All File Changes
v257_preview2 to v257_base (2011-09-13 to 2011-09-19) v257
- python/lib/ucscgenomics/bed.py
- lines changed 49, context: html, text, full: html, text
large-scale renaming change to allow python to be built into cluster/bin, also mkGeoPkg now renames files
- python/lib/ucscgenomics/compositetrack/CompositeTrack.py
- lines changed 228, context: html, text, full: html, text
large-scale renaming change to allow python to be built into cluster/bin, also mkGeoPkg now renames files
- python/lib/ucscgenomics/compositetrack/__init__.py
- lines changed 0, context: html, text, full: html, text
removed additional extra files
- python/lib/ucscgenomics/cv.py
- lines changed 507, context: html, text, full: html, text
large-scale renaming change to allow python to be built into cluster/bin, also mkGeoPkg now renames files
- python/lib/ucscgenomics/cvfile/CvFile.py
- lines changed 504, context: html, text, full: html, text
large-scale renaming change to allow python to be built into cluster/bin, also mkGeoPkg now renames files
- python/lib/ucscgenomics/cvfile/__init__.py
- python/lib/ucscgenomics/cvfile/unittest/input/Antibody/BlankKey.ra
- lines changed 25, context: html, text, full: html, text
large-scale renaming change to allow python to be built into cluster/bin, also mkGeoPkg now renames files
- python/lib/ucscgenomics/cvfile/unittest/input/Antibody/ExtraKey.ra
- lines changed 26, context: html, text, full: html, text
large-scale renaming change to allow python to be built into cluster/bin, also mkGeoPkg now renames files
- python/lib/ucscgenomics/cvfile/unittest/input/Antibody/MissingKey.ra
- lines changed 24, context: html, text, full: html, text
large-scale renaming change to allow python to be built into cluster/bin, also mkGeoPkg now renames files
- python/lib/ucscgenomics/cvfile/unittest/input/Antibody/NonmatchKey.ra
- lines changed 25, context: html, text, full: html, text
large-scale renaming change to allow python to be built into cluster/bin, also mkGeoPkg now renames files
- python/lib/ucscgenomics/cvfile/unittest/input/Antibody/ValidStanza.ra
- lines changed 36, context: html, text, full: html, text
large-scale renaming change to allow python to be built into cluster/bin, also mkGeoPkg now renames files
- python/lib/ucscgenomics/cvfile/unittest/input/CellLine/BlankKey.ra
- lines changed 34, context: html, text, full: html, text
large-scale renaming change to allow python to be built into cluster/bin, also mkGeoPkg now renames files
- python/lib/ucscgenomics/cvfile/unittest/input/CellLine/ExtraKey.ra
- lines changed 35, context: html, text, full: html, text
large-scale renaming change to allow python to be built into cluster/bin, also mkGeoPkg now renames files
- python/lib/ucscgenomics/cvfile/unittest/input/CellLine/MissingKey.ra
- lines changed 33, context: html, text, full: html, text
large-scale renaming change to allow python to be built into cluster/bin, also mkGeoPkg now renames files
- python/lib/ucscgenomics/cvfile/unittest/input/CellLine/NonmatchKey.ra
- lines changed 34, context: html, text, full: html, text
large-scale renaming change to allow python to be built into cluster/bin, also mkGeoPkg now renames files
- python/lib/ucscgenomics/cvfile/unittest/input/CellLine/ValidStanza.ra
- lines changed 33, context: html, text, full: html, text
large-scale renaming change to allow python to be built into cluster/bin, also mkGeoPkg now renames files
- python/lib/ucscgenomics/cvfile/unittest/input/Mouse/BlankKey.ra
- lines changed 37, context: html, text, full: html, text
large-scale renaming change to allow python to be built into cluster/bin, also mkGeoPkg now renames files
- python/lib/ucscgenomics/cvfile/unittest/input/Mouse/ExtraKey.ra
- lines changed 38, context: html, text, full: html, text
large-scale renaming change to allow python to be built into cluster/bin, also mkGeoPkg now renames files
- python/lib/ucscgenomics/cvfile/unittest/input/Mouse/MissingKey.ra
- lines changed 36, context: html, text, full: html, text
large-scale renaming change to allow python to be built into cluster/bin, also mkGeoPkg now renames files
- python/lib/ucscgenomics/cvfile/unittest/input/Mouse/NonmatchKey.ra
- lines changed 37, context: html, text, full: html, text
large-scale renaming change to allow python to be built into cluster/bin, also mkGeoPkg now renames files
- python/lib/ucscgenomics/cvfile/unittest/input/Mouse/ValidStanza.ra
- lines changed 37, context: html, text, full: html, text
large-scale renaming change to allow python to be built into cluster/bin, also mkGeoPkg now renames files
- python/lib/ucscgenomics/cvfile/unittest/testCvFile
- lines changed 95, context: html, text, full: html, text
large-scale renaming change to allow python to be built into cluster/bin, also mkGeoPkg now renames files
- python/lib/ucscgenomics/ordereddict.py
- lines changed 58, context: html, text, full: html, text
large-scale renaming change to allow python to be built into cluster/bin, also mkGeoPkg now renames files
- python/lib/ucscgenomics/ordereddict/OrderedDict.py
- lines changed 58, context: html, text, full: html, text
large-scale renaming change to allow python to be built into cluster/bin, also mkGeoPkg now renames files
- python/lib/ucscgenomics/ordereddict/__init__.py
- lines changed 0, context: html, text, full: html, text
removed additional extra files
- python/lib/ucscgenomics/ra.py
- lines changed 214, context: html, text, full: html, text
large-scale renaming change to allow python to be built into cluster/bin, also mkGeoPkg now renames files
- python/lib/ucscgenomics/rafile/RaFile.py
- lines changed 214, context: html, text, full: html, text
large-scale renaming change to allow python to be built into cluster/bin, also mkGeoPkg now renames files
- python/lib/ucscgenomics/rafile/__init__.py
- python/lib/ucscgenomics/rafile/unittest/testRaFile.py
- lines changed 205, context: html, text, full: html, text
large-scale renaming change to allow python to be built into cluster/bin, also mkGeoPkg now renames files
- python/lib/ucscgenomics/rafile/unittest/testoutput/BasicDiff.out
- lines changed 27, context: html, text, full: html, text
large-scale renaming change to allow python to be built into cluster/bin, also mkGeoPkg now renames files
- python/lib/ucscgenomics/rafile/unittest/testoutput/CommentsDiff.out
- lines changed 31, context: html, text, full: html, text
large-scale renaming change to allow python to be built into cluster/bin, also mkGeoPkg now renames files
- python/lib/ucscgenomics/rafile/unittest/testoutput/DeleteItem.out
- lines changed 39, context: html, text, full: html, text
large-scale renaming change to allow python to be built into cluster/bin, also mkGeoPkg now renames files
- python/lib/ucscgenomics/rafile/unittest/testoutput/ExtraneousWhitespace.out
- lines changed 70, context: html, text, full: html, text
large-scale renaming change to allow python to be built into cluster/bin, also mkGeoPkg now renames files
- python/lib/ucscgenomics/rafile/unittest/testoutput/GetItem.out
- lines changed 13, context: html, text, full: html, text
large-scale renaming change to allow python to be built into cluster/bin, also mkGeoPkg now renames files
- python/lib/ucscgenomics/rafile/unittest/testoutput/InlineCommentsDiff.out
- lines changed 27, context: html, text, full: html, text
large-scale renaming change to allow python to be built into cluster/bin, also mkGeoPkg now renames files
- python/lib/ucscgenomics/rafile/unittest/testoutput/IterEntryItems.out
- lines changed 27, context: html, text, full: html, text
large-scale renaming change to allow python to be built into cluster/bin, also mkGeoPkg now renames files
- python/lib/ucscgenomics/rafile/unittest/testoutput/IterEntryKeys.out
- lines changed 27, context: html, text, full: html, text
large-scale renaming change to allow python to be built into cluster/bin, also mkGeoPkg now renames files
- python/lib/ucscgenomics/rafile/unittest/testoutput/IterEntryValues.out
