hg/js/hui.js
- lines changed 8, context: html, text, full: html, text
Big checkin of jquery 1.5.1, jquery-ui 1.8 and ui-dropdownchecklist 1.3. Needs more testing and CSS work. DDCL is working on FF, Chrome and IE. Both Chrome and IE support required tiny changes to the DDCL wigit code. DDCL may still have problems with IE. Other jquery wigits have been tested at a cursory level and work fine. Ajax calls may need an extrat dataType: html param. Dialog (popup) needs CSS tuning.
- lines changed 21, context: html, text, full: html, text
IE is so damn slow. I had to limit the attempt by IE to gray invalid options in filterComposite boxes.
- src/hg/js/jquery-ui.js
- lines changed 403, context: html, text, full: html, text
Big checkin of jquery 1.5.1, jquery-ui 1.8 and ui-dropdownchecklist 1.3. Needs more testing and CSS work. DDCL is working on FF, Chrome and IE. Both Chrome and IE support required tiny changes to the DDCL wigit code. DDCL may still have problems with IE. Other jquery wigits have been tested at a cursory level and work fine. Ajax calls may need an extrat dataType: html param. Dialog (popup) needs CSS tuning.
- src/hg/js/jquery.js
- lines changed 16, context: html, text, full: html, text
Big checkin of jquery 1.5.1, jquery-ui 1.8 and ui-dropdownchecklist 1.3. Needs more testing and CSS work. DDCL is working on FF, Chrome and IE. Both Chrome and IE support required tiny changes to the DDCL wigit code. DDCL may still have problems with IE. Other jquery wigits have been tested at a cursory level and work fine. Ajax calls may need an extrat dataType: html param. Dialog (popup) needs CSS tuning.
- src/hg/js/ui.dropdownchecklist.js
- lines changed 790, context: html, text, full: html, text
Big checkin of jquery 1.5.1, jquery-ui 1.8 and ui-dropdownchecklist 1.3. Needs more testing and CSS work. DDCL is working on FF, Chrome and IE. Both Chrome and IE support required tiny changes to the DDCL wigit code. DDCL may still have problems with IE. Other jquery wigits have been tested at a cursory level and work fine. Ajax calls may need an extrat dataType: html param. Dialog (popup) needs CSS tuning.
- lines changed 4, context: html, text, full: html, text
Disabling the DDCL window.resize event code seems to make IE support sound.
- lines changed 0, context: html, text, full: html, text
Undos'ed this file which came from the DDCL people with CRLFs
- src/hg/js/utils.js
- lines changed 333, context: html, text, full: html, text
Big checkin of jquery 1.5.1, jquery-ui 1.8 and ui-dropdownchecklist 1.3. Needs more testing and CSS work. DDCL is working on FF, Chrome and IE. Both Chrome and IE support required tiny changes to the DDCL wigit code. DDCL may still have problems with IE. Other jquery wigits have been tested at a cursory level and work fine. Ajax calls may need an extrat dataType: html param. Dialog (popup) needs CSS tuning.
- lines changed 14, context: html, text, full: html, text
DDCL improvement on 'first is all' logic
- lines changed 2, context: html, text, full: html, text
Disabling the DDCL window.resize event code seems to make IE support sound.
- lines changed 6, context: html, text, full: html, text
Fix to redmine 2813 note 20. In IE8, the first 'advanced' track search often failed because 'any' was replaces with every option, thus producing a gigantic submit URL.
- lines changed 1, context: html, text, full: html, text
Must exclude noneIsAll too.
- src/hg/lib/fileUi.c
- lines changed 10, context: html, text, full: html, text
Big checkin of jquery 1.5.1, jquery-ui 1.8 and ui-dropdownchecklist 1.3. Needs more testing and CSS work. DDCL is working on FF, Chrome and IE. Both Chrome and IE support required tiny changes to the DDCL wigit code. DDCL may still have problems with IE. Other jquery wigits have been tested at a cursory level and work fine. Ajax calls may need an extrat dataType: html param. Dialog (popup) needs CSS tuning.
- src/hg/lib/hCommon.c
- lines changed 7, context: html, text, full: html, text
Adding parallel-fetch loading of remote bigDataUrl tracks using pthreads
- src/hg/lib/hVarSubst.c
- lines changed 1, context: html, text, full: html, text
Adding BORDER=1 back in, because Brooke pointed out the change in the table. While this is 'deprecated' in favor of style, the simple style used here did not reproduce the as desired and we are still ruinning 4.01 transitional anyway.
- src/hg/lib/hui.c
- lines changed 8, context: html, text, full: html, text
Big checkin of jquery 1.5.1, jquery-ui 1.8 and ui-dropdownchecklist 1.3. Needs more testing and CSS work. DDCL is working on FF, Chrome and IE. Both Chrome and IE support required tiny changes to the DDCL wigit code. DDCL may still have problems with IE. Other jquery wigits have been tested at a cursory level and work fine. Ajax calls may need an extrat dataType: html param. Dialog (popup) needs CSS tuning.
