All File Changes

v265_base to v266_preview (2012-03-27 to 2012-04-10) v266

• README
  • lines changed 119, context: html, text, full: html, text
    Splitting up README to populate higher level README.
  • lines changed 3, context: html, text, full: html, text
    Adding more information about source tree structure and revisiting list of useful library modules.
• python/lib/ucscgenomics/cv.py
  • lines changed 329, context: html, text, full: html, text
    bugfixes for ra and mdb to fix an ordering issue for mdb file values. Also added new changes to cv validation
  • lines changed 95, context: html, text, full: html, text
    added encode.py to store global constants and other encode stuff, and made all other libraries interface correctly with it
• python/lib/ucscgenomics/encode.py
  • lines changed 115, context: html, text, full: html, text
    added encode.py to store global constants and other encode stuff, and made all other libraries interface correctly with it
• python/lib/ucscgenomics/geo.py
  • lines changed 30, context: html, text, full: html, text
    added encode.py to store global constants and other encode stuff, and made all other libraries interface correctly with it
• python/lib/ucscgenomics/mdb.py
  • lines changed 64, context: html, text, full: html, text
    bugfixes for ra and mdb to fix an ordering issue for mdb file values. Also added new changes to cv validation
  • lines changed 77, context: html, text, full: html, text
    added encode.py to store global constants and other encode stuff, and made all other libraries interface correctly with it
• python/lib/ucscgenomics/ordereddict.py
  • lines changed 9, context: html, text, full: html, text
    bugfixes for ra and mdb to fix an ordering issue for mdb file values. Also added new changes to cv validation
• python/lib/ucscgenomics/qa.py
  • lines changed 19, context: html, text, full: html, text
    Made callHgsql function.
  • lines changed 39, context: html, text, full: html, text
    Changed hgsql calls to use callHgsql function, except for the one in countPerChrom, which needs more work before changing. Moved callHgsql to top of file.
• python/lib/ucscgenomics/ra.py
  • lines changed 9, context: html, text, full: html, text
    bugfixes for ra and mdb to fix an ordering issue for mdb file values. Also added new changes to cv validation
• python/lib/ucscgenomics/track.py
  • lines changed 114, context: html, text, full: html, text
    added encode.py to store global constants and other encode stuff, and made all other libraries interface correctly with it
• python/programs/mkGeoPkg/mkGeoPkg
  • lines changed 229, context: html, text, full: html, text
    added encode.py to store global constants and other encode stuff, and made all other libraries interface correctly with it
• python/style.txt
  • lines changed 2, context: html, text, full: html, text
    Fixed some typo's.
  • lines changed 1, context: html, text, full: html, text
    Removing 'rare' for the acronym case, since it's not so rare.
• src/README
  • lines changed 34, context: html, text, full: html, text
    Updating style guide a little to allow // comments mostly.
  • lines changed 23, context: html, text, full: html, text
    Adding recommendations against long lines and long functions.
  • lines changed 4, context: html, text, full: html, text
    Minor edits.
  • lines changed 18, context: html, text, full: html, text
    More wordsmithing
  • lines changed 27, context: html, text, full: html, text
    Adding a section on modules.
  • lines changed 116, context: html, text, full: html, text
    Splitting up README to populate higher level README.
  • lines changed 52, context: html, text, full: html, text
    Adding more information about source tree structure and revisiting list of useful library modules.
• src/TAGS
  • lines changed 18929, context: html, text, full: html, text
    added TAGS for kent library (c/o markd)
  • lines changed 18929, context: html, text, full: html, text
    more work on annoGratorGpVar and gpFx libraries.
• src/hg/autoDtd/autoDtd.c
  • lines changed 463, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 463, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/hg/autoDtd/doTest
  • lines changed 13, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 13, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/hg/autoDtd/makefile
  • lines changed 18, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 18, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/hg/autoDtd/test/chado/expected.atree
  • lines changed 77, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 77, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/hg/autoDtd/test/chado/expected.dtd
  • lines changed 183, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 183, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/hg/autoDtd/test/chado/expected.stats
  • lines changed 190, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 190, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/hg/autoDtd/test/chado/expected.tree
  • lines changed 77, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 77, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/hg/autoDtd/test/chado/in.xml
  • lines changed 1017, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 1017, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/hg/autoDtd/test/hotnews/expected.atree
  • lines changed 18, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 18, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/hg/autoDtd/test/hotnews/expected.dtd
  • lines changed 58, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 58, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/hg/autoDtd/test/hotnews/expected.stats
  • lines changed 49, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 49, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/hg/autoDtd/test/hotnews/expected.tree
  • lines changed 18, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 18, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/hg/autoDtd/test/hotnews/in.xml
  • lines changed 77, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 77, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/hg/autoDtd/test/shapes/expected.atree
  • lines changed 4, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 4, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/hg/autoDtd/test/shapes/expected.dtd
  • lines changed 23, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 23, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/hg/autoDtd/test/shapes/expected.stats
  • lines changed 22, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 22, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/hg/autoDtd/test/shapes/expected.tree
  • lines changed 4, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 4, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/hg/autoDtd/test/shapes/in.xml
  • lines changed 16, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 16, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/hg/autoSql/.gitignore
  • lines changed 1, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 1, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/hg/autoSql/autoSql.c
  • lines changed 128, context: html, text, full: html, text
    First cut of Django output for autoSql.
  • lines changed 1946, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 1946, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/hg/autoSql/autoSql.doc
  • lines changed 312, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 312, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/hg/autoSql/commonSh.c
  • lines changed 39, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 39, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/hg/autoSql/doc.as
  • lines changed 17, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 17, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/hg/autoSql/doc2.as
  • lines changed 33, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 33, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/hg/autoSql/eztok.c
  • lines changed 71, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 71, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/hg/autoSql/eztok.h
  • lines changed 18, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 18, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/hg/autoSql/makefile
  • lines changed 29, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 29, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/hg/autoSql/tests/.gitignore
  • lines changed 5, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 5, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/hg/autoSql/tests/dbLinkTest.c
  • lines changed 326, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 326, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/hg/autoSql/tests/expected/dbLinkTest.out
  • lines changed 5, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 5, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/hg/autoSql/tests/expected/doc.c
  • lines changed 336, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 336, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/hg/autoSql/tests/expected/doc.h
  • lines changed 135, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 135, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/hg/autoSql/tests/expected/doc.sql
  • lines changed 24, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 24, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/hg/autoSql/tests/expected/doc2.c
  • lines changed 622, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 622, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/hg/autoSql/tests/expected/doc2.h
  • lines changed 200, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 200, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/hg/autoSql/tests/expected/doc2.sql
  • lines changed 14, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 14, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/hg/autoSql/tests/expected/hardTest.c
  • lines changed 447, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 447, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/hg/autoSql/tests/expected/hardTest.h
  • lines changed 120, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 120, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/hg/autoSql/tests/expected/hardTest.sql
  • lines changed 26, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 26, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/hg/autoSql/tests/expected/jsonTest.out
  • lines changed 16, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 16, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/hg/autoSql/tests/expected/mainTest.c
  • lines changed 859, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 859, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/hg/autoSql/tests/expected/mainTest.h
  • lines changed 287, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 287, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/hg/autoSql/tests/expected/mainTest.sql
  • lines changed 33, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 33, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/hg/autoSql/tests/expected/newTest.c
  • lines changed 434, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 434, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/hg/autoSql/tests/expected/newTest.err
  • lines changed 2, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 2, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/hg/autoSql/tests/expected/newTest.h
  • lines changed 140, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 140, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/hg/autoSql/tests/expected/newTest.sql
  • lines changed 21, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 21, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/hg/autoSql/tests/expected/polyTest.c
  • lines changed 428, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 428, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/hg/autoSql/tests/expected/polyTest.h
  • lines changed 157, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 157, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/hg/autoSql/tests/expected/polyTest.sql
  • lines changed 23, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 23, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/hg/autoSql/tests/expected/simpleTest.c
  • lines changed 1037, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 1037, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/hg/autoSql/tests/expected/simpleTest.h
  • lines changed 399, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 399, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/hg/autoSql/tests/expected/simpleTest.sql
  • lines changed 12, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 12, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/hg/autoSql/tests/expected/symColsTest.tab
  • lines changed 6, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 6, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/hg/autoSql/tests/expected/symTest.c
  • lines changed 134, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 134, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/hg/autoSql/tests/expected/symTest.err
  • lines changed 0, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 0, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/hg/autoSql/tests/expected/symTest.h
  • lines changed 75, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 75, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/hg/autoSql/tests/expected/symTest.sql
  • lines changed 13, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 13, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/hg/autoSql/tests/expected/testHarness.out
  • lines changed 17, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 17, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/hg/autoSql/tests/input/doc.as
  • lines changed 17, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 17, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/hg/autoSql/tests/input/doc2.as
  • lines changed 33, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 33, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/hg/autoSql/tests/input/hardTest.as
  • lines changed 28, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 28, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/hg/autoSql/tests/input/mainTest.as
  • lines changed 51, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 51, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/hg/autoSql/tests/input/newTest.as
  • lines changed 22, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 22, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/hg/autoSql/tests/input/polyTest.as
  • lines changed 25, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 25, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/hg/autoSql/tests/input/simpleTest.as
  • lines changed 66, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 66, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/hg/autoSql/tests/input/symColsTest.tab
  • lines changed 6, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 6, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/hg/autoSql/tests/input/symTest.as
  • lines changed 8, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 8, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/hg/autoSql/tests/jsonTest.c
  • lines changed 114, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 114, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/hg/autoSql/tests/makefile
  • lines changed 118, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 118, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/hg/autoSql/tests/testHarness.c
  • lines changed 193, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 193, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/hg/autoSql/tests/testSymCols.c
  • lines changed 117, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 117, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/hg/autoXml/autoXml.c
  • lines changed 724, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 724, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/hg/autoXml/autoXml.doc
  • lines changed 190, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 190, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/hg/autoXml/dasBed.dtdx
  • lines changed 43, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 43, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/hg/autoXml/doTest
  • lines changed 5, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 5, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/hg/autoXml/makefile
  • lines changed 1, context: html, text, full: html, text
    Removing dependence on src/hg/lib
  • lines changed 17, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 17, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/hg/autoXml/polygon.dtdx
  • lines changed 9, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 9, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/hg/autoXml/t/makefile
  • lines changed 14, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 14, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/hg/autoXml/t/t.c
  • lines changed 255, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 255, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/hg/autoXml/test.dtdx
  • lines changed 36, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 36, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/hg/autoXml/test/dasGff/dasGff.dtd
  • lines changed 45, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 45, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/hg/autoXml/test/dasGff/expected/dasGff.c
  • lines changed 1281, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 1281, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/hg/autoXml/test/dasGff/expected/dasGff.h
  • lines changed 387, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 387, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/hg/autoXml/test/polygon/expected/polygon.c
  • lines changed 241, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 241, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/hg/autoXml/test/polygon/expected/polygon.h
  • lines changed 89, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 89, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/hg/autoXml/test/polygon/polygon.dtd
  • lines changed 11, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 11, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/hg/encode/DAFs/3.0/hg19/wgEncodeCaltechRnaSeq.daf
  • lines changed 6, context: html, text, full: html, text
    Improving dafs
• src/hg/encode/DAFs/3.0/hg19/wgEncodeCshlLongRnaSeq.daf
  • lines changed 5, context: html, text, full: html, text
    Improving dafs
• src/hg/encode/DAFs/3.0/hg19/wgEncodeCshlShortRnaSeq.daf
  • lines changed 2, context: html, text, full: html, text
    Improving dafs
• src/hg/encode/DAFs/3.0/hg19/wgEncodeGisRnaPet.daf
  • lines changed 16, context: html, text, full: html, text
    Improving dafs
• src/hg/encode/DAFs/3.0/hg19/wgEncodeRikenCage.daf
  • lines changed 6, context: html, text, full: html, text
    Improving dafs
• src/hg/encode/DAFs/3.0/hg19/wgEncodeUncBsuProt.daf
  • lines changed 23, context: html, text, full: html, text
    create new views for proteomGenomics experiments for search results on genome database, genecode annotation, modified peptides, bigbed file format
  • lines changed 1, context: html, text, full: html, text
    change version number from 2.0 to 3.1
  • lines changed 1, context: html, text, full: html, text
    change dafVersion from 2.0 to 3.1
  • lines changed 1, context: html, text, full: html, text
    change dafVersion from 3.1 to 3.0 as the former gets an error when upload
• src/hg/encode/DAFs/3.0/mm9/wgEncodeCshlLongRnaSeq.daf
  • lines changed 25, context: html, text, full: html, text
    Added in changes to the DAF.
• src/hg/encode/DAFs/3.0/mm9/wgEncodeFsuRepliSeq.daf
  • lines changed 44, context: html, text, full: html, text
    First pass of Mouse DAF for FSU Repli-seq. Redmine #6627.
  • lines changed 1, context: html, text, full: html, text
    incorrect assembly in daf for mouse
• src/hg/encode/DAFs/3.0/mm9/wgEncodePsuRnaSeq.daf
  • lines changed 14, context: html, text, full: html, text
    Fixed DAF for track. Redmine #107.
  • lines changed 2, context: html, text, full: html, text
    Added other terms in DDF for track. Redmine #107.