- lines changed 27, context: html, text, full: html, text
large-scale renaming change to allow python to be built into cluster/bin, also mkGeoPkg now renames files
- python/lib/ucscgenomics/rafile/unittest/testoutput/IterItems.out
- lines changed 19, context: html, text, full: html, text
large-scale renaming change to allow python to be built into cluster/bin, also mkGeoPkg now renames files
- python/lib/ucscgenomics/rafile/unittest/testoutput/IterKeys.out
- lines changed 11, context: html, text, full: html, text
large-scale renaming change to allow python to be built into cluster/bin, also mkGeoPkg now renames files
- python/lib/ucscgenomics/rafile/unittest/testoutput/IterValues.out
- lines changed 41, context: html, text, full: html, text
large-scale renaming change to allow python to be built into cluster/bin, also mkGeoPkg now renames files
- python/lib/ucscgenomics/rafile/unittest/tests/BasicDiff.ra
- lines changed 12, context: html, text, full: html, text
large-scale renaming change to allow python to be built into cluster/bin, also mkGeoPkg now renames files
- python/lib/ucscgenomics/rafile/unittest/tests/CommentsDiff.ra
- lines changed 14, context: html, text, full: html, text
large-scale renaming change to allow python to be built into cluster/bin, also mkGeoPkg now renames files
- python/lib/ucscgenomics/rafile/unittest/tests/DeleteItem.ra
- lines changed 18, context: html, text, full: html, text
large-scale renaming change to allow python to be built into cluster/bin, also mkGeoPkg now renames files
- python/lib/ucscgenomics/rafile/unittest/tests/DuplicateKeys.ra
- lines changed 8, context: html, text, full: html, text
large-scale renaming change to allow python to be built into cluster/bin, also mkGeoPkg now renames files
- python/lib/ucscgenomics/rafile/unittest/tests/FunctionalityCheck.ra
- lines changed 23, context: html, text, full: html, text
large-scale renaming change to allow python to be built into cluster/bin, also mkGeoPkg now renames files
- python/lib/ucscgenomics/rafile/unittest/tests/GetItem.ra
- lines changed 5, context: html, text, full: html, text
large-scale renaming change to allow python to be built into cluster/bin, also mkGeoPkg now renames files
- python/lib/ucscgenomics/rafile/unittest/tests/InlineCommentsDiff.ra
- lines changed 12, context: html, text, full: html, text
large-scale renaming change to allow python to be built into cluster/bin, also mkGeoPkg now renames files
- python/lib/ucscgenomics/rafile/unittest/tests/IterEntryItems.ra
- lines changed 12, context: html, text, full: html, text
large-scale renaming change to allow python to be built into cluster/bin, also mkGeoPkg now renames files
- python/lib/ucscgenomics/rafile/unittest/tests/IterEntryKeys.ra
- lines changed 12, context: html, text, full: html, text
large-scale renaming change to allow python to be built into cluster/bin, also mkGeoPkg now renames files
- python/lib/ucscgenomics/rafile/unittest/tests/IterEntryValues.ra
- lines changed 12, context: html, text, full: html, text
large-scale renaming change to allow python to be built into cluster/bin, also mkGeoPkg now renames files
- python/lib/ucscgenomics/rafile/unittest/tests/IterItems.ra
- lines changed 8, context: html, text, full: html, text
large-scale renaming change to allow python to be built into cluster/bin, also mkGeoPkg now renames files
- python/lib/ucscgenomics/rafile/unittest/tests/IterKeys.ra
- lines changed 4, context: html, text, full: html, text
large-scale renaming change to allow python to be built into cluster/bin, also mkGeoPkg now renames files
- python/lib/ucscgenomics/rafile/unittest/tests/IterValues.ra
- lines changed 19, context: html, text, full: html, text
large-scale renaming change to allow python to be built into cluster/bin, also mkGeoPkg now renames files
- python/lib/ucscgenomics/rafile/unittest/tests/MisplacedKeys.ra
- lines changed 8, context: html, text, full: html, text
large-scale renaming change to allow python to be built into cluster/bin, also mkGeoPkg now renames files
- python/lib/ucscgenomics/rafile/unittest/tests/NonNewlineFile.ra
- lines changed 5, context: html, text, full: html, text
large-scale renaming change to allow python to be built into cluster/bin, also mkGeoPkg now renames files
- python/lib/ucscgenomics/soft.py
- lines changed 392, context: html, text, full: html, text
large-scale renaming change to allow python to be built into cluster/bin, also mkGeoPkg now renames files
- python/lib/ucscgenomics/softfile/SoftFile.py
- lines changed 392, context: html, text, full: html, text
large-scale renaming change to allow python to be built into cluster/bin, also mkGeoPkg now renames files
- python/lib/ucscgenomics/softfile/__init__.py
- python/lib/ucscgenomics/softfile/unittest/testSoft
- lines changed 10, context: html, text, full: html, text
large-scale renaming change to allow python to be built into cluster/bin, also mkGeoPkg now renames files
- python/lib/ucscgenomics/styles.py
- lines changed 38, context: html, text, full: html, text
large-scale renaming change to allow python to be built into cluster/bin, also mkGeoPkg now renames files
- python/lib/ucscgenomics/test/test_cv
- lines changed 95, context: html, text, full: html, text
large-scale renaming change to allow python to be built into cluster/bin, also mkGeoPkg now renames files
- python/lib/ucscgenomics/test/test_cv_input/Antibody/BlankKey.ra
- lines changed 25, context: html, text, full: html, text
large-scale renaming change to allow python to be built into cluster/bin, also mkGeoPkg now renames files
- python/lib/ucscgenomics/test/test_cv_input/Antibody/ExtraKey.ra
- lines changed 26, context: html, text, full: html, text
large-scale renaming change to allow python to be built into cluster/bin, also mkGeoPkg now renames files
- python/lib/ucscgenomics/test/test_cv_input/Antibody/MissingKey.ra
- lines changed 24, context: html, text, full: html, text
large-scale renaming change to allow python to be built into cluster/bin, also mkGeoPkg now renames files
- python/lib/ucscgenomics/test/test_cv_input/Antibody/NonmatchKey.ra
- lines changed 25, context: html, text, full: html, text
large-scale renaming change to allow python to be built into cluster/bin, also mkGeoPkg now renames files
- python/lib/ucscgenomics/test/test_cv_input/Antibody/ValidStanza.ra
- lines changed 36, context: html, text, full: html, text
large-scale renaming change to allow python to be built into cluster/bin, also mkGeoPkg now renames files
- python/lib/ucscgenomics/test/test_cv_input/CellLine/BlankKey.ra
- lines changed 34, context: html, text, full: html, text
large-scale renaming change to allow python to be built into cluster/bin, also mkGeoPkg now renames files
- python/lib/ucscgenomics/test/test_cv_input/CellLine/ExtraKey.ra
- lines changed 35, context: html, text, full: html, text
large-scale renaming change to allow python to be built into cluster/bin, also mkGeoPkg now renames files
- python/lib/ucscgenomics/test/test_cv_input/CellLine/MissingKey.ra
- lines changed 33, context: html, text, full: html, text
large-scale renaming change to allow python to be built into cluster/bin, also mkGeoPkg now renames files
- python/lib/ucscgenomics/test/test_cv_input/CellLine/NonmatchKey.ra
- lines changed 34, context: html, text, full: html, text
large-scale renaming change to allow python to be built into cluster/bin, also mkGeoPkg now renames files
- python/lib/ucscgenomics/test/test_cv_input/CellLine/ValidStanza.ra
- lines changed 33, context: html, text, full: html, text
large-scale renaming change to allow python to be built into cluster/bin, also mkGeoPkg now renames files
- python/lib/ucscgenomics/test/test_cv_input/Mouse/BlankKey.ra
- lines changed 37, context: html, text, full: html, text
large-scale renaming change to allow python to be built into cluster/bin, also mkGeoPkg now renames files
- python/lib/ucscgenomics/test/test_cv_input/Mouse/ExtraKey.ra