- lines changed 5, context: html, text, full: html, text
Add links (just dummy for now) to preview browser in trackUI
- lines changed 4, context: html, text, full: html, text
Activate preview browser links on track UI
- lines changed 9, context: html, text, full: html, text
Changes after review by Katrina -- remove ENCODE top link on trackUi, instead link to image, etc.
- lines changed 3, context: html, text, full: html, text
Cosmetics on ENCODE track UI
- lines changed 107, context: html, text, full: html, text
Merge conflict resolution
- src/hg/lib/jsHelper.c
- lines changed 2, context: html, text, full: html, text
While debugging MLQ #4463, I noticed that jsMakeTrackingCheckBox wasimplemented in a way that would work if the checkbox was clicked a single
time (or odd number of times), but not if the checkbox was clicked an even
number of times. So if the user clicked the checkbox but changed their mind
and clicked again, and then changed the group or track, the checkbox would
change. Solution: make the variable toggle like the checkbox. Using +1 mod 2
so that our cart will see the expected 0 or 1 (not the logically inverted
true or false from ! negation).
- src/hg/makeDb/doc/bosTau6.txt
- lines changed 2, context: html, text, full: html, text
record result of 'featureBits -countGaps bosTau6 gap'
- src/hg/makeDb/doc/encodeDccHg19/broadHistoneBernstein.hg19.txt
- lines changed 67, context: html, text, full: html, text
A bit of note taking. HMM released, versioning Broad tracks broke Jim's reg tracks.
- src/hg/makeDb/doc/encodeDccHg19/wgEncodeHaibGenotype.release1.notes
- lines changed 4, context: html, text, full: html, text
Changeing the notes file to move the supplemental files from the files section to the other section
- src/hg/makeDb/doc/encodeDccHg19/wgEncodeSydhNsome.release1.notes
- lines changed 186, context: html, text, full: html, text
Sydh Nucleosome release1 notes added
- lines changed 192, context: html, text, full: html, text
error in generating the notes files, regenerated
- src/hg/makeDb/doc/encodeDccHg19/wgEncodeUncBsuProt.release1.notes
- lines changed 22, context: html, text, full: html, text
Updating the release notes for Release 1 of UncBsuProt
- src/hg/makeDb/doc/encodeDccMm9/wgEncodeSydhHistone.release1.notes
- lines changed 97, context: html, text, full: html, text
Added release 1 notes for track.
- src/hg/makeDb/doc/encodeDccMm9/wgEncodeSydhTfbs.release2.notes
- lines changed 568, context: html, text, full: html, text
First pass at the making notes file for release 2 of file.
- src/hg/makeDb/doc/encodeDccMm9/wgEncodeUwDnase.release1.notes
- lines changed 1, context: html, text, full: html, text
Fixed Total field to have 114 tables that should be passed to RR. The 165 tables that were there indicate some tables that are for attic files.
- src/hg/makeDb/doc/hg19.txt
- lines changed 6, context: html, text, full: html, text
redmine 4422 creaye rbest.chain file for hg19 vs panTro3
- src/hg/makeDb/doc/myoLuc2.txt
- lines changed 129, context: html, text, full: html, text
Finish new myoLuc2 assembly
- src/hg/makeDb/genbank/etc/genbank.conf
- lines changed 16, context: html, text, full: html, text
Added allMis0 (preliminary alligator )
- lines changed 1, context: html, text, full: html, text
no per chrom tables for allMis0
- src/hg/makeDb/genbank/src/lib/gbGenome.c
- src/hg/makeDb/schema/all.joiner
- lines changed 5, context: html, text, full: html, text
Finish new myoLuc2 assembly
- src/hg/makeDb/trackDb/README
- lines changed 2, context: html, text, full: html, text
Use new tag bamSkipPrintQualScore to skip printing quality score in bam item details page
- src/hg/makeDb/trackDb/cv/alpha/CD34+Mobilized_Stam_protocol.pdf
- lines changed 0, context: html, text, full: html, text
Added several new UW cell protocols
- src/hg/makeDb/trackDb/cv/alpha/HBVP_Stam_protocol.pdf
- lines changed 0, context: html, text, full: html, text
Added several new UW cell protocols
- src/hg/makeDb/trackDb/cv/alpha/HBVSMC_Stam_protocol.pdf
- lines changed 0, context: html, text, full: html, text
Added several new UW cell protocols
- src/hg/makeDb/trackDb/cv/alpha/HMVECdAd_Stam_protocol.pdf
- lines changed 0, context: html, text, full: html, text
Added several new UW cell protocols
- src/hg/makeDb/trackDb/cv/alpha/HPAEC_Stam_protocol.pdf
- lines changed 0, context: html, text, full: html, text
Added several new UW cell protocols
- src/hg/makeDb/trackDb/cv/alpha/NHBE_Stam_protocol.pdf
- lines changed 0, context: html, text, full: html, text
Added several new UW cell protocols
- src/hg/makeDb/trackDb/cv/alpha/cv.ra
- lines changed 130, context: html, text, full: html, text
Added several new UW cell types
- lines changed 1, context: html, text, full: html, text
replacing the 'decription' of the Fastq stanza with a 'description'
- lines changed 3, context: html, text, full: html, text
Fixed the spelling of the name of the Tullius lab
- lines changed 1, context: html, text, full: html, text
adding institution to USC
- lines changed 1, context: html, text, full: html, text
Renaming HMVEC_dAd to HMVEC-dAd, for consistency with the rest of the HMVEC cell lines.