• src/hg/encode/DAFs/3.0/mm9/wgEncodeSydhRnaSeq.daf
  • lines changed 17, context: html, text, full: html, text
    Updated DAF for new Signal data.
• src/hg/encode/antibodyWikiParser/antibodyWikiParser.py
  • lines changed 1, context: html, text, full: html, text
    Changed shebang to the correct syntax to be used for python code.
• src/hg/encode/encodeLoad/installSqlSchemas.pl
  • lines changed 23, context: html, text, full: html, text
    removed old bigBedTypes support (tagalign stuff), makes Tim's life easier
• src/hg/encode/encodeMkChangeNotes/encodeMkChangeNotes
  • lines changed 1, context: html, text, full: html, text
    changed hash bangs over to new styles
• src/hg/encode/encodeQaCheckHgdownloadFiles/encodeQaCheckHgdownloadFiles
  • lines changed 1, context: html, text, full: html, text
    changed hash bangs over to new styles
• src/hg/encode/encodeQaInit/encodeQaInit
  • lines changed 1, context: html, text, full: html, text
    changed hash bangs over to new styles
• src/hg/encode/encodeReport/gencodeStats
  • lines changed 18, context: html, text, full: html, text
    Fixed bug in code and found that querying Tag table for the PAR tag is a better way of identifying genes in the PAR regions.
  • lines changed 5, context: html, text, full: html, text
    Added code to calculate number of PAR genes using PAR tag. Removed some debugging code.
• src/hg/encode/encodeValidate/doEncodeValidate.pl
  • lines changed 1, context: html, text, full: html, text
    added insertLength to the or None pile
  • lines changed 17, context: html, text, full: html, text
    Removed the validateSAM since there never has been a validateFiles option for SAM. If this funtion were ever called, it would fail, and it is never alled anyehrew in the code
  • lines changed 31, context: html, text, full: html, text
    Removing validateBowtie. This is code to validate a format that the coder defined as unknown. We are not getting data of this form nor can I find evidence that we have any
  • lines changed 15, context: html, text, full: html, text
    Cleaning up the dispatch table
  • lines changed 5, context: html, text, full: html, text
    corrected some syntax errors, and changed conditional on bedRnaElements to allow a dot in the 8th field
  • lines changed 6, context: html, text, full: html, text
    added in conditional to always use the sex from ddf regardless of if it's a tissue or not
• src/hg/encode/qaAddTrackReferences/qaAddTrackReferences
  • lines changed 10, context: html, text, full: html, text
    some minor updates, changed how html is outputted, and all authors are used for alphabetizaio instead of just first
  • lines changed 26, context: html, text, full: html, text
    cleaned up the pubmed central path a bit
  • lines changed 1, context: html, text, full: html, text
    changed hash bangs over to new styles
  • lines changed 6, context: html, text, full: html, text
    changed variable name to be more descriptive, changed errors to print to stderr
• src/hg/encode/qaEncodeTracks2/qaEncodeTracks2
  • lines changed 1, context: html, text, full: html, text
    changed hashbang to new standard
• src/hg/encode/qaUpdateMetadata/qaUpdateMetadata
  • lines changed 1, context: html, text, full: html, text
    changed hash bangs over to new styles
• src/hg/encode/raDiff/raDiff
  • lines changed 1, context: html, text, full: html, text
    changed hash bangs over to new styles
• src/hg/encode/raMerge/raMerge
  • lines changed 1, context: html, text, full: html, text
    changed hash bangs over to new styles
• src/hg/encode/validateFiles/validateFilesUsage
  • lines changed 73, context: html, text, full: html, text
    Incorporating Galt's Changes and suggestion a better format
• src/hg/hgGateway/hgGateway.c
  • lines changed 29, context: html, text, full: html, text
    replace use of SUPPORT_EURONODE with geoMirrorEnabled()
  • lines changed 23, context: html, text, full: html, text
    redirect code has gotten pretty long, so I moved it out of main
• src/hg/hgTables/filterFields.c
  • lines changed 2, context: html, text, full: html, text
    made button text lower case in two places to conform to nearly all other Table Browser buttons
• src/hg/hgTracks/bedTrack.c
  • lines changed 7, context: html, text, full: html, text
    fix #7505 by adding a track handler for the pesky broken track
• src/hg/hgTracks/hgTracks.c
  • lines changed 1, context: html, text, full: html, text
    taking back menubar change of commit 0513e85cc01843ecc411b86dfce9180a8d1acf37
  • lines changed 2, context: html, text, full: html, text
    removing right-click sentence from pdf export page
• src/hg/hgTracks/hgTracks.h
  • lines changed 3, context: html, text, full: html, text
    fix #7505 by adding a track handler for the pesky broken track
• src/hg/hgTracks/simpleTracks.c
  • lines changed 38, context: html, text, full: html, text
    fixing performance issue with itemName/mapItem in squish/dense mode, loading extra fields now lazily in itemName/mapItem instead of loadItems
  • lines changed 1, context: html, text, full: html, text
    fix #7505 by adding a track handler for the pesky broken track
• src/hg/hgc/pubs.c
  • lines changed 28, context: html, text, full: html, text
    adding elsevier outlinks for sciverse app to hgc publications page
  • lines changed 35, context: html, text, full: html, text
    handling case of transmapped protein alignments
  • lines changed 16, context: html, text, full: html, text
    handling split codons and reverse strands
  • lines changed 21, context: html, text, full: html, text
    moving link to top of table
• src/hg/htdocs/ENCODE/dataMatrix/dataMatrix.css
  • lines changed 3, context: html, text, full: html, text
    Fixes to support floating column header on IE
  • lines changed 1, context: html, text, full: html, text
    Change cursor to hand when moused over experimentcells in matrix and rows in summary. (QA Item 21)
• src/hg/htdocs/ENCODE/dataMatrix/dataSummary.css
  • lines changed 1, context: html, text, full: html, text
    Change cursor to hand when moused over experimentcells in matrix and rows in summary. (QA Item 21)
• src/hg/htdocs/ENCODE/dataMatrix/encodeChipMatrixHuman.html
  • lines changed 1, context: html, text, full: html, text
    Fixes to support floating column header on IE
• src/hg/htdocs/ENCODE/dataMatrix/encodeChipMatrixInclude.html
  • lines changed 3, context: html, text, full: html, text
    1. Open header links to CV target window (QA item 25) 2. Fix IE vertical label problem
• src/hg/htdocs/ENCODE/dataMatrix/encodeDataMatrixHuman.html
  • lines changed 1, context: html, text, full: html, text
    Fixes to support floating column header on IE
• src/hg/htdocs/ENCODE/dataMatrix/encodeDataMatrixInclude.html
  • lines changed 1, context: html, text, full: html, text
    Fixes to support floating column header on IE
  • lines changed 2, context: html, text, full: html, text
    1. Open header links to CV target window (QA item 25) 2. Fix IE vertical label problem
• src/hg/htdocs/ENCODE/dataMatrix/encodeDataSummaryHuman.html
  • lines changed 2, context: html, text, full: html, text
    IE prefers DOCTYPE earlier, so move out of include file
• src/hg/htdocs/ENCODE/dataMatrix/encodeDataSummaryInclude.html
  • lines changed 1, context: html, text, full: html, text
    IE prefers DOCTYPE earlier, so move out of include file
• src/hg/htdocs/ENCODE/index.html
  • lines changed 4, context: html, text, full: html, text
    Redo -- this is the intended page with new links for Data Matrix
• src/hg/htdocs/ENCODE/pubs.html
  • lines changed 410, context: html, text, full: html, text
    Quarterly ENCODE portal update (redmine #7513)
  • lines changed 159, context: html, text, full: html, text
    Remove spurious nofollow property from links. Added unintentionally by qaAddTrackReferences
• src/hg/htdocs/FAQ/FAQformat.html
  • lines changed 3, context: html, text, full: html, text
    adding '(-log10)' to the peaks
• src/hg/htdocs/images/highlight.png
  • lines changed 0, context: html, text, full: html, text
    add highlighting png copied from http://cdn1.iconfinder.com/data/icons/CrystalClear/32x32/apps/highlight.png (GNU license) - #709
• src/hg/htdocs/makefile
  • lines changed 1, context: html, text, full: html, text
    Finished tRNA Genes track for mm10
• src/hg/inc/annoGrateWig.h
  • lines changed 11, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Tool): Added annoStreamWig and annoGrateWig,which led to some significant changes: annoRow is now polymorphic (words[] vs. wig float[]), annoFilter has a new function to apply filter(s) to a single number, and annoFormatTab can print out per-base wiggle values or average wiggle values (hardcoded to do per-base until a real config option is added). One puny test case was verified against mysql & table browser output.
• src/hg/inc/annoGratorGpVar.h
  • lines changed 23, context: html, text, full: html, text
    start on genepred / variant annoGrator. #6152
  • lines changed 12, context: html, text, full: html, text
    more work on annoGratorGpVar and gpFx libraries.
• src/hg/inc/annoStreamDb.h
  • lines changed 5, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Tool): instead of having a callercreate the sql connection outside of annoStreamDb, and have to remember not to share it, just allocate the connection inside annoStreamDb. This introduces a dependency on hdb, but I guess that's inevitable. :)
• src/hg/inc/annoStreamWig.h
  • lines changed 11, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Tool): Added annoStreamWig and annoGrateWig,which led to some significant changes: annoRow is now polymorphic (words[] vs. wig float[]), annoFilter has a new function to apply filter(s) to a single number, and annoFormatTab can print out per-base wiggle values or average wiggle values (hardcoded to do per-base until a real config option is added). One puny test case was verified against mysql & table browser output.
• src/hg/inc/cart.h
  • lines changed 3, context: html, text, full: html, text
    replace use of SUPPORT_EURONODE with geoMirrorEnabled()
• src/hg/inc/geoMirror.h
  • lines changed 12, context: html, text, full: html, text
    add support code for geographic based mirroring (#3000)
• src/hg/inc/gpFx.h
  • lines changed 28, context: html, text, full: html, text
    more work on annoGratorGpVar and gpFx libraries.
• src/hg/inc/wiggle.h
  • lines changed 19, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Tool): Added annoStreamWig and annoGrateWig,which led to some significant changes: annoRow is now polymorphic (words[] vs. wig float[]), annoFilter has a new function to apply filter(s) to a single number, and annoFormatTab can print out per-base wiggle values or average wiggle values (hardcoded to do per-base until a real config option is added). One puny test case was verified against mysql & table browser output.
• src/hg/js/encodeChipMatrix.js
  • lines changed 5, context: html, text, full: html, text
    Fixes to support floating column header on IE
  • lines changed 3, context: html, text, full: html, text
    Add header links for Antibody Targets (except for IE, where special handling of vertical headers generates inner div so additional work would be required to implement)
• src/hg/js/encodeDataMatrix.js
  • lines changed 6, context: html, text, full: html, text
    Fixes to support floating column header on IE
• src/hg/js/encodeDataSummary.js
  • lines changed 10, context: html, text, full: html, text
    Giving up on IE7 matrix display. Just show data summary
• src/hg/js/encodeMatrix.js
  • lines changed 2, context: html, text, full: html, text
    Add header links for Antibody Targets (except for IE, where special handling of vertical headers generates inner div so additional work would be required to implement)
• src/hg/js/encodeProject.js
  • lines changed 5, context: html, text, full: html, text
    Giving up on IE7 matrix display. Just show data summary
• src/hg/js/hgTracks.js
  • lines changed 54, context: html, text, full: html, text
    code cleanup and refactoring and remove some dead code
  • lines changed 13, context: html, text, full: html, text
    making pubs subtracks configurable, tdb changes + thanks to tim for help with javascript changes
• src/hg/js/utils.js
  • lines changed 1, context: html, text, full: html, text
    Removed tissueSourceType otherTerms.html link as the term is not present on the page. Redmine #7100.
• src/hg/lib/annoGrateWig.c
  • lines changed 78, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Tool): Added annoStreamWig and annoGrateWig,which led to some significant changes: annoRow is now polymorphic (words[] vs. wig float[]), annoFilter has a new function to apply filter(s) to a single number, and annoFormatTab can print out per-base wiggle values or average wiggle values (hardcoded to do per-base until a real config option is added). One puny test case was verified against mysql & table browser output.
  • lines changed 1, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Tool): Added annoStreamVcf, whichled to yet more significant changes to annoRow: instead of every row declaring its type and annoRow{Free,Clone} taking a numCols argument that is meaningless for wig, now annoRow{Free,Clone} take the row's source annoStreamer as an argument. The annoStreamer now has public members (rowType and numCols) that provide all information needed about the row. annoStreamer constructors need to set rowType.
• src/hg/lib/annoGratorGpVar.c
  • lines changed 133, context: html, text, full: html, text
    start on genepred / variant annoGrator. #6152
  • lines changed 54, context: html, text, full: html, text
    more work on annoGratorGpVar and gpFx libraries.
• src/hg/lib/annoStreamDb.c
  • lines changed 14, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Tool): instead of having a callercreate the sql connection outside of annoStreamDb, and have to remember not to share it, just allocate the connection inside annoStreamDb. This introduces a dependency on hdb, but I guess that's inevitable. :)
  • lines changed 3, context: html, text, full: html, text
    bugfix for #6152: was skipping the bin column twice, oops.