- lines changed 38, context: html, text, full: html, text
large-scale renaming change to allow python to be built into cluster/bin, also mkGeoPkg now renames files
- python/lib/ucscgenomics/test/test_cv_input/Mouse/MissingKey.ra
- lines changed 36, context: html, text, full: html, text
large-scale renaming change to allow python to be built into cluster/bin, also mkGeoPkg now renames files
- python/lib/ucscgenomics/test/test_cv_input/Mouse/NonmatchKey.ra
- lines changed 37, context: html, text, full: html, text
large-scale renaming change to allow python to be built into cluster/bin, also mkGeoPkg now renames files
- python/lib/ucscgenomics/test/test_cv_input/Mouse/ValidStanza.ra
- lines changed 37, context: html, text, full: html, text
large-scale renaming change to allow python to be built into cluster/bin, also mkGeoPkg now renames files
- python/lib/ucscgenomics/test/test_ra
- lines changed 206, context: html, text, full: html, text
large-scale renaming change to allow python to be built into cluster/bin, also mkGeoPkg now renames files
- python/lib/ucscgenomics/test/test_ra_file/testoutput/BasicDiff.out
- lines changed 27, context: html, text, full: html, text
large-scale renaming change to allow python to be built into cluster/bin, also mkGeoPkg now renames files
- python/lib/ucscgenomics/test/test_ra_file/testoutput/CommentsDiff.out
- lines changed 31, context: html, text, full: html, text
large-scale renaming change to allow python to be built into cluster/bin, also mkGeoPkg now renames files
- python/lib/ucscgenomics/test/test_ra_file/testoutput/DeleteItem.out
- lines changed 39, context: html, text, full: html, text
large-scale renaming change to allow python to be built into cluster/bin, also mkGeoPkg now renames files
- python/lib/ucscgenomics/test/test_ra_file/testoutput/ExtraneousWhitespace.out
- lines changed 70, context: html, text, full: html, text
large-scale renaming change to allow python to be built into cluster/bin, also mkGeoPkg now renames files
- python/lib/ucscgenomics/test/test_ra_file/testoutput/GetItem.out
- lines changed 13, context: html, text, full: html, text
large-scale renaming change to allow python to be built into cluster/bin, also mkGeoPkg now renames files
- python/lib/ucscgenomics/test/test_ra_file/testoutput/InlineCommentsDiff.out
- lines changed 27, context: html, text, full: html, text
large-scale renaming change to allow python to be built into cluster/bin, also mkGeoPkg now renames files
- python/lib/ucscgenomics/test/test_ra_file/testoutput/IterEntryItems.out
- lines changed 27, context: html, text, full: html, text
large-scale renaming change to allow python to be built into cluster/bin, also mkGeoPkg now renames files
- python/lib/ucscgenomics/test/test_ra_file/testoutput/IterEntryKeys.out
- lines changed 27, context: html, text, full: html, text
large-scale renaming change to allow python to be built into cluster/bin, also mkGeoPkg now renames files
- python/lib/ucscgenomics/test/test_ra_file/testoutput/IterEntryValues.out
- lines changed 27, context: html, text, full: html, text
large-scale renaming change to allow python to be built into cluster/bin, also mkGeoPkg now renames files
- python/lib/ucscgenomics/test/test_ra_file/testoutput/IterItems.out
- lines changed 19, context: html, text, full: html, text
large-scale renaming change to allow python to be built into cluster/bin, also mkGeoPkg now renames files
- python/lib/ucscgenomics/test/test_ra_file/testoutput/IterKeys.out
- lines changed 11, context: html, text, full: html, text
large-scale renaming change to allow python to be built into cluster/bin, also mkGeoPkg now renames files
- python/lib/ucscgenomics/test/test_ra_file/testoutput/IterValues.out
- lines changed 41, context: html, text, full: html, text
large-scale renaming change to allow python to be built into cluster/bin, also mkGeoPkg now renames files
- python/lib/ucscgenomics/test/test_ra_input/BasicDiff.ra
- lines changed 12, context: html, text, full: html, text
large-scale renaming change to allow python to be built into cluster/bin, also mkGeoPkg now renames files
- python/lib/ucscgenomics/test/test_ra_input/CommentsDiff.ra
- lines changed 14, context: html, text, full: html, text
large-scale renaming change to allow python to be built into cluster/bin, also mkGeoPkg now renames files
- python/lib/ucscgenomics/test/test_ra_input/DeleteItem.ra
- lines changed 18, context: html, text, full: html, text
large-scale renaming change to allow python to be built into cluster/bin, also mkGeoPkg now renames files
- python/lib/ucscgenomics/test/test_ra_input/DuplicateKeys.ra
- lines changed 8, context: html, text, full: html, text
large-scale renaming change to allow python to be built into cluster/bin, also mkGeoPkg now renames files
- python/lib/ucscgenomics/test/test_ra_input/FunctionalityCheck.ra
- lines changed 23, context: html, text, full: html, text
large-scale renaming change to allow python to be built into cluster/bin, also mkGeoPkg now renames files
- python/lib/ucscgenomics/test/test_ra_input/GetItem.ra
- lines changed 5, context: html, text, full: html, text
large-scale renaming change to allow python to be built into cluster/bin, also mkGeoPkg now renames files
- python/lib/ucscgenomics/test/test_ra_input/InlineCommentsDiff.ra
- lines changed 12, context: html, text, full: html, text
large-scale renaming change to allow python to be built into cluster/bin, also mkGeoPkg now renames files
- python/lib/ucscgenomics/test/test_ra_input/IterEntryItems.ra
- lines changed 12, context: html, text, full: html, text
large-scale renaming change to allow python to be built into cluster/bin, also mkGeoPkg now renames files
- python/lib/ucscgenomics/test/test_ra_input/IterEntryKeys.ra
- lines changed 12, context: html, text, full: html, text
large-scale renaming change to allow python to be built into cluster/bin, also mkGeoPkg now renames files
- python/lib/ucscgenomics/test/test_ra_input/IterEntryValues.ra
- lines changed 12, context: html, text, full: html, text
large-scale renaming change to allow python to be built into cluster/bin, also mkGeoPkg now renames files
- python/lib/ucscgenomics/test/test_ra_input/IterItems.ra
- lines changed 8, context: html, text, full: html, text
large-scale renaming change to allow python to be built into cluster/bin, also mkGeoPkg now renames files
- python/lib/ucscgenomics/test/test_ra_input/IterKeys.ra
- lines changed 4, context: html, text, full: html, text
large-scale renaming change to allow python to be built into cluster/bin, also mkGeoPkg now renames files
- python/lib/ucscgenomics/test/test_ra_input/IterValues.ra
- lines changed 19, context: html, text, full: html, text
large-scale renaming change to allow python to be built into cluster/bin, also mkGeoPkg now renames files
- python/lib/ucscgenomics/test/test_ra_input/MisplacedKeys.ra
- lines changed 8, context: html, text, full: html, text
large-scale renaming change to allow python to be built into cluster/bin, also mkGeoPkg now renames files
- python/lib/ucscgenomics/test/test_ra_input/NonNewlineFile.ra
- lines changed 5, context: html, text, full: html, text
large-scale renaming change to allow python to be built into cluster/bin, also mkGeoPkg now renames files
- python/lib/ucscgenomics/test/test_soft
- lines changed 10, context: html, text, full: html, text
large-scale renaming change to allow python to be built into cluster/bin, also mkGeoPkg now renames files
- python/lib/ucscgenomics/textstyle.py
- lines changed 40, context: html, text, full: html, text
large-scale renaming change to allow python to be built into cluster/bin, also mkGeoPkg now renames files
- python/lib/ucscgenomics/textstyle/TextStyle.py
- lines changed 40, context: html, text, full: html, text
large-scale renaming change to allow python to be built into cluster/bin, also mkGeoPkg now renames files
- python/lib/ucscgenomics/textstyle/__init__.py
- lines changed 0, context: html, text, full: html, text
removed additional extra files