- lines changed 4, context: html, text, full: html, text
Updated the Description for Yale-m to explictily state that Sherm Weissman did some of the experiments at Yale.
- lines changed 20, context: html, text, full: html, text
Housekeeping: accepted several provisional stanzas, removed one obsolete, commented-out stanza
- lines changed 6, context: html, text, full: html, text
making some label changes for Kate to match NHGRI
- lines changed 1, context: html, text, full: html, text
corrected gata3 sc269's tag
- lines changed 19, context: html, text, full: html, text
Added C2C12 cell line for Wold lab.
- lines changed 250, context: html, text, full: html, text
standardized protocol naming conventions. From now on, use protocol labPi:protocol.pdf ...
- src/hg/makeDb/trackDb/cv/beta/cv.ra
- lines changed 1283, context: html, text, full: html, text
Copying to beta post code review, now that everything looks stable
- src/hg/makeDb/trackDb/human/hg18/evoCpg.html
- lines changed 0, context: html, text, full: html, text
Fixed spacing in html, redmine #4430
- src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeHudsonalphaChipSeq.ra
- lines changed 48, context: html, text, full: html, text
Putting the expVars in matching order for hg18 and hg19
- lines changed 29, context: html, text, full: html, text
Trying to fix the HTB-11 goes to SK-N-SH issue and consolidate the Control versus Input issue to all control
- lines changed 48, context: html, text, full: html, text
Removed experiment 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.
- src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeSangerGencode.ra
- src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeYaleChIPseq.ra
- lines changed 3, context: html, text, full: html, text
This one replicate had the wrong metaData
- src/hg/makeDb/trackDb/human/hg18/metaDb/beta/wgEncodeSangerGencode.ra
- lines changed 12, context: html, text, full: html, text
fixing errors Cricket found in code review redmine#4442 and redmine#2390
- src/hg/makeDb/trackDb/human/hg18/metaDb/public/wgEncodeSangerGencode.ra
- lines changed 12, context: html, text, full: html, text
fixing errors Cricket found in code review redmine#4442 and redmine#2390
- src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaChipSeq.new.ra
- lines changed 8, context: html, text, full: html, text
Removed experiment 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.
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/makefile
- lines changed 2, context: html, text, full: html, text
restoring V4 metadata, labeling Gencode composites with V?, #2608
- lines changed 1, context: html, text, full: html, text
Adding a new composite subId 4444 and redmine ticket 4234
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCaltechRnaSeq.ra
- lines changed 243, context: html, text, full: html, text
repaired orig assembly where needed
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlShortRnaSeq.ra
- lines changed 30, context: html, text, full: html, text
Fixing the ExonGencV3c to ExonsGencV3c
- lines changed 2, context: html, text, full: html, text
Error in dataType, ShortRnaSeq to RnaSeq
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGencode.ra
- lines changed 26, context: html, text, full: html, text
dropped dataVersion per Venkat #2608
- lines changed 26, context: html, text, full: html, text
added objType per Cricket (#2608)
- lines changed 52, context: html, text, full: html, text
adding expIds and changing the expVars to reflect
- lines changed 27, context: html, text, full: html, text
restoring V4 metadata, labeling Gencode composites with V?, #2608
- lines changed 371, context: html, text, full: html, text
moving all Gencode metadata to files with the V? suffix
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGencodeV4.ra
- lines changed 98, context: html, text, full: html, text
move gencodeV4 metadata to properly named file, #2608
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGencodeV7.ra
- lines changed 371, context: html, text, full: html, text
is slowly getting this to work ;-)
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibGenotype.ra
- lines changed 30, context: html, text, full: html, text
Moving the Ballele and Gtype to be supplemental data, it is leaving the mdb
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethyl450.ra
- lines changed 248, context: html, text, full: html, text
Adding a new composite subId 4444 and redmine ticket 4234
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra
- lines changed 2, context: html, text, full: html, text
Putting the expVars in matching order for hg18 and hg19
- lines changed 3041, context: html, text, full: html, text
added in first few submissions to release 2
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhHistone.ra
- lines changed 317, context: html, text, full: html, text
renamed all ucd to usc expect subid=1831, that needs to be replaced
- lines changed 7, context: html, text, full: html, text
added expid for subid 1831
- lines changed 193, context: html, text, full: html, text
added in pbmc control and experiments
- lines changed 25, context: html, text, full: html, text
added expId and dcc's to sydh histone
- lines changed 350, context: html, text, full: html, text
changed names of k562b's to k562
- lines changed 7, context: html, text, full: html, text
corrected some controlId errors
- lines changed 109, context: html, text, full: html, text
changed controlId to matching dcc accession
- lines changed 253, context: html, text, full: html, text
reverted Usc > Ucd in filename, it was controlId not labId
- lines changed 301, context: html, text, full: html, text
forcome some k562b's to k562 last time finished the job
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra
- lines changed 10, context: html, text, full: html, text
removed bad dcc accessions
- lines changed 296, context: html, text, full: html, text
added origAssembly hg18 where needed
- lines changed 1229, context: html, text, full: html, text
added missing expIds and dcc accessions
- lines changed 33, context: html, text, full: html, text
added in last 6 submissions
- lines changed 1117, context: html, text, full: html, text
added in first submissions for release 2
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUncBsuProt.ra
- lines changed 5, context: html, text, full: html, text
Revised the restrictedUntil dates of two submissions that had been submitted earlier and revoked
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUw5C.ra
- lines changed 1, context: html, text, full: html, text
adding required dataType to the expVars
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDgf.ra
- lines changed 155, context: html, text, full: html, text
Removed meta-data for version 1 of files and stored Geo Sample number ind dccInternalNotes for the V2 of the file for reference.