  • lines changed 1, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Tool): Added annoStreamVcf, whichled to yet more significant changes to annoRow: instead of every row declaring its type and annoRow{Free,Clone} taking a numCols argument that is meaningless for wig, now annoRow{Free,Clone} take the row's source annoStreamer as an argument. The annoStreamer now has public members (rowType and numCols) that provide all information needed about the row. annoStreamer constructors need to set rowType.
• src/hg/lib/annoStreamWig.c
  • lines changed 152, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Tool): Added annoStreamWig and annoGrateWig,which led to some significant changes: annoRow is now polymorphic (words[] vs. wig float[]), annoFilter has a new function to apply filter(s) to a single number, and annoFormatTab can print out per-base wiggle values or average wiggle values (hardcoded to do per-base until a real config option is added). One puny test case was verified against mysql & table browser output.
  • lines changed 3, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Tool): Added annoStreamVcf, whichled to yet more significant changes to annoRow: instead of every row declaring its type and annoRow{Free,Clone} taking a numCols argument that is meaningless for wig, now annoRow{Free,Clone} take the row's source annoStreamer as an argument. The annoStreamer now has public members (rowType and numCols) that provide all information needed about the row. annoStreamer constructors need to set rowType.
• src/hg/lib/bigBed.as
  • lines changed 10, context: html, text, full: html, text
    adding in dummy as and sql files for bigBed
  • lines changed 10, context: html, text, full: html, text
    removing bigBed.as file
• src/hg/lib/bigBed.sql
  • lines changed 17, context: html, text, full: html, text
    adding in dummy as and sql files for bigBed
  • lines changed 1, context: html, text, full: html, text
    added in dummy column
  • lines changed 18, context: html, text, full: html, text
    removing bigBed.as file
• src/hg/lib/cart.c
  • lines changed 13, context: html, text, full: html, text
    replace use of SUPPORT_EURONODE with geoMirrorEnabled()
• src/hg/lib/geoMirror.c
  • lines changed 17, context: html, text, full: html, text
    add support code for geographic based mirroring (#3000)
• src/hg/lib/gpFx.c
  • lines changed 96, context: html, text, full: html, text
    more work on annoGratorGpVar and gpFx libraries.
• src/hg/lib/hvGfx.c
  • lines changed 16, context: html, text, full: html, text
    Adding commas to ruler on Genome Browser. Redmine #7559
• src/hg/lib/jsHelper.c
  • lines changed 1, context: html, text, full: html, text
    use double quotes in jsonHashAddString to conform to JSON standard
• src/hg/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Tool): Added annoStreamWig and annoGrateWig,which led to some significant changes: annoRow is now polymorphic (words[] vs. wig float[]), annoFilter has a new function to apply filter(s) to a single number, and annoFormatTab can print out per-base wiggle values or average wiggle values (hardcoded to do per-base until a real config option is added). One puny test case was verified against mysql & table browser output.
  • lines changed 1, context: html, text, full: html, text
    add support code for geographic based mirroring (#3000)
  • lines changed 1, context: html, text, full: html, text
    start on genepred / variant annoGrator. #6152
  • lines changed 1, context: html, text, full: html, text
    more work on annoGratorGpVar and gpFx libraries.
• src/hg/lib/pubsArticle.sql
  • lines changed 3, context: html, text, full: html, text
    adding new fields to sql files
  • lines changed 1, context: html, text, full: html, text
    adding a doi field to pubsArticle
• src/hg/lib/pubsSequenceAnnot.sql
  • lines changed 3, context: html, text, full: html, text
    adding new fields to sql files
• src/hg/lib/tests/annoGratorTester.c
  • lines changed 9, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Tool): instead of having a callercreate the sql connection outside of annoStreamDb, and have to remember not to share it, just allocate the connection inside annoStreamDb. This introduces a dependency on hdb, but I guess that's inevitable. :)
  • lines changed 74, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Tool): Added annoStreamWig and annoGrateWig,which led to some significant changes: annoRow is now polymorphic (words[] vs. wig float[]), annoFilter has a new function to apply filter(s) to a single number, and annoFormatTab can print out per-base wiggle values or average wiggle values (hardcoded to do per-base until a real config option is added). One puny test case was verified against mysql & table browser output.
  • lines changed 90, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Tool): Added annoStreamVcf, whichled to yet more significant changes to annoRow: instead of every row declaring its type and annoRow{Free,Clone} taking a numCols argument that is meaningless for wig, now annoRow{Free,Clone} take the row's source annoStreamer as an argument. The annoStreamer now has public members (rowType and numCols) that provide all information needed about the row. annoStreamer constructors need to set rowType.
  • lines changed 18, context: html, text, full: html, text
    start on genepred / variant annoGrator. #6152
  • lines changed 1, context: html, text, full: html, text
    more work on annoGratorGpVar and gpFx libraries.
• src/hg/lib/tests/annoGratorTests.mk
  • lines changed 5, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Tool): Added annoStreamWig and annoGrateWig,which led to some significant changes: annoRow is now polymorphic (words[] vs. wig float[]), annoFilter has a new function to apply filter(s) to a single number, and annoFormatTab can print out per-base wiggle values or average wiggle values (hardcoded to do per-base until a real config option is added). One puny test case was verified against mysql & table browser output.
  • lines changed 9, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Tool): Added annoStreamVcf, whichled to yet more significant changes to annoRow: instead of every row declaring its type and annoRow{Free,Clone} taking a numCols argument that is meaningless for wig, now annoRow{Free,Clone} take the row's source annoStreamer as an argument. The annoStreamer now has public members (rowType and numCols) that provide all information needed about the row. annoStreamer constructors need to set rowType.
  • lines changed 5, context: html, text, full: html, text
    start on genepred / variant annoGrator. #6152
• src/hg/lib/tests/expected/annoGrator/pgSnpKgDbToGpFx.txt
  • lines changed 4, context: html, text, full: html, text
    start on genepred / variant annoGrator. #6152
  • lines changed 5, context: html, text, full: html, text
    more work on annoGratorGpVar and gpFx libraries.
• src/hg/lib/tests/expected/annoGrator/snpConsDbToTabOutShort.txt
  • lines changed 39, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Tool): Added annoStreamWig and annoGrateWig,which led to some significant changes: annoRow is now polymorphic (words[] vs. wig float[]), annoFilter has a new function to apply filter(s) to a single number, and annoFormatTab can print out per-base wiggle values or average wiggle values (hardcoded to do per-base until a real config option is added). One puny test case was verified against mysql & table browser output.
• src/hg/lib/tests/expected/annoGrator/vcfEx1.txt
  • lines changed 110, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Tool): Added annoStreamVcf, whichled to yet more significant changes to annoRow: instead of every row declaring its type and annoRow{Free,Clone} taking a numCols argument that is meaningless for wig, now annoRow{Free,Clone} take the row's source annoStreamer as an argument. The annoStreamer now has public members (rowType and numCols) that provide all information needed about the row. annoStreamer constructors need to set rowType.
• src/hg/lib/tests/expected/annoGrator/vcfEx2.txt
  • lines changed 120, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Tool): Added annoStreamVcf, whichled to yet more significant changes to annoRow: instead of every row declaring its type and annoRow{Free,Clone} taking a numCols argument that is meaningless for wig, now annoRow{Free,Clone} take the row's source annoStreamer as an argument. The annoStreamer now has public members (rowType and numCols) that provide all information needed about the row. annoStreamer constructors need to set rowType.
• src/hg/lib/web.c
  • lines changed 17, context: html, text, full: html, text
    replace use of SUPPORT_EURONODE with geoMirrorEnabled()
• src/hg/makeDb/doc/chrPic1.txt
  • lines changed 349, context: html, text, full: html, text
    masking underway
  • lines changed 86, context: html, text, full: html, text
    done with masking, used the WM result
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeCaltechRnaSeq.release2.notes
  • lines changed 566, context: html, text, full: html, text
    notes for caltech rna seq
  • lines changed 566, context: html, text, full: html, text
    reverting to b9fbbd2f2d1db6c0a26c06712148113494b962bc for release 2 notes
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeCaltechRnaSeq.release3.notes
  • lines changed 1393, context: html, text, full: html, text
    release notes for caltech release 3
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeCshlLongRnaSeq.release2.notes
  • lines changed 3739, context: html, text, full: html, text
    adding notes foir cshl long release 2
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeOpenChromChip.release2.notes
  • lines changed 122, context: html, text, full: html, text
    updated notes files for open chrom chip
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeUwDgf.release4.notes
  • lines changed 739, context: html, text, full: html, text
    adding in notes for histone and dgf
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeUwDnase.release5.notes
  • lines changed 2201, context: html, text, full: html, text
    notes for uw dnase release 5
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeUwHistone.release4.notes
  • lines changed 2492, context: html, text, full: html, text
    adding in notes for histone and dgf
• src/hg/makeDb/doc/encodeDccMm9/wgEncodeLicrTfbs.release1.notes
  • lines changed 2, context: html, text, full: html, text
    Fixed issue regarding replicate 1 of an experiment should have been revoked and replicate 2 and 3 should be reclassified as 1 and 2 respectivley. Redmine #5394, Note #63.
• src/hg/makeDb/doc/encodeDccMm9/wgEncodeLicrTfbs.release2.notes
  • lines changed 38, context: html, text, full: html, text
    creating the notes file
  • lines changed 28, context: html, text, full: html, text
    create notes file
• src/hg/makeDb/doc/hg18.txt
  • lines changed 4, context: html, text, full: html, text
    Track #1656 (GWAS Catalog): bi-monthly update.
• src/hg/makeDb/doc/hg19.txt
  • lines changed 1, context: html, text, full: html, text
    Noting update of wgEncodeRegTfbsClustered
  • lines changed 4, context: html, text, full: html, text
    Track #1656 (GWAS Catalog): bi-monthly update.
  • lines changed 1, context: html, text, full: html, text
    added a comment about ISCA tracks to watch for second part
• src/hg/makeDb/doc/melUnd1.txt
  • lines changed 68, context: html, text, full: html, text
    download sequence for new browsers
  • lines changed 102, context: html, text, full: html, text
    initial browser build
  • lines changed 161, context: html, text, full: html, text
    masking underway
  • lines changed 99, context: html, text, full: html, text
    done with masking, used the WM result
• src/hg/makeDb/doc/mm10.txt
  • lines changed 11, context: html, text, full: html, text
    rn5 lastz done with abridged repeats
  • lines changed 359, context: html, text, full: html, text
    running reciprocal bests and starting triMan1 monDom5 sarHar1 melUnd1 lastz runs
  • lines changed 173, context: html, text, full: html, text
    done with lastz chain net runs for ornAna1 chrPic1 triMan1 monDom5 sarHar1 melUnd1 and most recip bests
  • lines changed 882, context: html, text, full: html, text
    starting lastz runs for the final set: galGal4 taeGut1 anoCar2 melGal1 xenTro3 latCha1 gadMor1 oreNil1 gasAcu1 fr3 tetNig2 danRer7 oryLat2 petMar1
  • lines changed 146, context: html, text, full: html, text
    done with all 60 lastz chain net alignments with swaps
• src/hg/makeDb/doc/oviAri1.txt
  • lines changed 5, context: html, text, full: html, text
    Bug# 7486 Fixed /gbdb/oviAri1/oviAri1.2bit symlink to point to masked sequence
• src/hg/makeDb/doc/triMan1.txt
  • lines changed 67, context: html, text, full: html, text
    download sequence for new browsers
  • lines changed 129, context: html, text, full: html, text
    initial browser build
  • lines changed 162, context: html, text, full: html, text
    masking underway
  • lines changed 53, context: html, text, full: html, text
    completed masking operations, used the RM result
  • lines changed 95, context: html, text, full: html, text
    starting genbank
  • lines changed 8, context: html, text, full: html, text
    completed genbank run
• src/hg/makeDb/doc/uniProt/sp120323.txt
  • lines changed 54, context: html, text, full: html, text
    build new uniProt database (#7045)
• src/hg/makeDb/genbank/etc/align.dbs
  • lines changed 1, context: html, text, full: html, text
    Added triMan1 - Manatee
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 17, context: html, text, full: html, text
    adding Trichechus manatus latirostris (Florida manatee) triMan1
  • lines changed 1, context: html, text, full: html, text
    adding Trichechus manatus latirostris (Florida manatee) triMan1
  • lines changed 16, context: html, text, full: html, text
    add strPur4 for Kord.
• src/hg/makeDb/genbank/etc/hgwdev.dbs
  • lines changed 1, context: html, text, full: html, text
    Added triMan1 - Manatee
• src/hg/makeDb/genbank/src/lib/gbGenome.c
  • lines changed 3, context: html, text, full: html, text
    adding Trichechus manatus latirostris (Florida manatee) triMan1
• src/hg/makeDb/hgLoadBed/hgLoadBed.c
  • lines changed 4, context: html, text, full: html, text
    Changing the dotIsNull to load -1
• src/hg/makeDb/hgLoadSeq/hgLoadSeq.c
  • lines changed 38, context: html, text, full: html, text
    fill in the size column with the sequence size instead of leaving at zero
• src/hg/makeDb/schema/all.joiner
  • lines changed 2, context: html, text, full: html, text
    Added two tables for the polyaseq track that were missing from tables ignored
• src/hg/makeDb/trackDb/birds/melUnd1/description.html
  • lines changed 132, context: html, text, full: html, text
    original source from makeGenomeDb.pl
• src/hg/makeDb/trackDb/birds/melUnd1/gap.html
  • lines changed 64, context: html, text, full: html, text
    original source from makeGenomeDb.pl
• src/hg/makeDb/trackDb/birds/melUnd1/gold.html
  • lines changed 23, context: html, text, full: html, text
    original source from makeGenomeDb.pl
• src/hg/makeDb/trackDb/birds/melUnd1/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    original source from makeGenomeDb.pl
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 99, context: html, text, full: html, text
    Added a few mouse cell registrations.
