Commits for kent

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

• Working on a program to help convert cv.ra to a relational database.
  • src/hg/oneShot/testCvToSql/testCvToSql.c - lines changed 277, context: html, text, full: html, text
• Removing no longer used code.
  • src/hg/oneShot/testCvToSql/testCvToSql.c - lines changed 98, context: html, text, full: html, text
• Improving usage message which was lacking 'from' clause.
  • src/utils/raSqlQuery/raSqlQuery.c - lines changed 2, 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.
  • src/hg/oneShot/testCvToSql/testCvToSql.c - lines changed 207, context: html, text, full: html, text
• Adding deprecated field to all tables lacking one.
  • src/hg/oneShot/testCvToSql/testCvToSql.c - lines changed 90, context: html, text, full: html, text
• Starting to output data as opposed to field structure. Starting to implement merging of fields.
  • src/hg/oneShot/testCvToSql/testCvToSql.c - lines changed 255, context: html, text, full: html, text
• Checking no tabs in wrong places in input. Removing some debugging.
  • src/hg/oneShot/testCvToSql/testCvToSql.c - lines changed 12, context: html, text, full: html, text
• Starting to make .as output.
  • src/hg/oneShot/testCvToSql/testCvToSql.c - lines changed 109, context: html, text, full: html, text
• Improving .as output. Still need to fill in field doc string.
  • src/hg/oneShot/testCvToSql/testCvToSql.c - lines changed 62, context: html, text, full: html, text
• Adding field descriptions.
  • src/hg/oneShot/testCvToSql/testCvToSql.c - lines changed 75, context: html, text, full: html, text
• Making autoSql output all in single file. Escaping some quotes. Dodging 'grant' reserved word in SQL.
  • src/hg/oneShot/testCvToSql/foo.c - lines changed 4302, context: html, text, full: html, text
  • src/hg/oneShot/testCvToSql/testCvToSql.c - lines changed 19, context: html, text, full: html, text
• Did not mean to commit that autoSql output!
  • src/hg/oneShot/testCvToSql/foo.c - lines changed 4302, context: html, text, full: html, text
• Improving comments.
  • src/inc/common.h - lines changed 1, context: html, text, full: html, text
  • src/inc/sqlNum.h - lines changed 7, context: html, text, full: html, text
  • src/lib/common.c - lines changed 3, context: html, text, full: html, text
• First cut of Django output for autoSql.
  • src/hg/autoSql/autoSql.c - lines changed 128, context: html, text, full: html, text
  • src/inc/asParse.h - lines changed 1, context: html, text, full: html, text
  • src/lib/asParse.c - lines changed 34, context: html, text, full: html, text
• Adding long string support.
  • src/hg/oneShot/testCvToSql/foo.c - lines changed 4305, context: html, text, full: html, text
  • src/hg/oneShot/testCvToSql/testCvToSql.c - lines changed 12, context: html, text, full: html, text
• Noting update of wgEncodeRegTfbsClustered
  • src/hg/makeDb/doc/hg19.txt - lines changed 1, context: html, text, full: html, text
• Starting to split antibody table.
  • src/hg/oneShot/testCvToSql/testCvToSql.c - lines changed 226, context: html, text, full: html, text
• Looks like split of antibody table may work as well as can automate. Will require some curation.....
  • src/hg/oneShot/testCvToSql/testCvToSql.c - lines changed 8, context: html, text, full: html, text
• Updating style guide a little to allow // comments mostly.
  • src/README - lines changed 34, context: html, text, full: html, text
• Adding recommendations against long lines and long functions.
  • src/README - lines changed 23, context: html, text, full: html, text
• Minor edits.
  • src/README - lines changed 4, context: html, text, full: html, text
• More wordsmithing
  • src/README - lines changed 18, context: html, text, full: html, text
• Adding a section on modules.
  • src/README - lines changed 27, context: html, text, full: html, text
• Splitting up README to populate higher level README.