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDnase.ra
- lines changed 1170, context: html, text, full: html, text
added in a whole bunch of uw entries
- lines changed 285, context: html, text, full: html, text
cleaned up ExpId's in uwDnase
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwHistone.ra
- lines changed 2712, context: html, text, full: html, text
added in a whole bunch of uw entries
- lines changed 249, context: html, text, full: html, text
added in missing expid's to uwhistone
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwTfbs.ra
- lines changed 1816, context: html, text, full: html, text
added in a whole bunch of uw entries
- lines changed 169, context: html, text, full: html, text
added in missing expids and dccaccesions to uw tfbs
- src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
- lines changed 3, context: html, text, full: html, text
Following up on the decision to NOT have separate releases of Version 1 of uncBsuProt (with two subtracks) and version 2 (with three additional subtracks), but instead to have one release with all five subtracks. Accordingly, we no longer need to stage separate .ra and .new.ra files. Updated the overall .ra file to reflect this
- lines changed 1, context: html, text, full: html, text
This went with the previous commit to add the composite Methyl450, I had forgotten to add to the trackDb.wgEncode.ra. I also cleaned up a few things in fileSortOrder and sortOrder.
- lines changed 1, context: html, text, full: html, text
take GencodeV5 off of alpha
- src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV4.new.ra
- lines changed 1, context: html, text, full: html, text
restoring V4 metadata, labeling Gencode composites with V?, #2608
- src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV7.html
- lines changed 9, context: html, text, full: html, text
put references in alphabetical order
- lines changed 41, context: html, text, full: html, text
added doc on track filters
- src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV7.ra
- lines changed 7, context: html, text, full: html, text
restoring V4 metadata, labeling Gencode composites with V?, #2608
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibGenotype.html
- lines changed 1, context: html, text, full: html, text
Moving the Ballele and Gtype to be supplemental data, it is leaving the mdb
- lines changed 1, context: html, text, full: html, text
Changing the links to go exactly to the supplemental materails directory
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethyl450.html
- lines changed 68, context: html, text, full: html, text
Adding track description
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethyl450.ra
- lines changed 136, context: html, text, full: html, text
Adding a new composite subId 4444 and redmine ticket 4234
- lines changed 6, context: html, text, full: html, text
This went with the previous commit to add the composite Methyl450, I had forgotten to add to the trackDb.wgEncode.ra. I also cleaned up a few things in fileSortOrder and sortOrder.
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.new.ra
- lines changed 6784, context: html, text, full: html, text
made .new.ra's for sydhtfbs and haib tfbs
- lines changed 896, context: html, text, full: html, text
added in first few submissions to release 2
- src/hg/makeDb/trackDb/human/hg19/wgEncodeMapability.new.html
- lines changed 5, context: html, text, full: html, text
Should have checked this in earlier.