  • lines changed 4, context: html, text, full: html, text
    Updating H1 vendorName,Id and Url
  • lines changed 2, context: html, text, full: html, text
    Correcting HEEpiC vendorId to 2720 from 2700
  • lines changed 2, context: html, text, full: html, text
    adding the monocytes parent back in
  • lines changed 102, context: html, text, full: html, text
    Registration of new cell lines and treatments for Gilbert lab.
  • lines changed 36, context: html, text, full: html, text
    make new views proteomGenomics experiments for search on genome database, gencode annotation, modified peptides, bigbed file
  • lines changed 17, context: html, text, full: html, text
    Added MEP cell line for Hardison lab.
  • lines changed 5, context: html, text, full: html, text
    Updated strain for ES-CJ7 to be a specific 129 strain.
  • lines changed 4, context: html, text, full: html, text
    Removed out dataed term displayName.
  • lines changed 16, context: html, text, full: html, text
    Registered HDAC6.
  • lines changed 3, context: html, text, full: html, text
    Fixed spelling of HDAC6 to be consistent with cv.ra.
  • lines changed 5, context: html, text, full: html, text
    Added Ribo-Zero RNA extract type protocol.
  • lines changed 8, context: html, text, full: html, text
    addingin FSU mouse tiling platform
  • lines changed 3, context: html, text, full: html, text
    description and type got merged for DBA/2
  • lines changed 25, context: html, text, full: html, text
    Removing PROVISIONAL tags from CV
  • lines changed 32, context: html, text, full: html, text
    Sovling merge conflict
  • lines changed 2, context: html, text, full: html, text
    Fixed spelling of organism.
  • lines changed 1, context: html, text, full: html, text
    Fixed error in protocol name.
  • lines changed 1, context: html, text, full: html, text
    Fixed lab designation for MEP cell type.
  • lines changed 4, context: html, text, full: html, text
    added in and corrected some labels
  • lines changed 1, context: html, text, full: html, text
    correcting capitalization error
  • lines changed 1, context: html, text, full: html, text
    more labels
  • lines changed 1, context: html, text, full: html, text
    qa fixes, and more labels in cv fun
  • lines changed 1, context: html, text, full: html, text
    Fixing typo in CV
  • lines changed 3, context: html, text, full: html, text
    more label changes for qa
  • lines changed 5, context: html, text, full: html, text
    Fixed typo's in cv.ra
  • lines changed 18, context: html, text, full: html, text
    Removed comma in Cell's multiple protocols, which is incorrect syntax.
  • lines changed 1, context: html, text, full: html, text
    Commented out T98G protocol that doesn't exist.
  • lines changed 1, context: html, text, full: html, text
    Fixed tag for diffProtD.
  • lines changed 28, context: html, text, full: html, text
    Adding B_cells_CD20+ parental line
  • lines changed 36, context: html, text, full: html, text
    Changing to childOf Lymphoblastoid cell line for Mike Pazin
  • lines changed 150, context: html, text, full: html, text
    added experimental optional & required variables to typeOfTerm stanzas to allow for data-driven validation of the CV
  • lines changed 1, context: html, text, full: html, text
    changed description at lab's behest
• src/hg/makeDb/trackDb/cv/beta/cv.ra
  • lines changed 18, context: html, text, full: html, text
    Removed comma in Cell's multiple protocols, which is incorrect syntax.
  • lines changed 1, context: html, text, full: html, text
    Commented out T98G protocol that doesn't exist.
  • lines changed 729, context: html, text, full: html, text
    Pushing changes in alpha cv to beta
• src/hg/makeDb/trackDb/cv/public/cv.ra
  • lines changed 17, context: html, text, full: html, text
    Removed comma in Cell's multiple protocols, which is incorrect syntax.
  • lines changed 1, context: html, text, full: html, text
    Commented out T98G protocol that doesn't exist.
  • lines changed 2, context: html, text, full: html, text
    Fixed error in order of tag and term in stanza.
  • lines changed 38, context: html, text, full: html, text
    Added in approved submissions from beta/cv.ra to public/cv.ra. Redmine #7433.
• src/hg/makeDb/trackDb/dog/canFam2/polyASeqSites.html
  • lines changed 59, context: html, text, full: html, text
    This was a copy/paste replacement of everything in these files (except the table) from the hg19 version of this file that I updated. So it included all the changes that were in there: html cleanup, link edit, minor grammar fix
  • lines changed 6, context: html, text, full: html, text
    Updated table formatting per the same change made on this file on hg19.
  • lines changed 1, context: html, text, full: html, text
    Removed an extraneous > character.
  • lines changed 1, context: html, text, full: html, text
    Added name of second person under credits per request from Adnan.
• src/hg/makeDb/trackDb/dog/canFam2/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    Removed Fan's PolyA-Seq track
• src/hg/makeDb/trackDb/human/hg18/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    Removed Fan's PolyA-Seq track
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
  • lines changed 8, context: html, text, full: html, text
    Matt made some metadata changes (redmine #7395)
• src/hg/makeDb/trackDb/human/hg18/wgEncodeCaltechRnaSeq.patch.ra
  • lines changed 1257, context: html, text, full: html, text
    Matt made some metadata changes (redmine #7395)
• src/hg/makeDb/trackDb/human/hg18/wgEncodeCaltechRnaSeq.ra
  • lines changed 139, context: html, text, full: html, text
    Matt made some metadata changes (redmine #7395)
• src/hg/makeDb/trackDb/human/hg18/wgEncodeGisRnaSeq.patch.ra
  • lines changed 301, context: html, text, full: html, text
    Matt made some metadata changes (redmine #7395)
• src/hg/makeDb/trackDb/human/hg18/wgEncodeGisRnaSeq.ra
  • lines changed 19, context: html, text, full: html, text
    Matt made some metadata changes (redmine #7395)
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaMethyl27.patch.ra
  • lines changed 92, context: html, text, full: html, text
    Matt made some metadata changes (redmine #7395)
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaMethyl27.ra
  • lines changed 7, context: html, text, full: html, text
    Matt made some metadata changes (redmine #7395)
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaMethylSeq.patch.ra
  • lines changed 324, context: html, text, full: html, text
    Matt made some metadata changes (redmine #7395)
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaMethylSeq.ra
  • lines changed 30, context: html, text, full: html, text
    Matt made some metadata changes (redmine #7395)
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeBroadHistone.ra
  • lines changed 2676, context: html, text, full: html, text
    added in new broad histone metaDb
  • lines changed 2676, context: html, text, full: html, text
    Errors in metaDb, not all submissions have an antibodyRevert "added in new broad histone metaDb" This reverts commit 6b7478127796dadd417430b7c59ab17af25b3692.
  • lines changed 2676, context: html, text, full: html, text
    adding in new tracks for broad histone metaDb
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCaltechRnaSeq.ra
  • lines changed 1476, context: html, text, full: html, text
    revoked data and added in replacement files
  • lines changed 121, context: html, text, full: html, text
    added expIds and accessiosn to caltech rnaseq
  • lines changed 549, context: html, text, full: html, text
    filling in the treatment = none holes
  • lines changed 118, context: html, text, full: html, text
    filling in holes for insert length (doesn't exist for non paired reads)
  • lines changed 181, context: html, text, full: html, text
    correcting date submitted and unrestricted
  • lines changed 171, context: html, text, full: html, text
    filled in holes for localization and rnaExtract
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra
  • lines changed 357, context: html, text, full: html, text
    added in more cshl long tracks
  • lines changed 4589, context: html, text, full: html, text
    Added lots of new data
  • lines changed 357, context: html, text, full: html, text
    added in metadata that i forgot to
  • lines changed 391, context: html, text, full: html, text
    added in md5sums for cshl long rna seq
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlShortRnaSeq.ra
  • lines changed 2588, context: html, text, full: html, text
    added in metadata for new cshl short tracks
  • lines changed 852, context: html, text, full: html, text
    added in new tracks for cshl short
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeDukeAffyExon.ra
  • lines changed 153, context: html, text, full: html, text
    fixed md5sums after another resubmit of all the data
  • lines changed 91, context: html, text, full: html, text
    adding in dcc Accessions
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeFsuRepliSeq.ra
  • lines changed 21, context: html, text, full: html, text
    Added md5sum's for all tracks after the ENCODE Freeze.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisRnaPet.ra
  • lines changed 3082, context: html, text, full: html, text
    adding in metadata for gisrnaper
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromChip.ra
  • lines changed 877, context: html, text, full: html, text
    added in new open chrom chip tracks
  • lines changed 43, context: html, text, full: html, text
    added in md5sums
  • lines changed 290, context: html, text, full: html, text
    converted controlIds to dccaccession
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromDnase.ra
  • lines changed 2, context: html, text, full: html, text
    missing 1 md5sum
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeRikenCage.ra
  • lines changed 1470, context: html, text, full: html, text
    added in metadata for new cshl short tracks
  • lines changed 5044, context: html, text, full: html, text
    added in metadata for new riken cage tracks
  • lines changed 446, context: html, text, full: html, text
    added in riken cage metaData part 2
  • lines changed 39, context: html, text, full: html, text
    last time there was a replacement file that didn't get the v4
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhHistone.ra
  • lines changed 577, context: html, text, full: html, text
    Added 5 new experiments for the track. Redmine #7510.
  • lines changed 28, context: html, text, full: html, text
    Added md5sum's for all tracks after the ENCODE Freeze.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra
  • lines changed 580, context: html, text, full: html, text
    Added meta-data that was forgotten to be checked in. Redmine #4486.
  • lines changed 68, context: html, text, full: html, text
    Removed HCT-116 control, which was meant for SYDH Histone track.
  • lines changed 334, context: html, text, full: html, text
    Added md5sum's for all tracks after the ENCODE Freeze.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDgf.ra
  • lines changed 1179, context: html, text, full: html, text
    added in new tracks for uw dgf
  • lines changed 181, context: html, text, full: html, text
    data came in with incorrect metadata, correcting
  • lines changed 61, context: html, text, full: html, text
    added in md5sums
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDnase.ra
  • lines changed 2551, context: html, text, full: html, text
    added in new metadata for UwDnase tracks
  • lines changed 409, context: html, text, full: html, text
    added in more uw dnase tracks
  • lines changed 146, context: html, text, full: html, text
    added in md5sums
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwHistone.ra
  • lines changed 1221, context: html, text, full: html, text
    added in emtadata for uwhistone new tracks
  • lines changed 11, context: html, text, full: html, text
    revoked old dataset, missed becuase the histone tag changed between releases h3k4 vs h3k04
  • lines changed 51, context: html, text, full: html, text
    added in md5sums
  • lines changed 11, context: html, text, full: html, text
    incorrectly revoked, turns out the repleacement was missing the treatment in the name
  • lines changed 11, context: html, text, full: html, text
    revoked objects that were missing treatment names, resubmitting
  • lines changed 255, context: html, text, full: html, text
    added in replacement tracks
  • lines changed 4, context: html, text, full: html, text
    putting an experiment without a rep2 into the attic, lab doesn't think it'll ever get rep2
  • lines changed 143, context: html, text, full: html, text
    added in controls as accessions, we dont' have all of them yet
  • lines changed 21, context: html, text, full: html, text
    adding in known accessions and expids
  • lines changed 51, context: html, text, full: html, text
    added in more controlIds
  • lines changed 101, context: html, text, full: html, text
    added in accessions and expids
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeDukeAffyExon.ra
  • lines changed 3531, context: html, text, full: html, text
    Staging Duke Affy Exon (Release 3) on beta (redmine #5648)
  • lines changed 91, context: html, text, full: html, text
    Matt added some missing UCSC Accession numbers
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeOpenChromChip.ra
  • lines changed 272, context: html, text, full: html, text
    staging the expIds for 3 tracks to beta for a metadata update
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeOpenChromDnase.ra
  • lines changed 2, context: html, text, full: html, text
    Matt changed one of the md5sums (redmine #4143)
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeOpenChromFaire.ra
  • lines changed 180, context: html, text, full: html, text
    staging the expIds for 3 tracks to beta for a metadata update
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeSunyAlbanyTiling.ra
  • lines changed 9, context: html, text, full: html, text
    staging the expIds for 3 tracks to beta for a metadata update
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeUwHistone.ra
  • lines changed 1790, context: html, text, full: html, text
    Staging UW Histone (Release 4) on beta (redmine #6809)
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeDukeAffyExon.ra
  • lines changed 3621, context: html, text, full: html, text
    Releasing Duke Affy Exon (Release 3) to the RR (redmine #5648)
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeOpenChromDnase.ra
  • lines changed 5699, context: html, text, full: html, text
    Releasing Open Chrom DNase (Release 2) to the RR (redmine #4143)
  • lines changed 2, context: html, text, full: html, text
    Matt changed one of the md5sums (redmine #4143)
• src/hg/makeDb/trackDb/human/hg19/polyASeqSites.html
  • lines changed 70, context: html, text, full: html, text
    Lots of changes: cleaned up and fixed html. Moved a paragraph for better flow. Restyled the table. Changed the text of a link for better flow.