- python/lib/ucscgenomics/track.py
- lines changed 234, context: html, text, full: html, text
large-scale renaming change to allow python to be built into cluster/bin, also mkGeoPkg now renames files
- python/programs/cvValidate/cvValidate
- lines changed 2, context: html, text, full: html, text
large-scale renaming change to allow python to be built into cluster/bin, also mkGeoPkg now renames files
- python/programs/mkChangeNotes/mkChangeNotes
- lines changed 123, context: html, text, full: html, text
large-scale renaming change to allow python to be built into cluster/bin, also mkGeoPkg now renames files
- python/programs/mkGeoPkg/mkGeoPkg
- lines changed 94, context: html, text, full: html, text
large-scale renaming change to allow python to be built into cluster/bin, also mkGeoPkg now renames files
- python/programs/mkGeoPkg/trackInfo
- lines changed 183, context: html, text, full: html, text
large-scale renaming change to allow python to be built into cluster/bin, also mkGeoPkg now renames files
- python/programs/trackInfo/trackInfo
- lines changed 179, context: html, text, full: html, text
large-scale renaming change to allow python to be built into cluster/bin, also mkGeoPkg now renames files
- src/hg/encode/DAFs/2.0/affyRnaChip.daf
- lines changed 38, context: html, text, full: html, text
Put replicate 5 in the attic and changed short labels according to Kate instructions on track 43
- src/hg/encode/DAFs/2.0/cshlLongElements.daf
- lines changed 76, context: html, text, full: html, text
Put replicate 5 in the attic and changed short labels according to Kate instructions on track 43
- src/hg/encode/DAFs/2.0/cshlLongSpikeIns.daf
- lines changed 42, context: html, text, full: html, text
Put replicate 5 in the attic and changed short labels according to Kate instructions on track 43
- src/hg/encode/DAFs/2.0/gisDnaPet.daf
- lines changed 73, context: html, text, full: html, text
Put replicate 5 in the attic and changed short labels according to Kate instructions on track 43
- src/hg/encode/DAFs/2.0/haibMethylRrbs.daf
- lines changed 34, context: html, text, full: html, text
Put replicate 5 in the attic and changed short labels according to Kate instructions on track 43
- src/hg/encode/DAFs/2.0/sunySwitchgear.daf
- lines changed 35, context: html, text, full: html, text
Put replicate 5 in the attic and changed short labels according to Kate instructions on track 43
- src/hg/encode/DAFs/2.0/wgEncodeAffyRnaChip.daf
- lines changed 38, context: html, text, full: html, text
Put replicate 5 in the attic and changed short labels according to Kate instructions on track 43
- src/hg/encode/DAFs/2.0/wgEncodeGisDnaPet.daf
- lines changed 73, context: html, text, full: html, text
Put replicate 5 in the attic and changed short labels according to Kate instructions on track 43
- src/hg/encode/DAFs/2.0/wgEncodeHaibMethylRrbs.daf
- lines changed 34, context: html, text, full: html, text
Put replicate 5 in the attic and changed short labels according to Kate instructions on track 43
- src/hg/encode/DAFs/2.0/wgEncodeSunySwitchgear.daf
- lines changed 35, context: html, text, full: html, text
Put replicate 5 in the attic and changed short labels according to Kate instructions on track 43
- src/hg/encode/DAFs/3.0/hg19/wgEncodeAffyRnaChip.daf
- lines changed 38, context: html, text, full: html, text
Moving the hg19 into the new directory
- lines changed 2, context: html, text, full: html, text
Starting the 3.0 DAF directory for hg19
- src/hg/encode/DAFs/3.0/hg19/wgEncodeBroadHistone.daf
- lines changed 54, context: html, text, full: html, text
Starting the 3.0 DAF directory for hg19
- src/hg/encode/DAFs/3.0/hg19/wgEncodeBroadHmm.daf
- lines changed 23, context: html, text, full: html, text
Starting the 3.0 DAF directory for hg19
- src/hg/encode/DAFs/3.0/hg19/wgEncodeCaltechRnaSeq.daf
- lines changed 146, context: html, text, full: html, text
Starting the 3.0 DAF directory for hg19
- src/hg/encode/DAFs/3.0/hg19/wgEncodeCshlLongRnaSeq.daf
- lines changed 62, context: html, text, full: html, text
Starting the 3.0 DAF directory for hg19
- src/hg/encode/DAFs/3.0/hg19/wgEncodeCshlShortRnaSeq.daf
- lines changed 81, context: html, text, full: html, text
Starting the 3.0 DAF directory for hg19
- src/hg/encode/DAFs/3.0/hg19/wgEncodeDukeAffyExon.daf
- lines changed 23, context: html, text, full: html, text
Starting the 3.0 DAF directory for hg19
- src/hg/encode/DAFs/3.0/hg19/wgEncodeGencodeV7.daf
- lines changed 0, context: html, text, full: html, text
Starting the 3.0 DAF directory for hg19
- src/hg/encode/DAFs/3.0/hg19/wgEncodeGisChiaPet.daf
- lines changed 60, context: html, text, full: html, text
Starting the 3.0 DAF directory for hg19
- src/hg/encode/DAFs/3.0/hg19/wgEncodeGisDnaPet.daf
- lines changed 73, context: html, text, full: html, text
Moving the hg19 into the new directory
- lines changed 1, context: html, text, full: html, text
Starting the 3.0 DAF directory for hg19
- src/hg/encode/DAFs/3.0/hg19/wgEncodeGisRnaPet.daf
- lines changed 72, context: html, text, full: html, text
Starting the 3.0 DAF directory for hg19
- src/hg/encode/DAFs/3.0/hg19/wgEncodeHaibGenotype.daf
- lines changed 44, context: html, text, full: html, text
Starting the 3.0 DAF directory for hg19
- src/hg/encode/DAFs/3.0/hg19/wgEncodeHaibMethyl27.daf
- lines changed 40, context: html, text, full: html, text
Starting the 3.0 DAF directory for hg19
- src/hg/encode/DAFs/3.0/hg19/wgEncodeHaibMethyl450.daf
- lines changed 39, context: html, text, full: html, text
Starting the 3.0 DAF directory for hg19
- src/hg/encode/DAFs/3.0/hg19/wgEncodeHaibMethylRrbs.daf
- lines changed 34, context: html, text, full: html, text
Moving the hg19 into the new directory
- lines changed 1, context: html, text, full: html, text
Starting the 3.0 DAF directory for hg19
- src/hg/encode/DAFs/3.0/hg19/wgEncodeHaibRnaSeq.daf
- lines changed 65, context: html, text, full: html, text
Starting the 3.0 DAF directory for hg19
- src/hg/encode/DAFs/3.0/hg19/wgEncodeHaibTfbs.daf
- lines changed 59, context: html, text, full: html, text
Starting the 3.0 DAF directory for hg19
- src/hg/encode/DAFs/3.0/hg19/wgEncodeMapability.daf
- lines changed 23, context: html, text, full: html, text
Starting the 3.0 DAF directory for hg19
- src/hg/encode/DAFs/3.0/hg19/wgEncodeOpenChromChip.daf
- lines changed 62, context: html, text, full: html, text
Starting the 3.0 DAF directory for hg19
- src/hg/encode/DAFs/3.0/hg19/wgEncodeOpenChromDnase.daf
- lines changed 63, context: html, text, full: html, text
Starting the 3.0 DAF directory for hg19
- src/hg/encode/DAFs/3.0/hg19/wgEncodeOpenChromFaire.daf
- lines changed 60, context: html, text, full: html, text
Starting the 3.0 DAF directory for hg19
- src/hg/encode/DAFs/3.0/hg19/wgEncodeRikenCage.daf
- lines changed 70, context: html, text, full: html, text
Starting the 3.0 DAF directory for hg19
- src/hg/encode/DAFs/3.0/hg19/wgEncodeSunyAlbanyGeneSt.daf
- lines changed 22, context: html, text, full: html, text
Starting the 3.0 DAF directory for hg19
- src/hg/encode/DAFs/3.0/hg19/wgEncodeSunyAlbanyTiling.daf
- lines changed 25, context: html, text, full: html, text
Starting the 3.0 DAF directory for hg19
- src/hg/encode/DAFs/3.0/hg19/wgEncodeSunyRipSeq.daf
- lines changed 51, context: html, text, full: html, text
Starting the 3.0 DAF directory for hg19
- src/hg/encode/DAFs/3.0/hg19/wgEncodeSunySwitchgear.daf
- lines changed 35, context: html, text, full: html, text
Moving the hg19 into the new directory
- lines changed 1, context: html, text, full: html, text
Starting the 3.0 DAF directory for hg19
- src/hg/encode/DAFs/3.0/hg19/wgEncodeSydhHistone.daf
- lines changed 58, context: html, text, full: html, text
Starting the 3.0 DAF directory for hg19
- src/hg/encode/DAFs/3.0/hg19/wgEncodeSydhNsome.daf
- lines changed 46, context: html, text, full: html, text
Starting the 3.0 DAF directory for hg19
- src/hg/encode/DAFs/3.0/hg19/wgEncodeSydhTfbs.daf
- lines changed 56, context: html, text, full: html, text