- src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.new.ra
- lines changed 30, context: html, text, full: html, text
Changing defualts, setting the extrafields
- src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhHistone.new.ra
- lines changed 62, context: html, text, full: html, text
renamed all ucd to usc expect subid=1831, that needs to be replaced
- lines changed 1, context: html, text, full: html, text
changed long label to havre usc
- lines changed 28, context: html, text, full: html, text
removed references to k562
- lines changed 32, context: html, text, full: html, text
added in pbmc control and experiments
- lines changed 18, context: html, text, full: html, text
changed names of k562b's to k562
- lines changed 73, context: html, text, full: html, text
reverted Usc > Ucd in filename, it was controlId not labId
- lines changed 36, context: html, text, full: html, text
fixed long labels in sydh histone
- lines changed 2, context: html, text, full: html, text
forcome some k562b's to k562 last time finished the job
- src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhNsome.html
- lines changed 32, context: html, text, full: html, text
added a blurb about the methods, and added references
- src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhNsome.ra
- lines changed 1, context: html, text, full: html, text
added BYU to the long label
- lines changed 4, context: html, text, full: html, text
corrected nucleosome's long and short labels
- src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.html
- lines changed 6, context: html, text, full: html, text
removed some lines from html
- src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.new.ra
- lines changed 5169, context: html, text, full: html, text
made .new.ra's for sydhtfbs and haib tfbs
- lines changed 423, context: html, text, full: html, text
added in first submissions for release 2
- src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.ra
- lines changed 225, context: html, text, full: html, text
added in last 6 submissions
- lines changed 1, context: html, text, full: html, text
corrected a tag error in sydh tfbs
- lines changed 537, context: html, text, full: html, text
fixed long labels for sydhtfbs
- lines changed 608, context: html, text, full: html, text
changed short labels and made all K562b's k562
- lines changed 2, context: html, text, full: html, text
removed an extra space in the views stanzas
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProt.new.ra
- lines changed 81, context: html, text, full: html, text
Following on the last commit, getting rid of the .new.ra file to avoid confusion with the .ra file
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProt.ra
- lines changed 32, context: html, text, full: html, text
During Morgan Gidding's recent visit, it was decided that we'd abandon our old plan of getting the first two subtracks on this track released (saving three additional subtracks for Version 2), and we'd instead try to release all five subtracks as part of Version 1. Accordingly, there's no need anymore to maintain separate .ra and .new.ra files. Getting rid of .new.ra
- lines changed 3, context: html, text, full: html, text
Changing the default subtrack visibility so that the Tier 1 subtracks are all on by default
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.new.ra
- lines changed 4, context: html, text, full: html, text
prepared the UW tracks for the mass loading that i'm doing tomorrow
- lines changed 325, context: html, text, full: html, text
added in a whole bunch of uw entries
- lines changed 21, context: html, text, full: html, text
cleaned up ExpId's in uwDnase
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.new.ra
- lines changed 227, context: html, text, full: html, text
prepared the UW tracks for the mass loading that i'm doing tomorrow
- lines changed 612, context: html, text, full: html, text
added in a whole bunch of uw entries
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwTfbs.new.ra
- lines changed 1, context: html, text, full: html, text
prepared the UW tracks for the mass loading that i'm doing tomorrow
- lines changed 391, context: html, text, full: html, text
added in a whole bunch of uw entries
- src/hg/makeDb/trackDb/human/omimDescriptionText.html
- lines changed 4, context: html, text, full: html, text
added disclaimer about omim updating all the time
- src/hg/makeDb/trackDb/human/trackDb.ra
- lines changed 1, context: html, text, full: html, text
Use new tag bamSkipPrintQualScore to skip printing quality score in bam item details page
- src/hg/makeDb/trackDb/microbat/myoLuc1/description.html
- lines changed 4, context: html, text, full: html, text
Add photo credit for myoLuc1
- src/hg/makeDb/trackDb/microbat/myoLuc2/description.html
- lines changed 78, context: html, text, full: html, text
Finished description.html for myoLuc2
- lines changed 3, context: html, text, full: html, text
Minor touchup of myoLuc2 description.html
- src/hg/makeDb/trackDb/microbat/myoLuc2/gap.html
- src/hg/makeDb/trackDb/microbat/myoLuc2/gold.html
- src/hg/makeDb/trackDb/microbat/myoLuc2/trackDb.ra
- lines changed 32, context: html, text, full: html, text
Finished description.html for myoLuc2
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/makefile
- lines changed 2, context: html, text, full: html, text
Added first 23 submissions for track.
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodePsuTfbs.ra
- lines changed 2, context: html, text, full: html, text
Fixed spelling of antibody in expVars.
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhHistone.ra
- lines changed 77, context: html, text, full: html, text
Added missing control IgG-Yale DMSO control for Histone track that was on TFBS track (Redmine 97). Fixed last open concatenated bam bug wgEncodeSydhTfbsMelInputDmso20StdAln using submission 4327. (Redmine #3216)
- lines changed 19, context: html, text, full: html, text
Fixed lab's from Stanford-m to Yale-m as suggested by lab.
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhRnaSeq.ra
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhTfbs.ra
- lines changed 4, context: html, text, full: html, text
Added missing control IgG-Yale DMSO control for Histone track that was on TFBS track (Redmine 97). Fixed last open concatenated bam bug wgEncodeSydhTfbsMelInputDmso20StdAln using submission 4327. (Redmine #3216)
- lines changed 147, context: html, text, full: html, text
Forgot to add meta-data for submission 2540.