  • lines changed 1, context: html, text, full: html, text
    Added name of second person under credits per request from Adnan.
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    Removed Fan's PolyA-Seq track
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
  • lines changed 2, context: html, text, full: html, text
    adding in new caltech rnaSeq release3.ra
  • lines changed 2, context: html, text, full: html, text
    Releasing Open Chrom DNase (Release 2) to the RR (redmine #4143)
  • lines changed 1, context: html, text, full: html, text
    bypassing patch.ra for replicate fix, and just going forward with release 5.
  • lines changed 2, context: html, text, full: html, text
    adding in release4.ra for uwhistone
  • lines changed 2, context: html, text, full: html, text
    Staging Duke Affy Exon (Release 3) on beta (redmine #5648)
  • lines changed 2, context: html, text, full: html, text
    split off release4 trackDb ra for uwDgf
  • lines changed 1, context: html, text, full: html, text
    added in new tracks for uw dgf
  • lines changed 2, context: html, text, full: html, text
    Releasing Duke Affy Exon (Release 3) to the RR (redmine #5648)
  • lines changed 1, context: html, text, full: html, text
    Removing CSHL Long so that we do not upset the build. CSHL long suffered a terrible merge conflict that I do not have time to recover fully from until after CGI release and so I do not want to have this track mucking up the works.
  • lines changed 2, context: html, text, full: html, text
    Staging UW Histone (Release 4) on beta (redmine #6809)
  • lines changed 1, context: html, text, full: html, text
    cleaned up trackDb in cshl long
• src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHistone.release3.html
  • lines changed 166, context: html, text, full: html, text
    Removed rel="nofollow" for current tracks being worked on. Redmine #7533.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHistone.release3.ra
  • lines changed 674, context: html, text, full: html, text
    adding in broad histone trackDb tracks
  • lines changed 1, context: html, text, full: html, text
    Removed rel="nofollow" for current tracks being worked on. Redmine #7533.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCaltechRnaSeq.release2.ra
  • lines changed 549, context: html, text, full: html, text
    removed bad signals from caltech rnaseq
  • lines changed 524, context: html, text, full: html, text
    added in replacement tracks for caltech rna seq
  • lines changed 1033, context: html, text, full: html, text
    reverting to 5a655dd525b84371e1e9c3326f741ce23e3e378a because it was really release 3
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCaltechRnaSeq.release3.ra
  • lines changed 2050, context: html, text, full: html, text
    adding in new caltech rnaSeq release3.ra
  • lines changed 674, context: html, text, full: html, text
    reworked long and short labels from previous release, also cleamed out commented lines
  • lines changed 1, context: html, text, full: html, text
    removed md5sum from filesort order
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.release2.ra
  • lines changed 33, context: html, text, full: html, text
    added in more cshl long tracks
  • lines changed 318, context: html, text, full: html, text
    Trying to resolve the merge conflict between Matt and I adding data. I think I have lost Matts changes
  • lines changed 33, context: html, text, full: html, text
    re-added in tracks for cshl long rna-seq lost in the merge
  • lines changed 157, context: html, text, full: html, text
    cleaned up trackDb in cshl long
  • lines changed 94, context: html, text, full: html, text
    fixed autogenerated long labels
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.release3.html
  • lines changed 2, context: html, text, full: html, text
    Removing nofollow
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.release3.ra
  • lines changed 1424, context: html, text, full: html, text
    added in new trackDb tracks for cshl short contigs and whatnot
  • lines changed 3, context: html, text, full: html, text
    didn't notice monocytes in the tier 3 cell lines, corrected
• src/hg/makeDb/trackDb/human/hg19/wgEncodeDukeAffyExon.release3.html
  • lines changed 30, context: html, text, full: html, text
    added in changes from lab
  • lines changed 11, context: html, text, full: html, text
    more html chagnes by lab
  • lines changed 1, context: html, text, full: html, text
    forgot to close ul tag
  • lines changed 27, context: html, text, full: html, text
    qa fixes
  • lines changed 35, context: html, text, full: html, text
    added in references to duke affy exon
  • lines changed 5, context: html, text, full: html, text
    qa fixes, and more labels in cv fun
• src/hg/makeDb/trackDb/human/hg19/wgEncodeDukeAffyExon.release3.ra
  • lines changed 1021, context: html, text, full: html, text
    qa fixes
  • lines changed 5, context: html, text, full: html, text
    more qa fixes to labels
  • lines changed 15, context: html, text, full: html, text
    found more errors
  • lines changed 3, context: html, text, full: html, text
    qa fixes, and more labels in cv fun
• src/hg/makeDb/trackDb/human/hg19/wgEncodeFsuRepliSeq.html
  • lines changed 6, context: html, text, full: html, text
    Removed rel="nofollow" for current tracks being worked on. Redmine #7533.
  • lines changed 4, context: html, text, full: html, text
    Updated track default and track description. Redmine #6626.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeFsuRepliSeq.ra
  • lines changed 28, context: html, text, full: html, text
    Updated track default and track description. Redmine #6626.
  • lines changed 1, context: html, text, full: html, text
    Fixed matrix link. Redmine#6626.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV11.html
  • lines changed 59, context: html, text, full: html, text
    Brooke found an issue with the gencode track description page html using the tables test robot. Did a quick clean up of the html for her.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGisChiaPet.html
  • lines changed 6, context: html, text, full: html, text
    Removing nofollow
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGisRnaPet.release2.ra
  • lines changed 2598, context: html, text, full: html, text
    added in new tracks from gis
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromChip.release2.ra
  • lines changed 145, context: html, text, full: html, text
    added in new open chrom chip tracks
  • lines changed 51, context: html, text, full: html, text
    reworked short labels
  • lines changed 66, context: html, text, full: html, text
    reworked short and long labels that were too long, and made all chagnes consistent
• src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.release3.ra
  • lines changed 3173, context: html, text, full: html, text
    added in tracks to riken cage release3 for freeze
  • lines changed 1, context: html, text, full: html, text
    flippign the matrix around, because ther'es too many cell lines now
  • lines changed 158, context: html, text, full: html, text
    added in new riken release 3 tracks part 2
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhHistone.release3.html
  • lines changed 3, context: html, text, full: html, text
    Removed rel="nofollow" for current tracks being worked on. Redmine #7533.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhHistone.release3.ra
  • lines changed 118, context: html, text, full: html, text
    Added 5 new experiments for the track. Redmine #7510.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.release2.html
  • lines changed 6, context: html, text, full: html, text
    Removed rel="nofollow" for current tracks being worked on. Redmine #7533.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.release2.ra
  • lines changed 79, context: html, text, full: html, text
    Added 5 experiments to the track. Redmine #4486.
  • lines changed 8, context: html, text, full: html, text
    Removed HCT-116 control as this is for the histone track.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDgf.release4.html
  • lines changed 167, context: html, text, full: html, text
    added in release notes and new html for uw dgf
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDgf.release4.ra
  • lines changed 1488, context: html, text, full: html, text
    split off release4 trackDb ra for uwDgf
  • lines changed 567, context: html, text, full: html, text
    added in new tracks for uw dgf
  • lines changed 40, context: html, text, full: html, text
    long labels for uw dgf
  • lines changed 1, context: html, text, full: html, text
    added in treatment to the cv list
  • lines changed 22, context: html, text, full: html, text
    fixed short labels
  • lines changed 1, context: html, text, full: html, text
    added in release notes and new html for uw dgf
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.patch.ra
  • lines changed 4562, context: html, text, full: html, text
    removing patch.ra, using release5.ra instead
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.release5.html
  • lines changed 132, context: html, text, full: html, text
    copying over release 4 html to 5
  • lines changed 2, context: html, text, full: html, text
    changing to release 5
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.release5.ra
  • lines changed 4562, context: html, text, full: html, text
    copying over wgEncodeUwDnase to release5 trackDb
  • lines changed 738, context: html, text, full: html, text
    added in new tracks to trackDb
  • lines changed 109, context: html, text, full: html, text
    added in more uw dnase tracks
  • lines changed 101, context: html, text, full: html, text
    new long labels for uw dnase
  • lines changed 510, context: html, text, full: html, text
    short labels for uwDnase
  • lines changed 7, context: html, text, full: html, text
    changed wi30O to wi38, same thing, treatment was embedded in cell name
  • lines changed 182, context: html, text, full: html, text
    removed fdr 1%, as everything is fdr 1%
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.release4.html
  • lines changed 96, context: html, text, full: html, text
    added in release notes and new html for uw histone
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.release4.ra
  • lines changed 5953, context: html, text, full: html, text
    adding in release4.ra for uwhistone
  • lines changed 301, context: html, text, full: html, text
    added in metadata for new cshl short tracks
  • lines changed 4, context: html, text, full: html, text
    changed matrix around
  • lines changed 102, context: html, text, full: html, text
    revoked old tracks, added in replacement tracks
  • lines changed 144, context: html, text, full: html, text
    reworked long labels
  • lines changed 1, context: html, text, full: html, text
    added in release notes and new html for uw histone
  • lines changed 37, context: html, text, full: html, text
    reded short labels
• src/hg/makeDb/trackDb/makefile
  • lines changed 3, context: html, text, full: html, text
    adding manatee, painted turtle, budgerigar
• src/hg/makeDb/trackDb/manatee/triMan1/description.html
  • lines changed 132, context: html, text, full: html, text
    original source from makeGenomeDb.pl
• src/hg/makeDb/trackDb/manatee/triMan1/gap.html
  • lines changed 64, context: html, text, full: html, text
    original source from makeGenomeDb.pl
• src/hg/makeDb/trackDb/manatee/triMan1/gold.html
  • lines changed 23, context: html, text, full: html, text
    original source from makeGenomeDb.pl
• src/hg/makeDb/trackDb/manatee/triMan1/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    original source from makeGenomeDb.pl
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.chainNet.ra
  • lines changed 483, context: html, text, full: html, text
    contents split up into separate files
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.gliersChainNet.ra
  • lines changed 66, context: html, text, full: html, text
    initial contents
  • lines changed 106, context: html, text, full: html, text
    glier subset
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.placentalsChainNet.ra
  • lines changed 338, context: html, text, full: html, text
    initial contents
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.previousVersionsChainNet.ra
  • lines changed 226, context: html, text, full: html, text
    initial contents
  • lines changed 185, context: html, text, full: html, text
    moved older genome release chain nets to this package
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.primatesChainNet.ra
  • lines changed 226, context: html, text, full: html, text
    initial contents
  • lines changed 5, context: html, text, full: html, text
    using otoGar3 instead of otoGar1
  • lines changed 1, context: html, text, full: html, text
    correct netOtoGar3 instead of netOtoGar1
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
  • lines changed 5, context: html, text, full: html, text
    five primary groups for chain net definitions
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.vertebrateChainNet.ra
  • lines changed 354, context: html, text, full: html, text
    initial contents
  • lines changed 1, context: html, text, full: html, text
    setting priority to get in line
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/makefile
  • lines changed 1, context: html, text, full: html, text
    Displaying the first 24 experiments from FSU for Mouse. Redmine #6627.
  • lines changed 1, context: html, text, full: html, text
    Added 3 submissions for RNA-seq track. Redmine #107.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeCaltechRnaSeq.ra
  • lines changed 203, context: html, text, full: html, text
    update with new submissions (got distracted to work on other things, this msg may not be accurate
  • lines changed 7, context: html, text, full: html, text
    Added md5sum's for files.
  • lines changed 39, context: html, text, full: html, text
    add expId
  • lines changed 15, context: html, text, full: html, text
    Renamed Alignment files, as there was an error in 2 submissions which had an older daf that didn't require replicates for alignment files. Redmine #4156.
  • lines changed 3, context: html, text, full: html, text
    Fixed typo in metadata surrouding spelling of replicate.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra
  • lines changed 1837, context: html, text, full: html, text
    Added 34 submissions for more processed non-displayed data. Redmine #7089.
  • lines changed 69, context: html, text, full: html, text
    Added md5sum's for all tracks after the ENCODE Freeze.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeFsuRepliSeq.ra
  • lines changed 1105, context: html, text, full: html, text
    Displaying the first 24 experiments from FSU for Mouse. Redmine #6627.
  • lines changed 35, context: html, text, full: html, text
    Fixed error in meta-data regarding reference to age.
  • lines changed 6, context: html, text, full: html, text
    Added trackDescription and metaData variables. Redmine #6627.
  • lines changed 49, context: html, text, full: html, text
    Added md5sum's for all tracks after the ENCODE Freeze.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrHistone.ra
  • lines changed 3121, context: html, text, full: html, text
    added in new mouse tracls
  • lines changed 3121, context: html, text, full: html, text
    Revert "added in new mouse tracls" This reverts commit be633f8017ea8465308013d3db3c016cf20e73fd.
  • lines changed 1249, context: html, text, full: html, text
    update those subtracks submitted before ADULT8WKS was changed to ADLT8W
  • lines changed 1873, context: html, text, full: html, text
    change ADULT8WKS to 1ADLT8W for ordering, update mdb
  • lines changed 241, context: html, text, full: html, text
    added expId
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrTfbs.ra
  • lines changed 136, context: html, text, full: html, text
    Fixed issue regarding replicate 1 of an experiment should have been revoked and replicate 2 and 3 should be reclassified as 1 and 2 respectivley. Redmine #5394, Note #63.