Starting the 3.0 DAF directory for hg19
- src/hg/encode/DAFs/3.0/hg19/wgEncodeUchicagoTfbs.daf
- lines changed 60, context: html, text, full: html, text
Starting the 3.0 DAF directory for hg19
- src/hg/encode/DAFs/3.0/hg19/wgEncodeUmMassWengTfbsValid.daf
- lines changed 25, context: html, text, full: html, text
Starting the 3.0 DAF directory for hg19
- src/hg/encode/DAFs/3.0/hg19/wgEncodeUmassDekker5C.daf
- lines changed 23, context: html, text, full: html, text
Starting the 3.0 DAF directory for hg19
- src/hg/encode/DAFs/3.0/hg19/wgEncodeUncBsuProt.daf
- lines changed 39, context: html, text, full: html, text
Starting the 3.0 DAF directory for hg19
- src/hg/encode/DAFs/3.0/hg19/wgEncodeUw5C.daf
- lines changed 28, context: html, text, full: html, text
Starting the 3.0 DAF directory for hg19
- src/hg/encode/DAFs/3.0/hg19/wgEncodeUwAffyExonArray.daf
- lines changed 35, context: html, text, full: html, text
Starting the 3.0 DAF directory for hg19
- src/hg/encode/DAFs/3.0/hg19/wgEncodeUwDgf.daf
- lines changed 70, context: html, text, full: html, text
Starting the 3.0 DAF directory for hg19
- src/hg/encode/DAFs/3.0/hg19/wgEncodeUwDnase.daf
- lines changed 61, context: html, text, full: html, text
Starting the 3.0 DAF directory for hg19
- src/hg/encode/DAFs/3.0/hg19/wgEncodeUwHistone.daf
- lines changed 58, context: html, text, full: html, text
Starting the 3.0 DAF directory for hg19
- src/hg/encode/DAFs/3.0/hg19/wgEncodebuOrchid.daf
- lines changed 33, context: html, text, full: html, text
Starting the 3.0 DAF directory for hg19
- src/hg/encode/DAFs/3.0/mm9/wgEncodeCaltechHist.daf
- lines changed 62, context: html, text, full: html, text
Making the 3.0 daf directory for mm9
- src/hg/encode/DAFs/3.0/mm9/wgEncodeCaltechHistone.daf
- lines changed 62, context: html, text, full: html, text
Making the 3.0 daf directory for mm9
- src/hg/encode/DAFs/3.0/mm9/wgEncodeCaltechTfbs.daf
- lines changed 62, context: html, text, full: html, text
Making the 3.0 daf directory for mm9
- src/hg/encode/DAFs/3.0/mm9/wgEncodeLicrHistone.daf
- lines changed 59, context: html, text, full: html, text
Making the 3.0 daf directory for mm9
- src/hg/encode/DAFs/3.0/mm9/wgEncodeLicrRnaSeq.daf
- lines changed 58, context: html, text, full: html, text
Making the 3.0 daf directory for mm9
- src/hg/encode/DAFs/3.0/mm9/wgEncodeLicrTfbs.daf
- lines changed 57, context: html, text, full: html, text
Making the 3.0 daf directory for mm9
- src/hg/encode/DAFs/3.0/mm9/wgEncodePsuHistone.daf
- lines changed 68, context: html, text, full: html, text
Making the 3.0 daf directory for mm9
- src/hg/encode/DAFs/3.0/mm9/wgEncodePsuTfbs.daf
- lines changed 67, context: html, text, full: html, text
Making the 3.0 daf directory for mm9
- src/hg/encode/DAFs/3.0/mm9/wgEncodeSydhHist.daf
- lines changed 63, context: html, text, full: html, text
Making the 3.0 daf directory for mm9
- src/hg/encode/DAFs/3.0/mm9/wgEncodeSydhRnaSeq.daf
- lines changed 57, context: html, text, full: html, text
Making the 3.0 daf directory for mm9
- src/hg/encode/DAFs/3.0/mm9/wgEncodeSydhTfbs.daf
- lines changed 63, context: html, text, full: html, text
Making the 3.0 daf directory for mm9
- src/hg/encode/DAFs/3.0/mm9/wgEncodeUwDfg.daf
- lines changed 76, context: html, text, full: html, text
Making the 3.0 daf directory for mm9
- src/hg/encode/DAFs/3.0/mm9/wgEncodeUwDnase.daf
- lines changed 63, context: html, text, full: html, text
Making the 3.0 daf directory for mm9
- src/hg/encode/DAFs/3.0/mm9/wgEncodeUwRnaSeq.daf
- lines changed 69, context: html, text, full: html, text
Making the 3.0 daf directory for mm9
- src/hg/encode/DAFs/3.0/mm9/wgEncodeUwTfbs.daf
- lines changed 65, context: html, text, full: html, text
Making the 3.0 daf directory for mm9
- src/hg/encode/DAFs/3.0/wgEncodeAffyRnaChip.daf
- lines changed 38, context: html, text, full: html, text
Moving to the next generation of DAFs
- lines changed 38, context: html, text, full: html, text
Moving the hg19 into the new directory
- src/hg/encode/DAFs/3.0/wgEncodeGisDnaPet.daf
- lines changed 73, context: html, text, full: html, text
Moving to the next generation of DAFs
- lines changed 73, context: html, text, full: html, text
Moving the hg19 into the new directory
- src/hg/encode/DAFs/3.0/wgEncodeHaibMethylRrbs.daf
- lines changed 34, context: html, text, full: html, text
Moving to the next generation of DAFs
- lines changed 34, context: html, text, full: html, text
Moving the hg19 into the new directory
- src/hg/encode/DAFs/3.0/wgEncodeSunySwitchgear.daf
- lines changed 35, context: html, text, full: html, text
Moving to the next generation of DAFs
- lines changed 35, context: html, text, full: html, text
Moving the hg19 into the new directory
- src/hg/encode/encodeMkChangeNotes/encodeMkChangeNotes
- lines changed 25, context: html, text, full: html, text
hacked encodeMkChangeNotes to remove duplicate entries, can't figure out why it's doing it, so no patch, just hack
- lines changed 1, context: html, text, full: html, text
Trying to make release 2 have the path information
- src/hg/encode/encodeMkFilesList/encodeMkFilesList
- lines changed 55, context: html, text, full: html, text
added in 3 functions, custom history file, silencing mdbupdates, and if updated metaDb, it will also attempt to print back out the .ra file
- src/hg/encode/hgEncodeVocab/hgEncodeVocab.c
- lines changed 18, context: html, text, full: html, text
Exclude deprecate terms from table unless requersted by name. Add tissue for cell line.
- src/hg/hgGene/hgGeneData/C_elegans/ce6/otherOrgs.ra
- lines changed 2, context: html, text, full: html, text
changing danRer6 to danRer7 and sacCer2 to sacCer3
- src/hg/hgGene/hgGeneData/D_melanogaster/dm3/otherOrgs.ra
- lines changed 2, context: html, text, full: html, text
changing danRer6 to danRer7 and sacCer2 to sacCer3
- src/hg/hgGene/hgGeneData/Human/hg19/otherOrgs.ra
- lines changed 2, context: html, text, full: html, text
changing danRer6 to danRer7 and sacCer2 to sacCer3
- src/hg/hgGene/hgGeneData/Mouse/mm9/otherOrgs.ra
- lines changed 2, context: html, text, full: html, text
changing danRer6 to danRer7 and sacCer2 to sacCer3
- src/hg/hgGene/hgGeneData/Rat/rn4/otherOrgs.ra
- lines changed 2, context: html, text, full: html, text
changing danRer6 to danRer7 and sacCer2 to sacCer3
- src/hg/hgHubConnect/hgHubConnect.c
- lines changed 2, context: html, text, full: html, text
don't show myHubs that don't support the current assembly #5253
- src/hg/hgTracks/bamTrack.c
- lines changed 9, context: html, text, full: html, text
labels on BAM tracks using tag coloring weren't drawing with an 0 alpha value #5338
- src/hg/hgTracks/gvfTrack.c
- lines changed 14, context: html, text, full: html, text
Track #34 (dbVar for human): Split ISCA Retrospective into 3subtracks by clinical interpretation (Benign, Pathogenic, Uncertain).
Data update required code update because of changes in keywords.
- src/hg/hgTracks/hgTracks.c
- lines changed 2, context: html, text, full: html, text
disable in-place navigation if advanced javascript features is turned off (see redmine 5279)
- src/hg/hgTracks/renderMain.c
- lines changed 11, context: html, text, full: html, text
show assembly and position by default
- src/hg/hgc/encodeClick.c
- lines changed 55, context: html, text, full: html, text
fixing peptideMapping - use name-and-position based query instead of just position to prevent picking up nearby peptides that are different, show all peptide mapping details, pull out peptideRepeatCount since it does not vary, show only unique alternate locations
- src/hg/hgc/gvfClick.c
- lines changed 8, context: html, text, full: html, text
Track #34 (dbVar for human): Split ISCA Retrospective into 3subtracks by clinical interpretation (Benign, Pathogenic, Uncertain).
Data update required code update because of changes in keywords.
- src/hg/hgc/hgc.c
- lines changed 4, context: html, text, full: html, text
Minor adjustment of <BR> due to removal of OMIM NCBI link.