- lines changed 191, context: html, text, full: html, text
Updated lab from Stanford-m to Yale-m for 3 experiemnts (MEL DMSO CTCF, CH12 CTCF, MEL DMSO Input). Updated control from Std to IgG-rab for 3 experiements (MEL p300 Std, MEL SMC3 Std and MEL CTCF Std). Also updated the antibody for MEL CTCF Std to CTCF_(SC-15914). Redmine #2726, note 3.
- lines changed 51, context: html, text, full: html, text
Replaced subId 1859 with submission 4451.
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeUwDnase.ra
- lines changed 49, context: html, text, full: html, text
Fixed one item that's meta-data didn't get renamed from Raw to Sig: wgEncodeUwDnaseLiverC57bl6MAdult8wksRawRep2. Fixes Redmine #191, Note:#31.
- lines changed 1189, context: html, text, full: html, text
Added 11 new submission for this track.
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeUwRnaSeq.ra
- lines changed 2743, context: html, text, full: html, text
Added first 23 submissions for track.
- lines changed 59, context: html, text, full: html, text
Fixed metadata for submission 4443 and 4441.
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/makefile
- lines changed 1, context: html, text, full: html, text
staging UW DNase on hgwbeta, redmine# 191
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/wgEncodeUwDnase.ra
- lines changed 6752, context: html, text, full: html, text
staging UW DNase on hgwbeta, redmine# 191
- lines changed 49, context: html, text, full: html, text
Venkat fixed missing metaDb for UW DNase, redmine #191
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/public/makefile
- lines changed 1, context: html, text, full: html, text
Releasing UW Dnase mm9, redmine #191
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/public/wgEncodeUwDnase.ra
- lines changed 6752, context: html, text, full: html, text
Releasing UW Dnase mm9, redmine #191
- src/hg/makeDb/trackDb/mouse/mm9/trackDb.ra
- lines changed 1, context: html, text, full: html, text
Use new tag bamSkipPrintQualScore to skip printing quality score in bam item details page
- src/hg/makeDb/trackDb/mouse/mm9/trackDb.wgEncode.ra
- lines changed 2, context: html, text, full: html, text
staging UW DNase on hgwbeta, redmine# 191
- lines changed 2, context: html, text, full: html, text
Added first 23 submissions for track.
- lines changed 1, context: html, text, full: html, text
Releasing UW Dnase mm9, redmine #191
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhHistone.ra
- lines changed 8, context: html, text, full: html, text
Updated colors of CH12 and MEL for the TFBS and Histone track. This conforms to the new colors in the cv.ra.
- lines changed 38, context: html, text, full: html, text
Updated notes for long and short labels. Update default tracks on and short and long labels for DMSO treated experiments.
- lines changed 9, context: html, text, full: html, text
Added missing control IgG-Yale DMSO control for Histone track that was on TFBS track (Redmine 97). Fixed last open concatenated bam bug wgEncodeSydhTfbsMelInputDmso20StdAln using submission 4327. (Redmine #3216)
- lines changed 6, context: html, text, full: html, text
Updated the DMSO tag's to match CV so that new items can easily be added into the track.
- lines changed 2, context: html, text, full: html, text
Updated track default settings and added fileSortOrder.
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhTfbs.newR2.ra
- lines changed 84, context: html, text, full: html, text
Updated colors of CH12 and MEL for the TFBS and Histone track. This conforms to the new colors in the cv.ra.
- lines changed 164, context: html, text, full: html, text
Updated notes of long, short labels and abbreviations. Also, updated subGroups treatment to force None to sort last. First pass at long and short labels.
- lines changed 9, context: html, text, full: html, text
Updated the DMSO tag's to match CV so that new items can easily be added into the track.
- lines changed 17, context: html, text, full: html, text
Updated default tracks on and off and accompanying notes. Aso updated p300sc584 -> p300sc584.
- lines changed 22, context: html, text, full: html, text
Updated lab from Stanford-m to Yale-m for 3 experiemnts (MEL DMSO CTCF, CH12 CTCF, MEL DMSO Input). Updated control from Std to IgG-rab for 3 experiements (MEL p300 Std, MEL SMC3 Std and MEL CTCF Std). Also updated the antibody for MEL CTCF Std to CTCF_(SC-15914). Redmine #2726, note 3.
- lines changed 2, context: html, text, full: html, text
Updated track default settings and added fileSortOrder.
- lines changed 38, context: html, text, full: html, text
Replaced subId 1859 with submission 4451.
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwDnase.html
- lines changed 3, context: html, text, full: html, text
removed release notes section and made the p lower case, redmine# 191
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwDnase.new.ra
- lines changed 477, context: html, text, full: html, text
Added 11 new submission for this track.
- lines changed 5, context: html, text, full: html, text
Added changes to Second release that were updated in Release 1 of track in Redmine #191. Also added Score Shading to both releases Redmine #191, note #33.
- lines changed 1, context: html, text, full: html, text
Added scoreMin for use to be able to change gray scale %. Redmine #191, note 36. Forgot in pervious commit.