  • lines changed 2, context: html, text, full: html, text
    add md5sums
  • lines changed 38, context: html, text, full: html, text
    try to resolve merge conflict
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodePsuRnaSeq.ra
  • lines changed 450, context: html, text, full: html, text
    Added 3 submissions for RNA-seq track. Redmine #107.
  • lines changed 19, context: html, text, full: html, text
    Added md5sum's for all tracks after the ENCODE Freeze.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodePsuTfbs.ra
  • lines changed 625, context: html, text, full: html, text
    Added 1 submission for release 2 of track. Redmine #7516.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhHist.ra
  • lines changed 1023, context: html, text, full: html, text
    update with new submissions
  • lines changed 2, context: html, text, full: html, text
    added series accession for SydHist
  • lines changed 43, context: html, text, full: html, text
    Added md5sum's for files.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhTfbs.ra
  • lines changed 1172, context: html, text, full: html, text
    added in new mouse metaDb for sydh tfbs
  • lines changed 67, context: html, text, full: html, text
    Added md5sum's for files.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeUwDgf.ra
  • lines changed 57, context: html, text, full: html, text
    Fixed metadata erore with age and strain for A20, 416B, MEL and mg/ER. Redmine #4469,#4468,#3631.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeUwDnase.ra
  • lines changed 79, context: html, text, full: html, text
    Fixed metadata erore with age and strain for A20, 416B, MEL and mg/ER. Redmine #4469,#4468,#3631.
  • lines changed 21, context: html, text, full: html, text
    Updated strain for ES-CJ7 to be a specific 129 strain.
  • lines changed 76, context: html, text, full: html, text
    Added md5sum's for all tracks after the ENCODE Freeze.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeUwRnaSeq.ra
  • lines changed 115, context: html, text, full: html, text
    Fixed metadata erore with age and strain for A20, 416B, MEL and mg/ER. Redmine #4469,#4468,#3631.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/wgEncodeLicrTfbs.ra
  • lines changed 140, context: html, text, full: html, text
    checking in Ruihuas updated metaDb changes on LICR TFBS, redmine# 5394
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/public/wgEncodeLicrHistone.ra
  • lines changed 12463, context: html, text, full: html, text
    Releasing LICR Histone (Release 2) to the RR (redmine #5393)
• src/hg/makeDb/trackDb/mouse/mm9/polyASeqSites.html
  • lines changed 59, context: html, text, full: html, text
    This was a copy/paste replacement of everything in these files (except the table) from the hg19 version of this file that I updated. So it included all the changes that were in there: html cleanup, link edit, minor grammar fix
  • lines changed 8, context: html, text, full: html, text
    Updated table formatting per the same change made on this file on hg19.
  • lines changed 1, context: html, text, full: html, text
    Added name of second person under credits per request from Adnan.
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    Removed Fan's PolyA-Seq track
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.wgEncode.ra
  • lines changed 2, context: html, text, full: html, text
    Releasing LICR Histone (Release 2) to the RR (redmine #5393)
  • lines changed 3, context: html, text, full: html, text
    Displaying the first 24 experiments from FSU for Mouse. Redmine #6627.
  • lines changed 2, context: html, text, full: html, text
    add alpha,beta at the end of xxxLicrHistone.release2, add xxxLicrHistone.release3
  • lines changed 2, context: html, text, full: html, text
    add public at the end of xxxLicrHistone.release2.ra and add alpha,beta to xxxLicrHistone.release3.ra
  • lines changed 2, context: html, text, full: html, text
    please ignore this change if you are reviewing the code for this section, change back to original as I can't access my sandbox, but it is probably a server error, it actually works fine, I'll need to add the change back after this commit
  • lines changed 2, context: html, text, full: html, text
    add beta,public to the end of xxxLicrHistone.release2 and alpha to the end of xxxLicrHistone.release3
  • lines changed 2, context: html, text, full: html, text
    remove LicrHistone.release3, add alpha,beta,product to the end of LicrHistone.release2
  • lines changed 1, context: html, text, full: html, text
    add LicrHistone.release3 alpha
  • lines changed 1, context: html, text, full: html, text
    change the end of LicrHistone.release2 from alpha,beta,product to beta,product
  • lines changed 4, context: html, text, full: html, text
    Added 3 submissions for RNA-seq track. Redmine #107.
  • lines changed 3, context: html, text, full: html, text
    added CaltechRnaSeq.release1.ra to include
  • lines changed 1, context: html, text, full: html, text
    fixed a typo
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCaltechRnaSeq.release1.html
  • lines changed 146, context: html, text, full: html, text
    create release1 files
  • lines changed 6, context: html, text, full: html, text
    update html
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCaltechRnaSeq.release1.ra
  • lines changed 91, context: html, text, full: html, text
    create release1 files
  • lines changed 45, context: html, text, full: html, text
    update with new submissions (got distracted to work on other things, this msg may not be accurate
  • lines changed 2, context: html, text, full: html, text
    trying to fix make error (note 29, ticket #4156, add rep=rep1 at the end of subGroups for Aln track of submission id 6081, 6082
  • lines changed 2, context: html, text, full: html, text
    removed fields with only one value from sortOrder and filedownload list
  • lines changed 16, context: html, text, full: html, text
    clean up short and long labels
  • lines changed 4, context: html, text, full: html, text
    clean up long labels
  • lines changed 4, context: html, text, full: html, text
    Renamed Alignment files, as there was an error in 2 submissions which had an older daf that didn't require replicates for alignment files. Redmine #4156.
  • lines changed 16, context: html, text, full: html, text
    modify labels
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCshlLongRnaSeq.release2.html
  • lines changed 123, context: html, text, full: html, text
    Removed rel="nofollow" for current tracks being worked on. Redmine #7533.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCshlLongRnaSeq.release2.ra
  • lines changed 1164, context: html, text, full: html, text
    Removed rel="nofollow" for current tracks being worked on. Redmine #7533.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeFsuRepliSeq.html
  • lines changed 149, context: html, text, full: html, text
    Added trackDescription and metaData variables. Redmine #6627.
  • lines changed 6, context: html, text, full: html, text
    Removed rel="nofollow" for current tracks being worked on. Redmine #7533.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeFsuRepliSeq.ra
  • lines changed 238, context: html, text, full: html, text
    Displaying the first 24 experiments from FSU for Mouse. Redmine #6627.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrHistone.release2.html
  • lines changed 14, context: html, text, full: html, text
    fixes according to Steve's comments in 153, #5393
  • lines changed 4, context: html, text, full: html, text
    fix methods
  • lines changed 1, context: html, text, full: html, text
    fixed Steve's comment 10, 11b, 16b in note 165 #5393
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrHistone.release2.ra
  • lines changed 44, context: html, text, full: html, text
    add Histone Modifications by to the long label of new submissions, responding to Steve's pont 4 in note 152 and note 155 in #5393
  • lines changed 1, context: html, text, full: html, text
    fixing long labels
  • lines changed 1, context: html, text, full: html, text
    fix order of the tissues
  • lines changed 3, context: html, text, full: html, text
    fix adult-24wks to 24w to be consistent with others
  • lines changed 4, context: html, text, full: html, text
    fix age in longLabel
  • lines changed 137, context: html, text, full: html, text
    fix order in file list
  • lines changed 120, context: html, text, full: html, text
    remove 1 before adult8wks, as it may have broken the pull down list below the matrix
  • lines changed 128, context: html, text, full: html, text
    add 1 in front of ADULT8WKS and 2 to ADULT24WKS, update the dimensionAchecked as well
  • lines changed 2, context: html, text, full: html, text
    fixed long labels
  • lines changed 10, context: html, text, full: html, text
    fixed the default check box, see Steve's point 5,6 in note 157 and Venkat note 168 in ticket 5393
  • lines changed 1, context: html, text, full: html, text
    fixing the greying box problem, see note 169, 173 in #5393
  • lines changed 2, context: html, text, full: html, text
    turn whole brain E14.5 off to fix the grey box problem but the lab wants to have whole brain E14.5 displayed by default, this is in conflict
  • lines changed 1, context: html, text, full: html, text
    turn off the whole brain E14.5 subtrack, missekd earlier
  • lines changed 362, context: html, text, full: html, text
    added in enw tracks for licr histone
  • lines changed 362, context: html, text, full: html, text
    Revert "added in enw tracks for licr histone" This reverts commit dcff6d1eccd504083b3c1194c50f1ac5ebb3ca2f.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrHistone.release3.html
  • lines changed 242, context: html, text, full: html, text
    change ADULT8WKS to ADLT8W in all the subtracks, add new html file
  • lines changed 1, context: html, text, full: html, text
    change release note 2 to 3, a test
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrHistone.release3.ra
  • lines changed 1756, context: html, text, full: html, text
    change ADULT8WKS to ADLT8W in all the subtracks, add new html file
  • lines changed 428, context: html, text, full: html, text
    change age=ADLT8W to age=ADULT8WKS to update those submissions loaded before ADULT8WKS is changed to ADLT8W
  • lines changed 36, context: html, text, full: html, text
    change ADULT8WKS to ADLT8W after update mdb of all the subtracks submitted before ADULT8WKS was changed to ADLT8W
  • lines changed 147, context: html, text, full: html, text
    change ADULT8WKS to 1ADLT8W for ordering, update mdb
  • lines changed 1, context: html, text, full: html, text
    change wrangler from Venkat to Ruihua in comment section
  • lines changed 5, context: html, text, full: html, text
    add 0 in front of BCELLxxx to force order
  • lines changed 40, context: html, text, full: html, text
    clean up long labels
  • lines changed 40, context: html, text, full: html, text
    clean up long labels
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrTfbs.release2.html
  • lines changed 23, context: html, text, full: html, text
    copy the html from LicrHistone which is the same as this track after correction in responding to all the points in Steve's note 153, points 11b, 16b in note 165 in ticket #5393
  • lines changed 3, context: html, text, full: html, text
    modified release note
  • lines changed 2, context: html, text, full: html, text
    fixed release note
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrTfbs.release2.ra
  • lines changed 77, context: html, text, full: html, text
    fixing cell name, age order, see Steve's point 1, 3 in note 152, ticket #5393 which are the same as this track
  • lines changed 5, context: html, text, full: html, text
    turn input signal off
  • lines changed 10, context: html, text, full: html, text
    add TFBS to MEL, BMDM longLabel
  • lines changed 1, context: html, text, full: html, text
    fixing the greying box problem, see note 169, 173 in #5393
  • lines changed 4, context: html, text, full: html, text
    turn whole brain E14.5 off to fix the grey box problem but the lab wants to have whole brain E14.5 displayed by default, this is in conflict
  • lines changed 1, context: html, text, full: html, text
    fix short label
  • lines changed 9, context: html, text, full: html, text
    remove stanza of Placenta adult-8wks Input, as its corresponding tfbs antibody dataset were not submitted
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuHistone.release2.html
  • lines changed 222, context: html, text, full: html, text
    Removed rel="nofollow" for current tracks being worked on. Redmine #7533.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuHistone.release2.ra
  • lines changed 1, context: html, text, full: html, text
    Removed rel="nofollow" for current tracks being worked on. Redmine #7533.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuRnaSeq.ra
  • lines changed 162, context: html, text, full: html, text
    Added 3 submissions for RNA-seq track. Redmine #107.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuTfbs.release2.html
  • lines changed 263, context: html, text, full: html, text
    Added 1 submission for release 2 of track. Redmine #7516.
  • lines changed 13, context: html, text, full: html, text
    Removed rel="nofollow" for current tracks being worked on. Redmine #7533.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuTfbs.release2.ra
  • lines changed 517, context: html, text, full: html, text
    Added 1 submission for release 2 of track. Redmine #7516.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhHist.release2.html
  • lines changed 147, context: html, text, full: html, text
    create trackDb and html files for release2
  • lines changed 6, context: html, text, full: html, text
    update html reference and release note
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhHist.release2.ra
  • lines changed 163, context: html, text, full: html, text
    create trackDb and html files for release2
  • lines changed 1, context: html, text, full: html, text
    update html reference and release note
  • lines changed 137, context: html, text, full: html, text
    update with new submissions
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhTfbs.release3.ra
  • lines changed 146, context: html, text, full: html, text
    added in tracks to sydh tfbs mm9 trackDb
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwDgf.html
  • lines changed 128, context: html, text, full: html, text
    Added track description for track. Redmine #3631.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwDgf.ra
  • lines changed 32, context: html, text, full: html, text
    Fixed metadata erore with age and strain for A20, 416B, MEL and mg/ER. Redmine #4469,#4468,#3631.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwDnase.release2.ra
  • lines changed 62, context: html, text, full: html, text
    Fixed metadata erore with age and strain for A20, 416B, MEL and mg/ER. Redmine #4469,#4468,#3631.
  • lines changed 7, context: html, text, full: html, text
    Updated strain for ES-CJ7 to be a specific 129 strain.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwRnaSeq.ra
  • lines changed 108, context: html, text, full: html, text
    Fixed metadata erore with age and strain for A20, 416B, MEL and mg/ER. Redmine #4469,#4468,#3631.