  • README - lines changed 119, context: html, text, full: html, text
  • src/README - lines changed 116, context: html, text, full: html, text
• Adding commas to ruler on Genome Browser. Redmine #7559
  • src/hg/lib/hvGfx.c - lines changed 16, context: html, text, full: html, text
• Adding more information about source tree structure and revisiting list of useful library modules.
  • README - lines changed 3, context: html, text, full: html, text
  • src/README - lines changed 52, context: html, text, full: html, text
• Removing dependence on src/hg/lib
  • src/hg/autoXml/makefile - lines changed 1, context: html, text, full: html, text
• Removing MySQL linking dependency.
  • src/hg/autoDtd/autoDtd.c - lines changed 463, context: html, text, full: html, text
  • src/hg/autoDtd/doTest - lines changed 13, context: html, text, full: html, text
  • src/hg/autoDtd/makefile - lines changed 18, context: html, text, full: html, text
  • src/hg/autoDtd/test/chado/expected.atree - lines changed 77, context: html, text, full: html, text
  • src/hg/autoDtd/test/chado/expected.dtd - lines changed 183, context: html, text, full: html, text
  • src/hg/autoDtd/test/chado/expected.stats - lines changed 190, context: html, text, full: html, text
  • src/hg/autoDtd/test/chado/expected.tree - lines changed 77, context: html, text, full: html, text
  • src/hg/autoDtd/test/chado/in.xml - lines changed 1017, context: html, text, full: html, text
  • src/hg/autoDtd/test/hotnews/expected.atree - lines changed 18, context: html, text, full: html, text
  • src/hg/autoDtd/test/hotnews/expected.dtd - lines changed 58, context: html, text, full: html, text
  • src/hg/autoDtd/test/hotnews/expected.stats - lines changed 49, context: html, text, full: html, text
  • src/hg/autoDtd/test/hotnews/expected.tree - lines changed 18, context: html, text, full: html, text
  • src/hg/autoDtd/test/hotnews/in.xml - lines changed 77, context: html, text, full: html, text
  • src/hg/autoDtd/test/shapes/expected.atree - lines changed 4, context: html, text, full: html, text
  • src/hg/autoDtd/test/shapes/expected.dtd - lines changed 23, context: html, text, full: html, text
  • src/hg/autoDtd/test/shapes/expected.stats - lines changed 22, context: html, text, full: html, text
  • src/hg/autoDtd/test/shapes/expected.tree - lines changed 4, context: html, text, full: html, text
  • src/hg/autoDtd/test/shapes/in.xml - lines changed 16, context: html, text, full: html, text
  • src/hg/autoSql/.gitignore - lines changed 1, context: html, text, full: html, text
  • src/hg/autoSql/autoSql.c - lines changed 1946, context: html, text, full: html, text
  • src/hg/autoSql/autoSql.doc - lines changed 312, context: html, text, full: html, text
  • src/hg/autoSql/commonSh.c - lines changed 39, context: html, text, full: html, text
  • src/hg/autoSql/doc.as - lines changed 17, context: html, text, full: html, text
  • src/hg/autoSql/doc2.as - lines changed 33, context: html, text, full: html, text
  • src/hg/autoSql/eztok.c - lines changed 71, context: html, text, full: html, text
  • src/hg/autoSql/eztok.h - lines changed 18, context: html, text, full: html, text
  • src/hg/autoSql/makefile - lines changed 29, context: html, text, full: html, text
  • src/hg/autoSql/tests/.gitignore - lines changed 5, context: html, text, full: html, text
  • src/hg/autoSql/tests/dbLinkTest.c - lines changed 326, context: html, text, full: html, text
  • src/hg/autoSql/tests/expected/dbLinkTest.out - lines changed 5, context: html, text, full: html, text
  • src/hg/autoSql/tests/expected/doc.c - lines changed 336, context: html, text, full: html, text
  • src/hg/autoSql/tests/expected/doc.h - lines changed 135, context: html, text, full: html, text
  • src/hg/autoSql/tests/expected/doc.sql - lines changed 24, context: html, text, full: html, text