- lines changed 3, context: html, text, full: html, text
Changed 'OMIM page at omim.org:' to 'OMIM:'.
- lines changed 16, context: html, text, full: html, text
Broke a complex query for omimGene2 into a combination of 2-step queries.
- src/hg/htdocs/FAQ/FAQformat.html
- lines changed 81, context: html, text, full: html, text
Added the peptide mapping format
- src/hg/htdocs/goldenPath/help/hgWiggleTrackHelp.html
- src/hg/htdocs/goldenPath/pubs.html
- lines changed 20, context: html, text, full: html, text
Added 2 new pubs for 2011.
- src/hg/htdocs/indexNews.html
- lines changed 4, context: html, text, full: html, text
Fixed incorrect info in news item -- thanks, Larry.
- src/hg/inc/hubConnect.h
- lines changed 3, context: html, text, full: html, text
don't show myHubs that don't support the current assembly #5253
- src/hg/inc/mdb.h
- lines changed 5, context: html, text, full: html, text
Added mdbPrint option to output ordered table of vars.
- src/hg/inc/versionInfo.h
- src/hg/js/hgTracks.js
- lines changed 62, context: html, text, full: html, text
make sure db is in external links (was missing from luNega links); more changes to experimental remote tracks code
- lines changed 1, context: html, text, full: html, text
disable in-place navigation if advanced javascript features is turned off (see redmine 5279)
- src/hg/lib/fileUi.c
- lines changed 14, context: html, text, full: html, text
Do not show objStatus 'rejected' or objStatus 'replaced' in hgFileUi or hgFileSearch. Do not show labels in extra metadata at the end of each downloadable file line.
- lines changed 2, context: html, text, full: html, text
Should have been 'revoked', not 'rejected'.
- lines changed 55, context: html, text, full: html, text
Fixed bai matching to second md5sum. Switched objStatus filtering to wildcard matching.
- src/hg/lib/hubConnect.c
- lines changed 13, context: html, text, full: html, text
don't show myHubs that don't support the current assembly #5253
- src/hg/lib/hui.c
- lines changed 3, context: html, text, full: html, text
Cricket noticed there was no easy way to set the default choice of a filterComp to all. Now defaults to all or, you can enter 'dimensionAchecked All'.
- src/hg/lib/mdb.c
- lines changed 80, context: html, text, full: html, text
Added mdbPrint option to output ordered table of vars.
- lines changed 1, context: html, text, full: html, text
Fix bad use of startsWith
- lines changed 6, context: html, text, full: html, text
Fixed bai matching to second md5sum. Switched objStatus filtering to wildcard matching.
- src/hg/makeDb/doc/encodeDccHg19/wgEncodeCshlLongRnaSeq.release1.notes
- lines changed 438, context: html, text, full: html, text
removed duplicated files
- lines changed 363, context: html, text, full: html, text
removed warings that aren't really warnings
- lines changed 7, context: html, text, full: html, text
I know the spikeins do not have bai files, they are not for display
- lines changed 5, context: html, text, full: html, text
Finishing the dropping of the 3 orphan files
- src/hg/makeDb/doc/encodeDccHg19/wgEncodeSydhTfbs.release1.notes
- lines changed 1572, context: html, text, full: html, text
hopefully this corrects the nfkb to nkfb error, there was a bad name change a while ago
- src/hg/makeDb/doc/encodeDccMm9/wgEncodeSydhTfbs.release2.notes
- lines changed 3, context: html, text, full: html, text
Added index.html file to be dropped.
- lines changed 115, context: html, text, full: html, text
Updated metaData and trackDb and notes files for release inorder to fall in line with Revoke Policy. To see a better explanation of what was changed refer to: Redmine #2725, note #24.
- src/hg/makeDb/doc/hg18.txt
- lines changed 26, context: html, text, full: html, text
Track #34 (dbVar for human): Split ISCA Retrospective into 3subtracks by clinical interpretation (Benign, Pathogenic, Uncertain).
Data update required code update because of changes in keywords.
- src/hg/makeDb/doc/proteins/101005.txt
- lines changed 62, context: html, text, full: html, text
(1) Removed an inaccurate sentence from the Unc/Bsu Prot track description page. (2) In the 101005.txt protein database script, added a shell variable to represent the base of the kent source tree. (3) In pbCalDistGlobal, there was an errAbort condition indicating that the number of proteins exceeded the max. number expected (10,000,000) and saying that it was time to raise the threshold. Instead, I changed the code to look at only the first 10,000,000 proteins, with the assumption that that had better be enough for estimating the distribution of amino acid properties
- src/hg/makeDb/doc/sacCer3.txt
- lines changed 3, context: html, text, full: html, text
added a comment about a table linked to growthCondition
- lines changed 1, context: html, text, full: html, text
small addition to a comment
- src/hg/makeDb/doc/ucscGenes/hg19.ucscGenes13.csh
- lines changed 72, context: html, text, full: html, text
Updates to UCSC Genes: (1) removed code to rebuild tables used by the proteome browser, now that the proteome browser is no longer used for hg19 (2) updated the code to parse the kegg tables, to adapt to what appears to be a change in format on kegg's side
- src/hg/makeDb/doc/xenTro3.txt
- lines changed 165, context: html, text, full: html, text
done with genbank and added cpgIslands and genscan
- lines changed 10, context: html, text, full: html, text
add microsatellite track
- lines changed 22, context: html, text, full: html, text
adding ucscToEnsembl table
- lines changed 38, context: html, text, full: html, text
construct download files and place in pushQ
- src/hg/makeDb/genbank/etc/align.dbs
- src/hg/makeDb/genbank/etc/hgwdev.dbs
- src/hg/makeDb/mdbUpdate/mdbPrint.c
- lines changed 18, context: html, text, full: html, text
Added mdbPrint option to output ordered table of vars.
- src/hg/makeDb/schema/all.joiner
- lines changed 14, context: html, text, full: html, text
Updated several places for rgdGene2 related IDs.
- lines changed 18, context: html, text, full: html, text
Track #5133 (dbSNP 134): added snp134 IDs to all.joiner (also correctedsome snp132 table names that changed during QA).
- src/hg/makeDb/trackDb/blastHg16KG.html
- lines changed 4, context: html, text, full: html, text
Capitalized 'BLAST'. Italicized organism name. Changed journal reference from default abstract on PubMed to direct URL to abstract on ScienceDirect.
- src/hg/makeDb/trackDb/blastHg18KG.html
- lines changed 3, context: html, text, full: html, text
Capitalized 'BLAST'. Changed journal reference from default abstract on PubMed to direct URL to abstract on ScienceDirect.
- src/hg/makeDb/trackDb/cpgIslandExt.html
- lines changed 1, context: html, text, full: html, text
Changed the journal link from the default abstract in PubMed to the direct abstract link to the ScienceDirect web site.
- lines changed 1, context: html, text, full: html, text
Corrected grammatical error
- src/hg/makeDb/trackDb/cv/alpha/cv.ra
- lines changed 70, context: html, text, full: html, text
Commenting out unused cell lines
- lines changed 2, context: html, text, full: html, text
Updating ProgFib cell line info
- lines changed 3, context: html, text, full: html, text
Adding donor ids to sorted blood cells
- lines changed 2, context: html, text, full: html, text
BioRep should not be just for transcriptome project
- lines changed 17, context: html, text, full: html, text
Returning bCStomach which has been used
- lines changed 5, context: html, text, full: html, text
Updated metadata for objects that have had antibodies renamed so the validation doesn't break. Also, haded renamed term in cv for objStatus for files that were renamed after release. Redmine #2726.