• src/hg/makeDb/trackDb/rat/rn4/polyASeqSites.html
  • lines changed 59, context: html, text, full: html, text
    This was a copy/paste replacement of everything in these files (except the table) from the hg19 version of this file that I updated. So it included all the changes that were in there: html cleanup, link edit, minor grammar fix
  • lines changed 5, context: html, text, full: html, text
    Updated table formatting per the same change made on this file on hg19.
  • lines changed 1, context: html, text, full: html, text
    Added name of second person under credits per request from Adnan.
• src/hg/makeDb/trackDb/rat/rn4/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    Removed Fan's PolyA-Seq track
• src/hg/makeDb/trackDb/rhesus/rheMac2/polyASeqSites.html
  • lines changed 59, context: html, text, full: html, text
    This was a copy/paste replacement of everything in these files (except the table) from the hg19 version of this file that I updated. So it included all the changes that were in there: html cleanup, link edit, minor grammar fix
  • lines changed 7, context: html, text, full: html, text
    Updated table formatting per the same change made on this file on hg19.
  • lines changed 1, context: html, text, full: html, text
    Oops. Missed getting rid of the old table header color. Gone now.
  • lines changed 1, context: html, text, full: html, text
    Added name of second person under credits per request from Adnan.
• src/hg/makeDb/trackDb/rhesus/rheMac2/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    Removed Fan's PolyA-Seq track
• src/hg/makeDb/trackDb/sacCer/sacCer1/description.html
  • lines changed 3, context: html, text, full: html, text
    The link to the photo credit was no longer valid for these assemblies. Searched for a replacement link, but could not fine one. Removed the link, but left the name.
• src/hg/makeDb/trackDb/sacCer/sacCer2/description.html
  • lines changed 3, context: html, text, full: html, text
    The link to the photo credit was no longer valid for these assemblies. Searched for a replacement link, but could not fine one. Removed the link, but left the name.
  • lines changed 1, context: html, text, full: html, text
    Fixed broken link
• src/hg/makeDb/trackDb/sacCer/sacCer3/description.html
  • lines changed 3, context: html, text, full: html, text
    The link to the photo credit was no longer valid for these assemblies. Searched for a replacement link, but could not fine one. Removed the link, but left the name.
• src/hg/makeDb/trackDb/seaHare/aplCal1/description.html
  • lines changed 3, context: html, text, full: html, text
    The link to the photo credit was no longer valid for these assemblies. Searched for a replacement link, but could not fine one. Removed the link, but left the name.
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 10, context: html, text, full: html, text
    changing order, inheritance and colors for pubs track
  • lines changed 7, context: html, text, full: html, text
    making pubs subtracks configurable, tdb changes + thanks to tim for help with javascript changes
• src/hg/makeDb/trackDb/turtle/chrPic1/description.html
  • lines changed 132, context: html, text, full: html, text
    original source from makeGenomeDb.pl
• src/hg/makeDb/trackDb/turtle/chrPic1/gap.html
  • lines changed 64, context: html, text, full: html, text
    original source from makeGenomeDb.pl
• src/hg/makeDb/trackDb/turtle/chrPic1/gold.html
  • lines changed 23, context: html, text, full: html, text
    original source from makeGenomeDb.pl
• src/hg/makeDb/trackDb/turtle/chrPic1/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    original source from makeGenomeDb.pl
• src/hg/makeDb/trackDb/zebrafish/danRer3/rhMap.html
  • lines changed 1, context: html, text, full: html, text
    Fixed broken links
• src/hg/makeDb/trackDb/zebrafish/danRer4/rhMap.html
  • lines changed 1, context: html, text, full: html, text
    Fixed broken links
• src/hg/oneShot/testCvToSql/foo.c
  • lines changed 4302, context: html, text, full: html, text
    Making autoSql output all in single file. Escaping some quotes. Dodging 'grant' reserved word in SQL.
  • lines changed 4302, context: html, text, full: html, text
    Did not mean to commit that autoSql output!
  • lines changed 4305, context: html, text, full: html, text
    Adding long string support.
  • lines changed 4305, context: html, text, full: html, text
    Making a more literal translation of cv.ra into database.
• src/hg/oneShot/testCvToSql/testCvToSql.c
  • lines changed 277, context: html, text, full: html, text
    Working on a program to help convert cv.ra to a relational database.
  • lines changed 98, context: html, text, full: html, text
    Removing no longer used code.
  • lines changed 207, context: html, text, full: html, text
    Making it so that it creates an 'atree' type output that is somewhat rearranged from order and name of fields in cv.ra.
  • lines changed 90, context: html, text, full: html, text
    Adding deprecated field to all tables lacking one.
  • lines changed 255, context: html, text, full: html, text
    Starting to output data as opposed to field structure. Starting to implement merging of fields.
  • lines changed 12, context: html, text, full: html, text
    Checking no tabs in wrong places in input. Removing some debugging.
  • lines changed 109, context: html, text, full: html, text
    Starting to make .as output.
  • lines changed 62, context: html, text, full: html, text
    Improving .as output. Still need to fill in field doc string.
  • lines changed 75, context: html, text, full: html, text
    Adding field descriptions.
  • lines changed 19, context: html, text, full: html, text
    Making autoSql output all in single file. Escaping some quotes. Dodging 'grant' reserved word in SQL.
  • lines changed 12, context: html, text, full: html, text
    Adding long string support.
  • lines changed 226, context: html, text, full: html, text
    Starting to split antibody table.
  • lines changed 8, context: html, text, full: html, text
    Looks like split of antibody table may work as well as can automate. Will require some curation.....
  • lines changed 15, context: html, text, full: html, text
    Making a more literal translation of cv.ra into database.
• src/hg/utils/automation/Encode.pm
  • lines changed 8, context: html, text, full: html, text
    removed daf version check
  • lines changed 1, context: html, text, full: html, text
    removed old bigBedTypes support (tagalign stuff), makes Tim's life easier
• src/hg/utils/automation/grcIncidentDb.pl
  • lines changed 3, context: html, text, full: html, text
    issue.sql has added two new fields
• src/hg/utils/automation/ncbiIncidentDb.pl
  • lines changed 3, context: html, text, full: html, text
    issue.sql has added two new fields
• src/hg/utils/omim/validateOmim.sh
  • lines changed 8, context: html, text, full: html, text
    don't check "numbering" field in omimGeneMap because it changes arbitrarily #6943
• src/hg/utils/phyloTrees/61way.nh
  • lines changed 25, context: html, text, full: html, text
    adding manatee triMan1
• src/hg/utils/phyloTrees/62way.nh
  • lines changed 25, context: html, text, full: html, text
    adding melUnd1 budgie
• src/hg/utils/phyloTrees/primates.txt
  • lines changed 23, context: html, text, full: html, text
    updated with newer listings from NCBI taxonomy
• src/inc/annoFilter.h
  • lines changed 5, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Tool): Added annoStreamWig and annoGrateWig,which led to some significant changes: annoRow is now polymorphic (words[] vs. wig float[]), annoFilter has a new function to apply filter(s) to a single number, and annoFormatTab can print out per-base wiggle values or average wiggle values (hardcoded to do per-base until a real config option is added). One puny test case was verified against mysql & table browser output.
• src/inc/annoFormatter.h
  • lines changed 14, context: html, text, full: html, text
    Fixing style errors found by Brian in code review: public methodsdefined in structs are functions, so the comment should go below the definition not above.
• src/inc/annoGrator.h
  • lines changed 1, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Tool): Added annoStreamVcf, whichled to yet more significant changes to annoRow: instead of every row declaring its type and annoRow{Free,Clone} taking a numCols argument that is meaningless for wig, now annoRow{Free,Clone} take the row's source annoStreamer as an argument. The annoStreamer now has public members (rowType and numCols) that provide all information needed about the row. annoStreamer constructors need to set rowType.
  • lines changed 5, context: html, text, full: html, text
    Fixing style errors found by Brian in code review: public methodsdefined in structs are functions, so the comment should go below the definition not above.
• src/inc/annoRow.h
  • lines changed 16, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Tool): Added annoStreamWig and annoGrateWig,which led to some significant changes: annoRow is now polymorphic (words[] vs. wig float[]), annoFilter has a new function to apply filter(s) to a single number, and annoFormatTab can print out per-base wiggle values or average wiggle values (hardcoded to do per-base until a real config option is added). One puny test case was verified against mysql & table browser output.
  • lines changed 8, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Tool): Added annoStreamVcf, whichled to yet more significant changes to annoRow: instead of every row declaring its type and annoRow{Free,Clone} taking a numCols argument that is meaningless for wig, now annoRow{Free,Clone} take the row's source annoStreamer as an argument. The annoStreamer now has public members (rowType and numCols) that provide all information needed about the row. annoStreamer constructors need to set rowType.
• src/inc/annoStreamVcf.h
  • lines changed 12, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Tool): Added annoStreamVcf, whichled to yet more significant changes to annoRow: instead of every row declaring its type and annoRow{Free,Clone} taking a numCols argument that is meaningless for wig, now annoRow{Free,Clone} take the row's source annoStreamer as an argument. The annoStreamer now has public members (rowType and numCols) that provide all information needed about the row. annoStreamer constructors need to set rowType.
• src/inc/annoStreamer.h
  • lines changed 1, context: html, text, full: html, text
    Comment tweak.
  • lines changed 4, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Tool): Added annoStreamVcf, whichled to yet more significant changes to annoRow: instead of every row declaring its type and annoRow{Free,Clone} taking a numCols argument that is meaningless for wig, now annoRow{Free,Clone} take the row's source annoStreamer as an argument. The annoStreamer now has public members (rowType and numCols) that provide all information needed about the row. annoStreamer constructors need to set rowType.
  • lines changed 17, context: html, text, full: html, text
    Fixing style errors found by Brian in code review: public methodsdefined in structs are functions, so the comment should go below the definition not above.
• src/inc/asParse.h
  • lines changed 1, context: html, text, full: html, text
    First cut of Django output for autoSql.
• src/inc/common.h
  • lines changed 1, context: html, text, full: html, text
    Improving comments.
• src/inc/sqlNum.h
  • lines changed 7, context: html, text, full: html, text
    Improving comments.
• src/inc/vcf.h
  • lines changed 17, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Tool): Added annoStreamVcf, whichled to yet more significant changes to annoRow: instead of every row declaring its type and annoRow{Free,Clone} taking a numCols argument that is meaningless for wig, now annoRow{Free,Clone} take the row's source annoStreamer as an argument. The annoStreamer now has public members (rowType and numCols) that provide all information needed about the row. annoStreamer constructors need to set rowType.
• src/kehayden/alphaChain/alphaChain.c
  • lines changed 429, context: html, text, full: html, text
    Starting to adapt wordChain.c to alphaChain.c for sequence generation
  • lines changed 44, context: html, text, full: html, text
    updated input to treat each line separately\n
  • lines changed 57, context: html, text, full: html, text
    adapting to centromere DYZ3 dataset
• src/kehayden/learningLibs/.learningLibs.c.swp
  • lines changed 0, context: html, text, full: html, text
    created during tags tutorial with markd
• src/kehayden/learningLibs/learningLibs.c
  • lines changed 36, context: html, text, full: html, text
    added TAGS for kent library (c/o markd)
  • lines changed 61, context: html, text, full: html, text
    KEH: updated version of learningLibs. Breaks lines into words and loads words into memory. Segmentation fault when looping through elements of the array to count occurence in hash data structure
  • lines changed 54, context: html, text, full: html, text
    JK/KH update of learningLibs from Mtg2
• src/kehayden/learningLibs/makefile
  • lines changed 18, context: html, text, full: html, text
    added TAGS for kent library (c/o markd)
• src/kehayden/tokenizerLib/makefile
  • lines changed 18, context: html, text, full: html, text
    KEH added tokenizerLib as a practice assignment for Jim Mtg 3
• src/kehayden/tokenizerLib/tokenizerLib.c
  • lines changed 151, context: html, text, full: html, text
    KEH added tokenizerLib as a practice assignment for Jim Mtg 3
  • lines changed 38, context: html, text, full: html, text
    switching from linefile to tokenizer
• src/lib/annoFilter.c
  • lines changed 29, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Tool): Added annoStreamWig and annoGrateWig,which led to some significant changes: annoRow is now polymorphic (words[] vs. wig float[]), annoFilter has a new function to apply filter(s) to a single number, and annoFormatTab can print out per-base wiggle values or average wiggle values (hardcoded to do per-base until a real config option is added). One puny test case was verified against mysql & table browser output.
• src/lib/annoFormatTab.c
  • lines changed 81, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Tool): Added annoStreamWig and annoGrateWig,which led to some significant changes: annoRow is now polymorphic (words[] vs. wig float[]), annoFilter has a new function to apply filter(s) to a single number, and annoFormatTab can print out per-base wiggle values or average wiggle values (hardcoded to do per-base until a real config option is added). One puny test case was verified against mysql & table browser output.
  • lines changed 10, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Tool): Added annoStreamVcf, whichled to yet more significant changes to annoRow: instead of every row declaring its type and annoRow{Free,Clone} taking a numCols argument that is meaningless for wig, now annoRow{Free,Clone} take the row's source annoStreamer as an argument. The annoStreamer now has public members (rowType and numCols) that provide all information needed about the row. annoStreamer constructors need to set rowType.