  • src/hg/autoSql/tests/expected/doc2.c - lines changed 622, context: html, text, full: html, text
  • src/hg/autoSql/tests/expected/doc2.h - lines changed 200, context: html, text, full: html, text
  • src/hg/autoSql/tests/expected/doc2.sql - lines changed 14, context: html, text, full: html, text
  • src/hg/autoSql/tests/expected/hardTest.c - lines changed 447, context: html, text, full: html, text
  • src/hg/autoSql/tests/expected/hardTest.h - lines changed 120, context: html, text, full: html, text
  • src/hg/autoSql/tests/expected/hardTest.sql - lines changed 26, context: html, text, full: html, text
  • src/hg/autoSql/tests/expected/jsonTest.out - lines changed 16, context: html, text, full: html, text
  • src/hg/autoSql/tests/expected/mainTest.c - lines changed 859, context: html, text, full: html, text
  • src/hg/autoSql/tests/expected/mainTest.h - lines changed 287, context: html, text, full: html, text
  • src/hg/autoSql/tests/expected/mainTest.sql - lines changed 33, context: html, text, full: html, text
  • src/hg/autoSql/tests/expected/newTest.c - lines changed 434, context: html, text, full: html, text
  • src/hg/autoSql/tests/expected/newTest.err - lines changed 2, context: html, text, full: html, text
  • src/hg/autoSql/tests/expected/newTest.h - lines changed 140, context: html, text, full: html, text
  • src/hg/autoSql/tests/expected/newTest.sql - lines changed 21, context: html, text, full: html, text
  • src/hg/autoSql/tests/expected/polyTest.c - lines changed 428, context: html, text, full: html, text
  • src/hg/autoSql/tests/expected/polyTest.h - lines changed 157, context: html, text, full: html, text
  • src/hg/autoSql/tests/expected/polyTest.sql - lines changed 23, context: html, text, full: html, text
  • src/hg/autoSql/tests/expected/simpleTest.c - lines changed 1037, context: html, text, full: html, text
  • src/hg/autoSql/tests/expected/simpleTest.h - lines changed 399, context: html, text, full: html, text
  • src/hg/autoSql/tests/expected/simpleTest.sql - lines changed 12, context: html, text, full: html, text
  • src/hg/autoSql/tests/expected/symColsTest.tab - lines changed 6, context: html, text, full: html, text
  • src/hg/autoSql/tests/expected/symTest.c - lines changed 134, context: html, text, full: html, text
  • src/hg/autoSql/tests/expected/symTest.err - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
  • src/hg/autoSql/tests/expected/symTest.h - lines changed 75, context: html, text, full: html, text
  • src/hg/autoSql/tests/expected/symTest.sql - lines changed 13, context: html, text, full: html, text
  • src/hg/autoSql/tests/expected/testHarness.out - lines changed 17, context: html, text, full: html, text
  • src/hg/autoSql/tests/input/doc.as - lines changed 17, context: html, text, full: html, text
  • src/hg/autoSql/tests/input/doc2.as - lines changed 33, context: html, text, full: html, text
  • src/hg/autoSql/tests/input/hardTest.as - lines changed 28, context: html, text, full: html, text
  • src/hg/autoSql/tests/input/mainTest.as - lines changed 51, context: html, text, full: html, text
  • src/hg/autoSql/tests/input/newTest.as - lines changed 22, context: html, text, full: html, text
  • src/hg/autoSql/tests/input/polyTest.as - lines changed 25, context: html, text, full: html, text
  • src/hg/autoSql/tests/input/simpleTest.as - lines changed 66, context: html, text, full: html, text
  • src/hg/autoSql/tests/input/symColsTest.tab - lines changed 6, context: html, text, full: html, text
  • src/hg/autoSql/tests/input/symTest.as - lines changed 8, context: html, text, full: html, text
  • src/hg/autoSql/tests/jsonTest.c - lines changed 114, context: html, text, full: html, text
  • src/hg/autoSql/tests/makefile - lines changed 118, context: html, text, full: html, text
  • src/hg/autoSql/tests/testHarness.c - lines changed 193, context: html, text, full: html, text