- lines changed 2, context: html, text, full: html, text
added provisional tags to 5c's cv entries
- src/hg/makeDb/trackDb/human/gwasCatalog.html
- lines changed 3, context: html, text, full: html, text
Made some minor grammatical corrections
- src/hg/makeDb/trackDb/human/hg18/wgEncodeAffyRnaChip.ra
- lines changed 1, context: html, text, full: html, text
Adding in the commented out fileSortOrder line in case we want to leak this ever
- src/hg/makeDb/trackDb/human/hg18/wgEncodeCaltechRnaSeq.new.ra
- lines changed 1, context: html, text, full: html, text
Adding in the commented out fileSortOrder line in case we want to leak this ever
- src/hg/makeDb/trackDb/human/hg18/wgEncodeCshlLongRnaSeq.ra
- lines changed 1, context: html, text, full: html, text
Adding in the commented out fileSortOrder line in case we want to leak this ever
- src/hg/makeDb/trackDb/human/hg18/wgEncodeCshlShortRnaSeq.ra
- lines changed 1, context: html, text, full: html, text
Adding in the commented out fileSortOrder line in case we want to leak this ever
- src/hg/makeDb/trackDb/human/hg18/wgEncodeGisDnaPet.ra
- lines changed 1, context: html, text, full: html, text
Adding in the commented out fileSortOrder line in case we want to leak this ever
- src/hg/makeDb/trackDb/human/hg18/wgEncodeGisPet.ra
- lines changed 1, context: html, text, full: html, text
Adding in the commented out fileSortOrder line in case we want to leak this ever
- src/hg/makeDb/trackDb/human/hg18/wgEncodeGisRnaSeq.ra
- lines changed 1, context: html, text, full: html, text
Adding in the commented out fileSortOrder line in case we want to leak this ever
- src/hg/makeDb/trackDb/human/hg18/wgEncodeHelicosRnaSeq.ra
- lines changed 1, context: html, text, full: html, text
Adding in the commented out fileSortOrder line in case we want to leak this ever
- src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaChipSeq.new.ra
- lines changed 2, context: html, text, full: html, text
Adding in the commented out fileSortOrder line in case we want to leak this ever
- src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaMethylSeq.new.ra
- lines changed 1, context: html, text, full: html, text
Adding in the commented out fileSortOrder line in case we want to leak this ever
- src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaRnaSeq.ra
- lines changed 1, context: html, text, full: html, text
Adding in the commented out fileSortOrder line in case we want to leak this ever
- src/hg/makeDb/trackDb/human/hg18/wgEncodeMapability.ra
- lines changed 1, context: html, text, full: html, text
Adding in the commented out fileSortOrder line in case we want to leak this ever
- src/hg/makeDb/trackDb/human/hg18/wgEncodeRikenCage.ra
- lines changed 1, context: html, text, full: html, text
Adding in the commented out fileSortOrder line in case we want to leak this ever
- src/hg/makeDb/trackDb/human/hg18/wgEncodeUwChIPSeq.ra
- lines changed 1, context: html, text, full: html, text
Adding in the commented out fileSortOrder line in case we want to leak this ever
- src/hg/makeDb/trackDb/human/hg18/wgEncodeUwDGF.ra
- lines changed 1, context: html, text, full: html, text
Adding in the commented out fileSortOrder line in case we want to leak this ever
- src/hg/makeDb/trackDb/human/hg18/wgEncodeYaleChIPseq.new.ra
- lines changed 1, context: html, text, full: html, text
Adding in the commented out fileSortOrder line in case we want to leak this ever
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra
- lines changed 71, context: html, text, full: html, text
Put replicate 5 in the attic and changed short labels according to Kate instructions on track 43
- lines changed 15, context: html, text, full: html, text
removed Rep5 stuff from Cshl Long, tablename and objtype=file
- lines changed 62, context: html, text, full: html, text
removed tableName from GencV7 entries
- lines changed 276, context: html, text, full: html, text
Adding the bioRep and labId to the Protocol Docs
- lines changed 78, context: html, text, full: html, text
removing 3 orphan objects, see track #43
- lines changed 53, context: html, text, full: html, text
Finishing the dropping of the 3 orphan files
- lines changed 55, context: html, text, full: html, text
reput in tablenames for junctions, that got rolled back with a bad make
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisChiaPet.ra
- lines changed 17, context: html, text, full: html, text
removing run from the file, storing in labExpId
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhHistone.ra
- lines changed 109, context: html, text, full: html, text
Willys changes to add geo accession numbers to Sydh submissions
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra
- lines changed 19, context: html, text, full: html, text
Willys changes to add geo accession numbers to Sydh submissions
- lines changed 191, context: html, text, full: html, text
hopefully this corrects the nfkb to nkfb error, there was a bad name change a while ago
- lines changed 7, context: html, text, full: html, text
updated md5sums for SYDH TFBS
- src/hg/makeDb/trackDb/human/hg19/metaDb/beta/makefile
- lines changed 1, context: html, text, full: html, text
staging CSHL Long RNA-seq on beta, redmine 43
- src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeCshlLongRnaSeq.ra
- lines changed 35525, context: html, text, full: html, text
staging CSHL Long RNA-seq on beta, redmine 43
- src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
- lines changed 1, context: html, text, full: html, text
staging CSHL Long RNA-seq on beta, redmine 43
- src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.html
- lines changed 5, context: html, text, full: html, text
Changed the min and max display, dropped the reference to pink and purple, dropped some of the color tools
- src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.ra
- lines changed 101, context: html, text, full: html, text
Put replicate 5 in the attic and changed short labels according to Kate instructions on track 43
- lines changed 107, context: html, text, full: html, text
changed shortlabels to be consistent and changed the method to handle Lab Rep in long and short, and some long label changes to be consistent
- lines changed 17, context: html, text, full: html, text
something went wrong with my last long label attempt. this one is good.
- lines changed 7, context: html, text, full: html, text
Changed the min and max display, dropped the reference to pink and purple, dropped some of the color tools
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.new.ra
- lines changed 28, context: html, text, full: html, text
revoked in the wrong trackDb, rolled back .ra revoked in .new.ra
- lines changed 4, context: html, text, full: html, text
the E2f6 > E2f6sc22823 didn't make it to the .new.ra
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.ra
- lines changed 14, context: html, text, full: html, text
revoked in the wrong trackDb, rolled back .ra revoked in .new.ra
- lines changed 14, context: html, text, full: html, text
prety sure I made the same mistake with leaking out a revoke for rep 1 on august 8's commit, re adding it now
- src/hg/makeDb/trackDb/human/hg19/wgEncodeProtGenoSuper.html
- lines changed 5, context: html, text, full: html, text
removing commas and adding some periods, redmine #4944
- lines changed 10, context: html, text, full: html, text
rewriting confusing sentences
- src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyAlbanyGeneSt.new.html
- lines changed 7, context: html, text, full: html, text
changing single view wording - since not a multi-view, i think it's best not to mention views at all; changed release month; slight wording change to release notes ('the' to 'an')
- src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyAlbanyGeneSt.new.ra
- lines changed 6, context: html, text, full: html, text
Getting rid of the - in H1-hESC
- src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyAlbanyGeneSt.ra
- lines changed 3, context: html, text, full: html, text
I meant to make these changes on .new.ra
- src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.new.ra
- lines changed 5425, context: html, text, full: html, text
merged release 1 settings with release 2 stub
- lines changed 2, context: html, text, full: html, text
corrected some filtering options that was blocking checkboxes
- src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.ra
- lines changed 18, context: html, text, full: html, text
hopefully this corrects the nfkb to nkfb error, there was a bad name change a while ago
- lines changed 28, context: html, text, full: html, text
turned on defaults on SYDH TFBS Rad21 Pol2 TBP and CHD@ on K562 and GM12878
- lines changed 2, context: html, text, full: html, text
corrected some filtering options that was blocking checkboxes
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProt.html
- lines changed 3, context: html, text, full: html, text
(1) Removed an inaccurate sentence from the Unc/Bsu Prot track description page. (2) In the 101005.txt protein database script, added a shell variable to represent the base of the kent source tree. (3) In pbCalDistGlobal, there was an errAbort condition indicating that the number of proteins exceeded the max. number expected (10,000,000) and saying that it was time to raise the threshold. Instead, I changed the code to look at only the first 10,000,000 proteins, with the assumption that that had better be enough for estimating the distribution of amino acid properties
- lines changed 5, context: html, text, full: html, text
Addressing some QA comments on this track details page
- lines changed 8, context: html, text, full: html, text
Reordered the extra bed6+ fields to make them consistent with the order in which they appear in the schema
- lines changed 105, context: html, text, full: html, text
Cleaning up a conflicted merge
- lines changed 11, context: html, text, full: html, text
Set the useScore .ra file variable to render the uncBsuProt track items in grayscale, according to the score. Updated the track description page to reflect this change
- lines changed 1, context: html, text, full: html, text
fixing typo (missing e at the end of sequence) that galt found, redmine #141
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProt.new.ra
- lines changed 1, context: html, text, full: html, text
Set the useScore .ra file variable to render the uncBsuProt track items in grayscale, according to the score. Updated the track description page to reflect this change
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProt.ra
- lines changed 1, context: html, text, full: html, text
Set the useScore .ra file variable to render the uncBsuProt track items in grayscale, according to the score. Updated the track description page to reflect this change
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUw5C.html
- src/hg/makeDb/trackDb/human/iscaRetrospectiveComposite.html
- lines changed 123, context: html, text, full: html, text
Track #34 (dbVar for human): Split ISCA Retrospective into 3subtracks by clinical interpretation (Benign, Pathogenic, Uncertain).