• src/lib/annoGrator.c
  • lines changed 7, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Tool): Added annoStreamVcf, whichled to yet more significant changes to annoRow: instead of every row declaring its type and annoRow{Free,Clone} taking a numCols argument that is meaningless for wig, now annoRow{Free,Clone} take the row's source annoStreamer as an argument. The annoStreamer now has public members (rowType and numCols) that provide all information needed about the row. annoStreamer constructors need to set rowType.
  • lines changed 2, context: html, text, full: html, text
    start on genepred / variant annoGrator. #6152
  • lines changed 2, context: html, text, full: html, text
    fix bug in annoGratorClose
• src/lib/annoGratorQuery.c
  • lines changed 1, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Tool): Added annoStreamWig and annoGrateWig,which led to some significant changes: annoRow is now polymorphic (words[] vs. wig float[]), annoFilter has a new function to apply filter(s) to a single number, and annoFormatTab can print out per-base wiggle values or average wiggle values (hardcoded to do per-base until a real config option is added). One puny test case was verified against mysql & table browser output.
  • lines changed 3, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Tool): Added annoStreamVcf, whichled to yet more significant changes to annoRow: instead of every row declaring its type and annoRow{Free,Clone} taking a numCols argument that is meaningless for wig, now annoRow{Free,Clone} take the row's source annoStreamer as an argument. The annoStreamer now has public members (rowType and numCols) that provide all information needed about the row. annoStreamer constructors need to set rowType.
• src/lib/annoRow.c
  • lines changed 57, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Tool): Added annoStreamWig and annoGrateWig,which led to some significant changes: annoRow is now polymorphic (words[] vs. wig float[]), annoFilter has a new function to apply filter(s) to a single number, and annoFormatTab can print out per-base wiggle values or average wiggle values (hardcoded to do per-base until a real config option is added). One puny test case was verified against mysql & table browser output.
  • lines changed 16, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Tool): Added annoStreamVcf, whichled to yet more significant changes to annoRow: instead of every row declaring its type and annoRow{Free,Clone} taking a numCols argument that is meaningless for wig, now annoRow{Free,Clone} take the row's source annoStreamer as an argument. The annoStreamer now has public members (rowType and numCols) that provide all information needed about the row. annoStreamer constructors need to set rowType.
• src/lib/annoStreamVcf.c
  • lines changed 135, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Tool): Added annoStreamVcf, whichled to yet more significant changes to annoRow: instead of every row declaring its type and annoRow{Free,Clone} taking a numCols argument that is meaningless for wig, now annoRow{Free,Clone} take the row's source annoStreamer as an argument. The annoStreamer now has public members (rowType and numCols) that provide all information needed about the row. annoStreamer constructors need to set rowType.
• src/lib/annoStreamer.c
  • lines changed 1, context: html, text, full: html, text
    Comment tweak.
  • lines changed 1, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Tool): Added annoStreamVcf, whichled to yet more significant changes to annoRow: instead of every row declaring its type and annoRow{Free,Clone} taking a numCols argument that is meaningless for wig, now annoRow{Free,Clone} take the row's source annoStreamer as an argument. The annoStreamer now has public members (rowType and numCols) that provide all information needed about the row. annoStreamer constructors need to set rowType.
• src/lib/asParse.c
  • lines changed 34, context: html, text, full: html, text
    First cut of Django output for autoSql.
• src/lib/common.c
  • lines changed 3, context: html, text, full: html, text
    Improving comments.
• src/lib/linefile.c
  • lines changed 1, context: html, text, full: html, text
    lineFileTabixMayOpen: initialize lf->tabixIter to ti_iter_first sowe can start reading lines from the beginning of the tabix-indexed file, without having to make an iterator for a specific region.
• src/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Tool): Added annoStreamVcf, whichled to yet more significant changes to annoRow: instead of every row declaring its type and annoRow{Free,Clone} taking a numCols argument that is meaningless for wig, now annoRow{Free,Clone} take the row's source annoStreamer as an argument. The annoStreamer now has public members (rowType and numCols) that provide all information needed about the row. annoStreamer constructors need to set rowType.
• src/lib/pipeline.c
  • lines changed 227, context: html, text, full: html, text
    checking Mark's changes back in. #1201
  • lines changed 1, context: html, text, full: html, text
    removed outdated FIXME comment
• src/lib/tests/expected/pipelineExecError.err
  • lines changed 2, context: html, text, full: html, text
    checking Mark's changes back in. #1201
• src/lib/tests/expected/pipelineExecError.parent.err
  • lines changed 2, context: html, text, full: html, text
    checking Mark's changes back in. #1201
• src/lib/tests/makefile
  • lines changed 9, context: html, text, full: html, text
    checking Mark's changes back in. #1201
• src/lib/vcf.c
  • lines changed 60, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Tool): Added annoStreamVcf, whichled to yet more significant changes to annoRow: instead of every row declaring its type and annoRow{Free,Clone} taking a numCols argument that is meaningless for wig, now annoRow{Free,Clone} take the row's source annoStreamer as an argument. The annoStreamer now has public members (rowType and numCols) that provide all information needed about the row. annoStreamer constructors need to set rowType.
• src/utils/autoDtd/autoDtd.c
  • lines changed 463, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 463, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/utils/autoDtd/doTest
  • lines changed 13, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 13, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/utils/autoDtd/makefile
  • lines changed 18, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 18, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/utils/autoDtd/test/chado/expected.atree
  • lines changed 77, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 77, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/utils/autoDtd/test/chado/expected.dtd
  • lines changed 183, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 183, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/utils/autoDtd/test/chado/expected.stats
  • lines changed 190, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 190, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/utils/autoDtd/test/chado/expected.tree
  • lines changed 77, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 77, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/utils/autoDtd/test/chado/in.xml
  • lines changed 1017, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 1017, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/utils/autoDtd/test/hotnews/expected.atree
  • lines changed 18, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 18, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/utils/autoDtd/test/hotnews/expected.dtd
  • lines changed 58, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 58, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/utils/autoDtd/test/hotnews/expected.stats
  • lines changed 49, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 49, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/utils/autoDtd/test/hotnews/expected.tree
  • lines changed 18, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 18, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/utils/autoDtd/test/hotnews/in.xml
  • lines changed 77, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 77, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/utils/autoDtd/test/shapes/expected.atree
  • lines changed 4, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 4, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/utils/autoDtd/test/shapes/expected.dtd
  • lines changed 23, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 23, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/utils/autoDtd/test/shapes/expected.stats
  • lines changed 22, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 22, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/utils/autoDtd/test/shapes/expected.tree
  • lines changed 4, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 4, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/utils/autoDtd/test/shapes/in.xml
  • lines changed 16, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 16, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/utils/autoSql/.gitignore
  • lines changed 1, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 1, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/utils/autoSql/autoSql.c
  • lines changed 1946, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 1946, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/utils/autoSql/autoSql.doc
  • lines changed 312, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 312, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/utils/autoSql/commonSh.c
  • lines changed 39, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 39, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/utils/autoSql/doc.as
  • lines changed 17, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 17, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/utils/autoSql/doc2.as
  • lines changed 33, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 33, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/utils/autoSql/eztok.c
  • lines changed 71, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 71, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/utils/autoSql/eztok.h
  • lines changed 18, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 18, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/utils/autoSql/makefile
  • lines changed 29, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 29, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/utils/autoSql/tests/.gitignore
  • lines changed 5, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 5, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/utils/autoSql/tests/dbLinkTest.c
  • lines changed 326, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 326, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/utils/autoSql/tests/expected/dbLinkTest.out
  • lines changed 5, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 5, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/utils/autoSql/tests/expected/doc.c
  • lines changed 336, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 336, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/utils/autoSql/tests/expected/doc.h
  • lines changed 135, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 135, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/utils/autoSql/tests/expected/doc.sql
  • lines changed 24, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 24, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/utils/autoSql/tests/expected/doc2.c
  • lines changed 622, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 622, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/utils/autoSql/tests/expected/doc2.h
  • lines changed 200, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 200, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/utils/autoSql/tests/expected/doc2.sql
  • lines changed 14, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 14, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/utils/autoSql/tests/expected/hardTest.c
  • lines changed 447, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 447, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/utils/autoSql/tests/expected/hardTest.h
  • lines changed 120, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 120, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/utils/autoSql/tests/expected/hardTest.sql
  • lines changed 26, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 26, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/utils/autoSql/tests/expected/jsonTest.out
  • lines changed 16, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 16, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/utils/autoSql/tests/expected/mainTest.c
  • lines changed 859, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 859, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/utils/autoSql/tests/expected/mainTest.h
  • lines changed 287, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 287, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/utils/autoSql/tests/expected/mainTest.sql
  • lines changed 33, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 33, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/utils/autoSql/tests/expected/newTest.c
  • lines changed 434, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 434, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/utils/autoSql/tests/expected/newTest.err
  • lines changed 2, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 2, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/utils/autoSql/tests/expected/newTest.h
  • lines changed 140, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 140, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/utils/autoSql/tests/expected/newTest.sql
  • lines changed 21, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 21, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/utils/autoSql/tests/expected/polyTest.c
  • lines changed 428, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 428, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/utils/autoSql/tests/expected/polyTest.h
  • lines changed 157, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 157, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/utils/autoSql/tests/expected/polyTest.sql
  • lines changed 23, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 23, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/utils/autoSql/tests/expected/simpleTest.c
  • lines changed 1037, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 1037, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/utils/autoSql/tests/expected/simpleTest.h
  • lines changed 399, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 399, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/utils/autoSql/tests/expected/simpleTest.sql
  • lines changed 12, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 12, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/utils/autoSql/tests/expected/symColsTest.tab
  • lines changed 6, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 6, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/utils/autoSql/tests/expected/symTest.c
  • lines changed 134, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 134, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/utils/autoSql/tests/expected/symTest.err
  • lines changed 0, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 0, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/utils/autoSql/tests/expected/symTest.h
  • lines changed 75, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 75, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/utils/autoSql/tests/expected/symTest.sql
  • lines changed 13, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 13, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/utils/autoSql/tests/expected/testHarness.out
  • lines changed 17, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 17, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/utils/autoSql/tests/input/doc.as
  • lines changed 17, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 17, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/utils/autoSql/tests/input/doc2.as
  • lines changed 33, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 33, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/utils/autoSql/tests/input/hardTest.as
  • lines changed 28, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 28, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/utils/autoSql/tests/input/mainTest.as
  • lines changed 51, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 51, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/utils/autoSql/tests/input/newTest.as
  • lines changed 22, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 22, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/utils/autoSql/tests/input/polyTest.as
  • lines changed 25, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 25, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/utils/autoSql/tests/input/simpleTest.as
  • lines changed 66, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 66, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/utils/autoSql/tests/input/symColsTest.tab
  • lines changed 6, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 6, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/utils/autoSql/tests/input/symTest.as
  • lines changed 8, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 8, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/utils/autoSql/tests/jsonTest.c
  • lines changed 114, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 114, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/utils/autoSql/tests/makefile
  • lines changed 118, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 118, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/utils/autoSql/tests/testHarness.c
  • lines changed 193, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 193, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/utils/autoSql/tests/testSymCols.c
  • lines changed 117, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 117, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/utils/autoXml/autoXml.c
  • lines changed 724, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 724, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/utils/autoXml/autoXml.doc
  • lines changed 190, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 190, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/utils/autoXml/dasBed.dtdx
  • lines changed 43, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 43, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/utils/autoXml/doTest
  • lines changed 5, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 5, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/utils/autoXml/makefile
  • lines changed 17, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 17, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/utils/autoXml/polygon.dtdx
  • lines changed 9, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 9, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/utils/autoXml/t/makefile
  • lines changed 14, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 14, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/utils/autoXml/t/t.c
  • lines changed 255, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 255, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/utils/autoXml/test.dtdx
  • lines changed 36, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 36, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/utils/autoXml/test/dasGff/dasGff.dtd
  • lines changed 45, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 45, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/utils/autoXml/test/dasGff/expected/dasGff.c
  • lines changed 1281, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 1281, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/utils/autoXml/test/dasGff/expected/dasGff.h
  • lines changed 387, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 387, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/utils/autoXml/test/polygon/expected/polygon.c
  • lines changed 241, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 241, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/utils/autoXml/test/polygon/expected/polygon.h
  • lines changed 89, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 89, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/utils/autoXml/test/polygon/polygon.dtd
  • lines changed 11, context: html, text, full: html, text
    Removing MySQL linking dependency.
  • lines changed 11, context: html, text, full: html, text
    Moving autoSql and autoDtd and autoXml back to just under hg. A little autoSql -django fix.
• src/utils/qa/bigPush.csh
  • lines changed 5, context: html, text, full: html, text
    Changed usage statement slightly now that admins have set sudo timeout length to 30 min.
  • lines changed 7, context: html, text, full: html, text
    Removed more of the warnings about re-typing password.
• src/utils/qa/countPerChrom.csh
  • lines changed 4, context: html, text, full: html, text
    Changed some exits to exit with an error status and added an onintr to keep tables from being left behind when the command is interrupted.
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    v266 preview1
• src/utils/raSqlQuery/raSqlQuery.c
  • lines changed 2, context: html, text, full: html, text
    Improving usage message which was lacking 'from' clause.

• lines changed: 272862
• files changed: 984