  • src/hg/autoSql/tests/testSymCols.c - lines changed 117, context: html, text, full: html, text
  • src/hg/autoXml/autoXml.c - lines changed 724, context: html, text, full: html, text
  • src/hg/autoXml/autoXml.doc - lines changed 190, context: html, text, full: html, text
  • src/hg/autoXml/dasBed.dtdx - lines changed 43, context: html, text, full: html, text
  • src/hg/autoXml/doTest - lines changed 5, context: html, text, full: html, text
  • src/hg/autoXml/makefile - lines changed 17, context: html, text, full: html, text
  • src/hg/autoXml/polygon.dtdx - lines changed 9, context: html, text, full: html, text
  • src/hg/autoXml/t/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/autoXml/t/t.c - lines changed 255, context: html, text, full: html, text
  • src/hg/autoXml/test.dtdx - lines changed 36, context: html, text, full: html, text
  • src/hg/autoXml/test/dasGff/dasGff.dtd - lines changed 45, context: html, text, full: html, text
  • src/hg/autoXml/test/dasGff/expected/dasGff.c - lines changed 1281, context: html, text, full: html, text
  • src/hg/autoXml/test/dasGff/expected/dasGff.h - lines changed 387, context: html, text, full: html, text
  • src/hg/autoXml/test/polygon/expected/polygon.c - lines changed 241, context: html, text, full: html, text
  • src/hg/autoXml/test/polygon/expected/polygon.h - lines changed 89, context: html, text, full: html, text
  • src/hg/autoXml/test/polygon/polygon.dtd - lines changed 11, context: html, text, full: html, text
  • src/utils/autoDtd/autoDtd.c - lines changed 463, context: html, text, full: html, text
  • src/utils/autoDtd/doTest - lines changed 13, context: html, text, full: html, text
  • src/utils/autoDtd/makefile - lines changed 18, context: html, text, full: html, text
  • src/utils/autoDtd/test/chado/expected.atree - lines changed 77, context: html, text, full: html, text
  • src/utils/autoDtd/test/chado/expected.dtd - lines changed 183, context: html, text, full: html, text
  • src/utils/autoDtd/test/chado/expected.stats - lines changed 190, context: html, text, full: html, text
  • src/utils/autoDtd/test/chado/expected.tree - lines changed 77, context: html, text, full: html, text
  • src/utils/autoDtd/test/chado/in.xml - lines changed 1017, context: html, text, full: html, text
  • src/utils/autoDtd/test/hotnews/expected.atree - lines changed 18, context: html, text, full: html, text
  • src/utils/autoDtd/test/hotnews/expected.dtd - lines changed 58, context: html, text, full: html, text
  • src/utils/autoDtd/test/hotnews/expected.stats - lines changed 49, context: html, text, full: html, text
  • src/utils/autoDtd/test/hotnews/expected.tree - lines changed 18, context: html, text, full: html, text
  • src/utils/autoDtd/test/hotnews/in.xml - lines changed 77, context: html, text, full: html, text
  • src/utils/autoDtd/test/shapes/expected.atree - lines changed 4, context: html, text, full: html, text
  • src/utils/autoDtd/test/shapes/expected.dtd - lines changed 23, context: html, text, full: html, text
  • src/utils/autoDtd/test/shapes/expected.stats - lines changed 22, context: html, text, full: html, text
  • src/utils/autoDtd/test/shapes/expected.tree - lines changed 4, context: html, text, full: html, text
  • src/utils/autoDtd/test/shapes/in.xml - lines changed 16, context: html, text, full: html, text
  • src/utils/autoSql/.gitignore - lines changed 1, context: html, text, full: html, text
  • src/utils/autoSql/autoSql.c - lines changed 1946, context: html, text, full: html, text
  • src/utils/autoSql/autoSql.doc - lines changed 312, context: html, text, full: html, text
  • src/utils/autoSql/commonSh.c - lines changed 39, context: html, text, full: html, text
  • src/utils/autoSql/doc.as - lines changed 17, context: html, text, full: html, text
  • src/utils/autoSql/doc2.as - lines changed 33, context: html, text, full: html, text
  • src/utils/autoSql/eztok.c - lines changed 71, context: html, text, full: html, text