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwDnase.ra
- lines changed 1, context: html, text, full: html, text
Added changes to Second release that were updated in Release 1 of track in Redmine #191. Also added Score Shading to both releases Redmine #191, note #33.
- lines changed 1, context: html, text, full: html, text
Added scoreMin for use to be able to change gray scale %. Redmine #191, note 36. Forgot in pervious commit.
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwRnaSeq.ra
- lines changed 937, context: html, text, full: html, text
Added first 23 submissions for track.
- lines changed 144, context: html, text, full: html, text
Fixed metadata for submission 4443 and 4441.
- src/hg/makeDb/trackDb/sacCer/sacCer2/trackDb.ra
- lines changed 3, context: html, text, full: html, text
Removed obsolete longLabel about lifting ensGene from sacCer1. Redmine #4464.
- src/hg/makeDb/trackDb/tagTypes.tab
- lines changed 2, context: html, text, full: html, text
Use new tag bamSkipPrintQualScore to skip printing quality score in bam item details page
- src/hg/makefile
- lines changed 1, context: html, text, full: html, text
add hgHubConnect to CGI build
- src/hg/pslCDnaFilter/cDnaAligns.c
- lines changed 69, context: html, text, full: html, text
fixed bug with haplotype filtesrs were some global need best were not correctly dropped and where some local near best where incorrectly dropped. Make -uniqueMapped haplotype chroms
- src/hg/pslCDnaFilter/cDnaAligns.h
- lines changed 76, context: html, text, full: html, text
fixed bug with haplotype filtesrs were some global need best were not correctly dropped and where some local near best where incorrectly dropped. Make -uniqueMapped haplotype chroms
- src/hg/pslCDnaFilter/cDnaReader.c
- lines changed 26, context: html, text, full: html, text
fixed bug with haplotype filtesrs were some global need best were not correctly dropped and where some local near best where incorrectly dropped. Make -uniqueMapped haplotype chroms
- src/hg/pslCDnaFilter/cDnaReader.h
- lines changed 6, context: html, text, full: html, text
fixed bug with haplotype filtesrs were some global need best were not correctly dropped and where some local near best where incorrectly dropped. Make -uniqueMapped haplotype chroms
- src/hg/pslCDnaFilter/cDnaStats.c
- lines changed 2, context: html, text, full: html, text
added filter to drop non-uniquely mapped cDNAs
- src/hg/pslCDnaFilter/cDnaStats.h
- lines changed 1, context: html, text, full: html, text
added filter to drop non-uniquely mapped cDNAs
- lines changed 6, context: html, text, full: html, text
fixed bug with haplotype filtesrs were some global need best were not correctly dropped and where some local near best where incorrectly dropped. Make -uniqueMapped haplotype chroms
- src/hg/pslCDnaFilter/globalNearBestFilter.c
- lines changed 48, context: html, text, full: html, text
fixed bug with haplotype filtesrs were some global need best were not correctly dropped and where some local near best where incorrectly dropped. Make -uniqueMapped haplotype chroms
- src/hg/pslCDnaFilter/globalNearBestFilter.h
- lines changed 7, context: html, text, full: html, text
fixed bug with haplotype filtesrs were some global need best were not correctly dropped and where some local near best where incorrectly dropped. Make -uniqueMapped haplotype chroms
- src/hg/pslCDnaFilter/hapRegions.c
- lines changed 225, context: html, text, full: html, text
fixed bug with haplotype filtesrs were some global need best were not correctly dropped and where some local near best where incorrectly dropped. Make -uniqueMapped haplotype chroms
- src/hg/pslCDnaFilter/hapRegions.h
- lines changed 13, context: html, text, full: html, text
fixed bug with haplotype filtesrs were some global need best were not correctly dropped and where some local near best where incorrectly dropped. Make -uniqueMapped haplotype chroms
- src/hg/pslCDnaFilter/localNearBestFilter.c
- lines changed 100, context: html, text, full: html, text
fixed bug with haplotype filtesrs were some global need best were not correctly dropped and where some local near best where incorrectly dropped. Make -uniqueMapped haplotype chroms
- src/hg/pslCDnaFilter/localNearBestFilter.h
- lines changed 9, context: html, text, full: html, text
fixed bug with haplotype filtesrs were some global need best were not correctly dropped and where some local near best where incorrectly dropped. Make -uniqueMapped haplotype chroms
- src/hg/pslCDnaFilter/makefile
- lines changed 6, context: html, text, full: html, text
fixed bug with haplotype filtesrs were some global need best were not correctly dropped and where some local near best where incorrectly dropped. Make -uniqueMapped haplotype chroms
- src/hg/pslCDnaFilter/overlapFilter.c
- lines changed 9, context: html, text, full: html, text
fixed bug with haplotype filtesrs were some global need best were not correctly dropped and where some local near best where incorrectly dropped. Make -uniqueMapped haplotype chroms
