kent: changes by commit

branch to review (2010-01-05 to 2010-01-12) v223

• Implementing mode=replace
  • src/hg/encode/encodePatchTdb/encodePatchTdb.c 1.4 - lines changed: 35, context: html, text, full: html, text
• Removing unused routine.
  • src/hg/encode/encodePatchTdb/encodePatchTdb.c 1.5 - lines changed: 33, context: html, text, full: html, text
• Getting rid of unused command line options.
  • src/hg/encode/encodePatchTdb/encodePatchTdb.c 1.6 - lines changed: 5, context: html, text, full: html, text
• Fixing stanza merge problem when there is no line before stanza in patch file. Fixing replace eating a stanza. Making replace just comment out old stanza by default, but there's a noComment option. Putting in test suite.
  • src/hg/encode/encodePatchTdb/encodePatchTdb.c 1.7 - lines changed: 93, context: html, text, full: html, text
  • src/hg/encode/encodePatchTdb/makefile 1.3 - lines changed: 3, context: html, text, full: html, text
  • src/hg/encode/encodePatchTdb/tests/expected/add1.ra 1.1 - lines changed: 0, context: html, text, full: html, text
  • src/hg/encode/encodePatchTdb/tests/expected/add3.ra 1.1 - lines changed: 0, context: html, text, full: html, text
  • src/hg/encode/encodePatchTdb/tests/expected/replace1.ra 1.1 - lines changed: 0, context: html, text, full: html, text
  • src/hg/encode/encodePatchTdb/tests/expected/replace3.ra 1.1 - lines changed: 0, context: html, text, full: html, text
  • src/hg/encode/encodePatchTdb/tests/expected/replace3NoComment.ra 1.1 - lines changed: 0, context: html, text, full: html, text
  • src/hg/encode/encodePatchTdb/tests/in/add1.ra 1.1 - lines changed: 0, context: html, text, full: html, text
  • src/hg/encode/encodePatchTdb/tests/in/add3.ra 1.1 - lines changed: 0, context: html, text, full: html, text
  • src/hg/encode/encodePatchTdb/tests/in/replace1.ra 1.1 - lines changed: 0, context: html, text, full: html, text
  • src/hg/encode/encodePatchTdb/tests/in/replace3.ra 1.1 - lines changed: 0, context: html, text, full: html, text
  • src/hg/encode/encodePatchTdb/tests/test.sh 1.1 - lines changed: 2, context: html, text, full: html, text
  • src/hg/encode/encodePatchTdb/tests/trackDb.ra 1.1 - lines changed: 0, context: html, text, full: html, text
• Adding another test case.
  • src/hg/encode/encodePatchTdb/tests/expected/composite.ra 1.1 - lines changed: 0, context: html, text, full: html, text
  • src/hg/encode/encodePatchTdb/tests/in/composite.ra 1.1 - lines changed: 0, context: html, text, full: html, text
  • src/hg/encode/encodePatchTdb/tests/test.sh 1.2 - lines changed: 2, context: html, text, full: html, text
• Removing some unused code.
  • src/hg/encode/encodePatchTdb/encodePatchTdb.c 1.8 - lines changed: 24, context: html, text, full: html, text
• Utility to convert wigs to bedGraphs seems to be working in basic tests at least.
  • src/utils/wigToBedGraph/makefile 1.1 - lines changed: 0, context: html, text, full: html, text
  • src/utils/wigToBedGraph/testFixed.bedGraph 1.1 - lines changed: 0, context: html, text, full: html, text
  • src/utils/wigToBedGraph/testFixed.wig 1.1 - lines changed: 0, context: html, text, full: html, text
  • src/utils/wigToBedGraph/testVar.bedGraph 1.1 - lines changed: 0, context: html, text, full: html, text
  • src/utils/wigToBedGraph/testVar.wig 1.1 - lines changed: 0, context: html, text, full: html, text
  • src/utils/wigToBedGraph/wigToBedGraph.c 1.1 - lines changed: 0, context: html, text, full: html, text
• Fixing indentation. Removing an unused define/ifdef. Adding braces for readability in a couple of places.
  • src/hg/hgTracks/altGraphXTrack.c 1.16 - lines changed: 2, context: html, text, full: html, text
  • src/hg/hgTracks/hgTracks.c 1.1618 - lines changed: 41, context: html, text, full: html, text
• Rescuing conservation track and others that have "subTrack parentTrack on" rather than just "subTrack parentTrack"
  • src/hg/makeDb/hgTrackDb/hgTrackDb.c 1.60 - lines changed: 2, context: html, text, full: html, text