  • src/utils/autoSql/eztok.h - lines changed 18, context: html, text, full: html, text
  • src/utils/autoSql/makefile - lines changed 29, context: html, text, full: html, text
  • src/utils/autoSql/tests/.gitignore - lines changed 5, context: html, text, full: html, text
  • src/utils/autoSql/tests/dbLinkTest.c - lines changed 326, context: html, text, full: html, text
  • src/utils/autoSql/tests/expected/dbLinkTest.out - lines changed 5, context: html, text, full: html, text
  • src/utils/autoSql/tests/expected/doc.c - lines changed 336, context: html, text, full: html, text
  • src/utils/autoSql/tests/expected/doc.h - lines changed 135, context: html, text, full: html, text
  • src/utils/autoSql/tests/expected/doc.sql - lines changed 24, context: html, text, full: html, text
  • src/utils/autoSql/tests/expected/doc2.c - lines changed 622, context: html, text, full: html, text
  • src/utils/autoSql/tests/expected/doc2.h - lines changed 200, context: html, text, full: html, text
  • src/utils/autoSql/tests/expected/doc2.sql - lines changed 14, context: html, text, full: html, text
  • src/utils/autoSql/tests/expected/hardTest.c - lines changed 447, context: html, text, full: html, text
  • src/utils/autoSql/tests/expected/hardTest.h - lines changed 120, context: html, text, full: html, text
  • src/utils/autoSql/tests/expected/hardTest.sql - lines changed 26, context: html, text, full: html, text
  • src/utils/autoSql/tests/expected/jsonTest.out - lines changed 16, context: html, text, full: html, text
  • src/utils/autoSql/tests/expected/mainTest.c - lines changed 859, context: html, text, full: html, text
  • src/utils/autoSql/tests/expected/mainTest.h - lines changed 287, context: html, text, full: html, text
  • src/utils/autoSql/tests/expected/mainTest.sql - lines changed 33, context: html, text, full: html, text
  • src/utils/autoSql/tests/expected/newTest.c - lines changed 434, context: html, text, full: html, text
  • src/utils/autoSql/tests/expected/newTest.err - lines changed 2, context: html, text, full: html, text
  • src/utils/autoSql/tests/expected/newTest.h - lines changed 140, context: html, text, full: html, text
  • src/utils/autoSql/tests/expected/newTest.sql - lines changed 21, context: html, text, full: html, text
  • src/utils/autoSql/tests/expected/polyTest.c - lines changed 428, context: html, text, full: html, text
  • src/utils/autoSql/tests/expected/polyTest.h - lines changed 157, context: html, text, full: html, text
  • src/utils/autoSql/tests/expected/polyTest.sql - lines changed 23, context: html, text, full: html, text
  • src/utils/autoSql/tests/expected/simpleTest.c - lines changed 1037, context: html, text, full: html, text
  • src/utils/autoSql/tests/expected/simpleTest.h - lines changed 399, context: html, text, full: html, text
  • src/utils/autoSql/tests/expected/simpleTest.sql - lines changed 12, context: html, text, full: html, text
  • src/utils/autoSql/tests/expected/symColsTest.tab - lines changed 6, context: html, text, full: html, text
  • src/utils/autoSql/tests/expected/symTest.c - lines changed 134, context: html, text, full: html, text
  • src/utils/autoSql/tests/expected/symTest.err - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
  • src/utils/autoSql/tests/expected/symTest.h - lines changed 75, context: html, text, full: html, text
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  • src/utils/autoSql/tests/expected/testHarness.out - lines changed 17, context: html, text, full: html, text
  • src/utils/autoSql/tests/input/doc.as - lines changed 17, context: html, text, full: html, text
  • src/utils/autoSql/tests/input/doc2.as - lines changed 33, context: html, text, full: html, text
  • src/utils/autoSql/tests/input/hardTest.as - lines changed 28, context: html, text, full: html, text