Data update required code update because of changes in keywords.
- src/hg/makeDb/trackDb/human/trackDb.ra
- lines changed 48, context: html, text, full: html, text
Track #34 (dbVar for human): Split ISCA Retrospective into 3subtracks by clinical interpretation (Benign, Pathogenic, Uncertain).
Data update required code update because of changes in keywords.
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhTfbs.ra
- lines changed 797, context: html, text, full: html, text
Updated metaData and trackDb and notes files for release inorder to fall in line with Revoke Policy. To see a better explanation of what was changed refer to: Redmine #2725, note #24.
- lines changed 19, context: html, text, full: html, text
Updated metadata for objects that have had antibodies renamed so the validation doesn't break. Also, haded renamed term in cv for objStatus for files that were renamed after release. Redmine #2726.
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/wgEncodeSydhTfbs.ra
- lines changed 3136, context: html, text, full: html, text
staging SYDH TFBS on beta, redmine# 2726
- lines changed 797, context: html, text, full: html, text
updating the metaDb to reflect the new ENCODE revoke policy, redmine# 2726
- lines changed 19, context: html, text, full: html, text
updating the metaDb to reflect the new ENCODE revoke policy (forgot to do a pull to reflect the latest changes so here goes round 2), redmine# 2726
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/public/wgEncodeSydhTfbs.ra
- lines changed 3801, context: html, text, full: html, text
releasing SYDH TFBS Redmine# 2726
- src/hg/makeDb/trackDb/mouse/mm9/trackDb.wgEncode.ra
- lines changed 2, context: html, text, full: html, text
staging SYDH TFBS on beta, redmine# 2726
- lines changed 2, context: html, text, full: html, text
releasing SYDH TFBS Redmine# 2726
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhTfbs.html
- lines changed 33, context: html, text, full: html, text
releasing SYDH TFBS Redmine# 2726
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhTfbs.new.html
- lines changed 4, context: html, text, full: html, text
changed release date, replaced character with a ascii equivilant, removed non breaking spaces and replaced with <p>
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhTfbs.newR2.ra
- lines changed 4, context: html, text, full: html, text
Updated metaData and trackDb and notes files for release inorder to fall in line with Revoke Policy. To see a better explanation of what was changed refer to: Redmine #2725, note #24.
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhTfbs.ra
- lines changed 728, context: html, text, full: html, text
releasing SYDH TFBS Redmine# 2726
- src/hg/makeDb/trackDb/nestedRepeats.html
- lines changed 3, context: html, text, full: html, text
Changed the journal links from the default abstract in PubMed to the direct abstract link to the ScienceDirect web site.
- src/hg/makeDb/trackDb/rmsk.html
- lines changed 3, context: html, text, full: html, text
Changed the journal links from the default abstract in PubMed to the direct abstract link to the ScienceDirect web site.
- src/hg/makeDb/trackDb/sacCer/blastHg18KG.html
- lines changed 3, context: html, text, full: html, text
Capitalized 'BLAST'. Replaced journal link to PubMed with URL to abstract on the ScienceDirect web site.
- src/hg/makeDb/trackDb/sacCer/sacCer2/gap.html
- lines changed 1, context: html, text, full: html, text
Removed unnecessary parentheses
- src/hg/makeDb/trackDb/sacCer/sacCer2/gold.html
- lines changed 1, context: html, text, full: html, text
Added italics to the organism name
- lines changed 1, context: html, text, full: html, text
Removed unnecessary parentheses
- src/hg/makeDb/trackDb/sacCer/sacCer3/gap.html
- lines changed 1, context: html, text, full: html, text
Removed unnecessary parentheses
- src/hg/makeDb/trackDb/sacCer/sgdClone.html
- lines changed 3, context: html, text, full: html, text
Corrected link to Stanford server on description page
- lines changed 3, context: html, text, full: html, text
Steve fixed link to Stanford ... I'm commiting for him.
- src/hg/makeDb/trackDb/sacCer/trackDb.ra
- lines changed 4, context: html, text, full: html, text
add searching for transRegCodeProbe
- src/hg/makeDb/trackDb/sacCer/transRegCode.html
- lines changed 6, context: html, text, full: html, text
Fixed grammatical errors. Journal article had 20 authors, but only 5 were listed on the page. Changed to 10. Journal link went to PubMed abstract, but free article was available, so changed URL to link straight to the free article.
- lines changed 1, context: html, text, full: html, text
Added hyphen to 'well conserved'.
- lines changed 1, context: html, text, full: html, text
Removed comma before 'et al' in transRegCode.html. Fixed grammatical errors in transRegCodeProbe.html. Journal article had 20 authors, but only 5 listed. Changed to 10. Journal link was to PubMed abstract, but free article available. Changed URL to point to the free article.
- lines changed 1, context: html, text, full: html, text
Changed link to journal article to the direct URL to the Nature web site
- lines changed 1, context: html, text, full: html, text
Journal article on Nature is not free to the public. Changed the URL back to the full text article on PubMed Central.
- lines changed 1, context: html, text, full: html, text
Changed the journal link to point to the abstract on Nature's web site
- src/hg/makeDb/trackDb/sacCer/transRegCodeProbe.html
- lines changed 3, context: html, text, full: html, text
Removed comma before 'et al' in transRegCode.html. Fixed grammatical errors in transRegCodeProbe.html. Journal article had 20 authors, but only 5 listed. Changed to 10. Journal link was to PubMed abstract, but free article available. Changed URL to point to the free article.
- lines changed 1, context: html, text, full: html, text
Changed link to journal article to the direct URL to the Nature web site
- lines changed 1, context: html, text, full: html, text
Journal article on Nature is not free to the public. Changed the URL back to the full text article on PubMed Central.
- lines changed 1, context: html, text, full: html, text
Changed the journal link to point to the abstract on Nature's web site
- src/hg/makeDb/trackDb/trackDb.ra
- lines changed 32, context: html, text, full: html, text
Track #5133 (dbSNP 134): adding search specs.
- src/hg/oneShot/doOmimAv/doOmimAv.c
- lines changed 7, context: html, text, full: html, text
Corrected replacement string processing logic to pick up only the first AA replacement string.
- src/hg/protein/pbCalDistGlobal/pbCalDistGlobal.c
- lines changed 4, context: html, text, full: html, text
(1) Removed an inaccurate sentence from the Unc/Bsu Prot track description page. (2) In the 101005.txt protein database script, added a shell variable to represent the base of the kent source tree. (3) In pbCalDistGlobal, there was an errAbort condition indicating that the number of proteins exceeded the max. number expected (10,000,000) and saying that it was time to raise the threshold. Instead, I changed the code to look at only the first 10,000,000 proteins, with the assumption that that had better be enough for estimating the distribution of amino acid properties
- src/hg/utils/cpAndLinkToResourceFiles.pl
- lines changed 83, context: html, text, full: html, text
use cgi versioned copies of files instead of softlinks for production files (see redmine 5104)
- src/hg/utils/pslMap/README
- lines changed 3, context: html, text, full: html, text
output unmapped psls in info file
- src/hg/utils/pslMap/pslMap.c
- lines changed 24, context: html, text, full: html, text
output unmapped psls in info file
- src/hg/utils/pslMap/tests/expected/mrnaMapOver.mapinfo
- lines changed 1, context: html, text, full: html, text
output unmapped psls in info file
- src/hg/utils/pslMap/tests/expected/mrnaMapOverSwap.mapinfo
- lines changed 1, context: html, text, full: html, text
output unmapped psls in info file
- src/hg/utils/pslMap/tests/input/mrnaToMm6.psl
- lines changed 1, context: html, text, full: html, text
output unmapped psls in info file
- src/hg/utils/pslMap/tests/makefile
- lines changed 1, context: html, text, full: html, text
output unmapped psls in info file
- src/hg/utils/pslMap/usage.txt
- lines changed 1, context: html, text, full: html, text
output unmapped psls in info file
- src/product/scripts/updateHtml.sh
- lines changed 10, context: html, text, full: html, text
add rsync of cgi-bin/encode/ directory
- src/utils/bedToBigBed/bedToBigBed.c
- lines changed 14, context: html, text, full: html, text
allow for an R,G,B field (normally field 9). #5287
- src/utils/qa/weeklybld/buildEnv.csh
- lines changed: 66096
- files changed: 375