- src/hg/pslCDnaFilter/overlapFilter.h
- lines changed 7, context: html, text, full: html, text
fixed bug with haplotype filtesrs were some global need best were not correctly dropped and where some local near best where incorrectly dropped. Make -uniqueMapped haplotype chroms
- src/hg/pslCDnaFilter/pslCDnaFilter.c
- lines changed 26, context: html, text, full: html, text
added filter to drop non-uniquely mapped cDNAs
- lines changed 264, context: html, text, full: html, text
fixed bug with haplotype filtesrs were some global need best were not correctly dropped and where some local near best where incorrectly dropped. Make -uniqueMapped haplotype chroms
- src/hg/pslCDnaFilter/tests/expected/hapGlobalTest/filt.out
- lines changed 3, context: html, text, full: html, text
fixed bug with haplotype filtesrs were some global need best were not correctly dropped and where some local near best where incorrectly dropped. Make -uniqueMapped haplotype chroms
- src/hg/pslCDnaFilter/tests/expected/hapGlobalTest/keep.psl
- lines changed 3, context: html, text, full: html, text
fixed bug with haplotype filtesrs were some global need best were not correctly dropped and where some local near best where incorrectly dropped. Make -uniqueMapped haplotype chroms
- src/hg/pslCDnaFilter/tests/expected/hapLocalTest/filt.out
- lines changed 2, context: html, text, full: html, text
fixed bug with haplotype filtesrs were some global need best were not correctly dropped and where some local near best where incorrectly dropped. Make -uniqueMapped haplotype chroms
- src/hg/pslCDnaFilter/tests/expected/hapLocalTest/keep.psl
- lines changed 7, context: html, text, full: html, text
fixed bug with haplotype filtesrs were some global need best were not correctly dropped and where some local near best where incorrectly dropped. Make -uniqueMapped haplotype chroms
- src/hg/pslCDnaFilter/tests/expected/uniqueMappedHapTest/filt.out
- lines changed 6, context: html, text, full: html, text
fixed bug with haplotype filtesrs were some global need best were not correctly dropped and where some local near best where incorrectly dropped. Make -uniqueMapped haplotype chroms
- src/hg/pslCDnaFilter/tests/expected/uniqueMappedHapTest/keep.psl
- lines changed 10, context: html, text, full: html, text
fixed bug with haplotype filtesrs were some global need best were not correctly dropped and where some local near best where incorrectly dropped. Make -uniqueMapped haplotype chroms
- src/hg/pslCDnaFilter/tests/expected/uniqueMappedTest/filt.out
- lines changed 7, context: html, text, full: html, text
added filter to drop non-uniquely mapped cDNAs
- src/hg/pslCDnaFilter/tests/expected/uniqueMappedTest/keep.psl
- lines changed 15, context: html, text, full: html, text
added filter to drop non-uniquely mapped cDNAs
- src/hg/pslCDnaFilter/tests/makefile
- lines changed 8, context: html, text, full: html, text
added filter to drop non-uniquely mapped cDNAs
- lines changed 3, context: html, text, full: html, text
fixed bug with haplotype filtesrs were some global need best were not correctly dropped and where some local near best where incorrectly dropped. Make -uniqueMapped haplotype chroms
- src/hg/pslCDnaFilter/usage.txt
- lines changed 3, context: html, text, full: html, text
added filter to drop non-uniquely mapped cDNAs
- lines changed 21, context: html, text, full: html, text
fixed bug with haplotype filtesrs were some global need best were not correctly dropped and where some local near best where incorrectly dropped. Make -uniqueMapped haplotype chroms
- src/inc/common.mk
- lines changed 4, context: html, text, full: html, text
Adding parallel-fetch loading of remote bigDataUrl tracks using pthreads
- src/lib/bigBed.c
- lines changed 1, context: html, text, full: html, text
Adding parallel-fetch loading of remote bigDataUrl tracks using pthreads
- src/lib/errCatch.c
- lines changed 4, context: html, text, full: html, text
Adding parallel-fetch loading of remote bigDataUrl tracks using pthreads
- src/lib/errabort.c
- lines changed 82, context: html, text, full: html, text
Adding parallel-fetch loading of remote bigDataUrl tracks using pthreads
- src/lib/https.c
- lines changed 126, context: html, text, full: html, text
Adding parallel-fetch loading of remote bigDataUrl tracks using pthreads
- src/lib/net.c
- lines changed 56, context: html, text, full: html, text
Adding parallel-fetch loading of remote bigDataUrl tracks using pthreads
- src/lib/portimpl.c
- lines changed 27, context: html, text, full: html, text
Adding parallel-fetch loading of remote bigDataUrl tracks using pthreads
- src/lib/vcf.c
- lines changed 5, context: html, text, full: html, text
#986 (VCF): Loosening regexes for parsing VCF header to accomodate 1000 Genomes pilot release trio indel files.
- src/utils/qa/weeklybld/buildEnv.csh
- lines changed: 69529
- files changed: 457