  • src/utils/autoSql/tests/input/mainTest.as - lines changed 51, context: html, text, full: html, text
  • src/utils/autoSql/tests/input/newTest.as - lines changed 22, context: html, text, full: html, text
  • src/utils/autoSql/tests/input/polyTest.as - lines changed 25, context: html, text, full: html, text
  • src/utils/autoSql/tests/input/simpleTest.as - lines changed 66, context: html, text, full: html, text
  • src/utils/autoSql/tests/input/symColsTest.tab - lines changed 6, context: html, text, full: html, text
  • src/utils/autoSql/tests/input/symTest.as - lines changed 8, context: html, text, full: html, text
  • src/utils/autoSql/tests/jsonTest.c - lines changed 114, context: html, text, full: html, text
  • src/utils/autoSql/tests/makefile - lines changed 118, context: html, text, full: html, text
  • src/utils/autoSql/tests/testHarness.c - lines changed 193, context: html, text, full: html, text
  • src/utils/autoSql/tests/testSymCols.c - lines changed 117, context: html, text, full: html, text
  • src/utils/autoXml/autoXml.c - lines changed 724, context: html, text, full: html, text
  • src/utils/autoXml/autoXml.doc - lines changed 190, context: html, text, full: html, text
  • src/utils/autoXml/dasBed.dtdx - lines changed 43, context: html, text, full: html, text
  • src/utils/autoXml/doTest - lines changed 5, context: html, text, full: html, text
  • src/utils/autoXml/makefile - lines changed 17, context: html, text, full: html, text
  • src/utils/autoXml/polygon.dtdx - lines changed 9, context: html, text, full: html, text
  • src/utils/autoXml/t/makefile - lines changed 14, context: html, text, full: html, text
  • src/utils/autoXml/t/t.c - lines changed 255, context: html, text, full: html, text
  • src/utils/autoXml/test.dtdx - lines changed 36, context: html, text, full: html, text
  • src/utils/autoXml/test/dasGff/dasGff.dtd - lines changed 45, context: html, text, full: html, text
  • src/utils/autoXml/test/dasGff/expected/dasGff.c - lines changed 1281, context: html, text, full: html, text
  • src/utils/autoXml/test/dasGff/expected/dasGff.h - lines changed 387, context: html, text, full: html, text
  • src/utils/autoXml/test/polygon/expected/polygon.c - lines changed 241, context: html, text, full: html, text
  • src/utils/autoXml/test/polygon/expected/polygon.h - lines changed 89, context: html, text, full: html, text
  • src/utils/autoXml/test/polygon/polygon.dtd - 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/autoDtd/autoDtd.c - lines changed 463, context: html, text, full: html, text
  • src/hg/autoDtd/doTest - lines changed 13, context: html, text, full: html, text
  • src/hg/autoDtd/makefile - lines changed 18, context: html, text, full: html, text
  • src/hg/autoDtd/test/chado/expected.atree - lines changed 77, context: html, text, full: html, text
  • src/hg/autoDtd/test/chado/expected.dtd - lines changed 183, context: html, text, full: html, text
  • src/hg/autoDtd/test/chado/expected.stats - lines changed 190, context: html, text, full: html, text
  • src/hg/autoDtd/test/chado/expected.tree - lines changed 77, context: html, text, full: html, text
  • src/hg/autoDtd/test/chado/in.xml - lines changed 1017, context: html, text, full: html, text
  • src/hg/autoDtd/test/hotnews/expected.atree - lines changed 18, context: html, text, full: html, text
  • src/hg/autoDtd/test/hotnews/expected.dtd - lines changed 58, context: html, text, full: html, text
  • src/hg/autoDtd/test/hotnews/expected.stats - lines changed 49, context: html, text, full: html, text
  • src/hg/autoDtd/test/hotnews/expected.tree - lines changed 18, context: html, text, full: html, text
  • src/hg/autoDtd/test/hotnews/in.xml - lines changed 77, context: html, text, full: html, text
  • src/hg/autoDtd/test/shapes/expected.atree - lines changed 4, context: html, text, full: html, text
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