kent: changes by commit

branch to review (2010-05-25 to 2010-06-01) v233

• Removing stray 'ES' from label of non-ES cells in wgEncodeReg track.
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.984 - lines changed: 76, context: html, text, full: html, text
• Renaming aliTrack to aliTable to help clarify track/table confusion.
  • src/hg/archaeStuff/chooseorg/chooseorg.c 1.5 - lines changed: 1, context: html, text, full: html, text
  • src/hg/archaeStuff/tooltip/tooltip.c 1.9 - lines changed: 1, context: html, text, full: html, text
• Improving usage message.
  • src/utils/wigSetSpanOrStep/wigSetSpanOrStep.c 1.2 - lines changed: 1, context: html, text, full: html, text
• Adding transformFunc to wig and bigWig types.
  • src/hg/makeDb/trackDb/tagTypes.tab 1.28 - lines changed: 1, context: html, text, full: html, text
• Adding docs on new tags.
  • src/hg/makeDb/trackDb/README 1.107 - lines changed: 14, context: html, text, full: html, text
• Making log transform work with whiskers.
  • src/hg/hgTracks/wigTrack.c 1.113 - lines changed: 44, context: html, text, full: html, text
• Adding info on showSubtrackColorOnUi
  • src/hg/makeDb/trackDb/README 1.108 - lines changed: 3, context: html, text, full: html, text
• Cleaning up the conservation track default settings a little. Commenting out some '_v2' versions of the conservation wiggles that have been up along side the normal one for months now.
  • src/hg/makeDb/trackDb/human/hg18/trackDb.ra 1.490 - lines changed: 61, context: html, text, full: html, text
• Making it so wigToBigWig will default span to step size.
  • src/lib/bwgCreate.c 1.24 - lines changed: 5, context: html, text, full: html, text
• Making wigEncode default the span to the stepSize in fixedStep wigs.
  • src/hg/lib/wigAsciiToBinary.c 1.34 - lines changed: 3, context: html, text, full: html, text
• Still half baked, but it compiles at least.
  • src/utils/wigCorrelate/makefile 1.1 - lines changed: 18, context: html, text, full: html, text
  • src/utils/wigCorrelate/wigCorrelate.c 1.1 - lines changed: 389, context: html, text, full: html, text
• Cleaned up a bit and tested more. Fixed a bug that made it hang after about 25 pairwise correlations.
  • src/utils/wigCorrelate/wigCorrelate.c 1.2 - lines changed: 63, context: html, text, full: html, text
• Matrix plotter seems to work.
  • src/utils/plotDataMatrix/enh.tab 1.1 - lines changed: 28, context: html, text, full: html, text
  • src/utils/plotDataMatrix/enhCol.tab 1.1 - lines changed: 8, context: html, text, full: html, text
  • src/utils/plotDataMatrix/enhRow.tab 1.1 - lines changed: 8, context: html, text, full: html, text
  • src/utils/plotDataMatrix/makefile 1.1 - lines changed: 21, context: html, text, full: html, text
  • src/utils/plotDataMatrix/plotDataMatrix.c 1.1 - lines changed: 240, context: html, text, full: html, text
• Seems to work.
  • src/utils/correlate/correlate.c 1.1 - lines changed: 58, context: html, text, full: html, text
  • src/utils/correlate/expected 1.1 - lines changed: 1, context: html, text, full: html, text
  • src/utils/correlate/makefile 1.1 - lines changed: 22, context: html, text, full: html, text
  • src/utils/correlate/test.tab 1.1 - lines changed: 10, context: html, text, full: html, text
• Adding clampMax option.
  • src/utils/wigCorrelate/wigCorrelate.c 1.3 - lines changed: 20, context: html, text, full: html, text
• Putting timing notes under CVS.
  • src/utils/wigTestMaker/timeNotes 1.1 - lines changed: 168, context: html, text, full: html, text
• Renaming wgEncodeRegMarkEnhancer subtracks to have the expected prefix rather than 'jkEnh'
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.998 - lines changed: 25, context: html, text, full: html, text
• Improving indentation. Improving an error message, and the test that triggers it.
  • src/hg/makeDb/trackDbPatch/trackDbPatch.c 1.6 - lines changed: 18, context: html, text, full: html, text
• Adding some const to string function parameters to better work with C standard library code as callbacks.
  • src/inc/common.h 1.173 - lines changed: 10, context: html, text, full: html, text
  • src/lib/common.c 1.150 - lines changed: 18, context: html, text, full: html, text
• Adding correlateNextMulti
  • src/inc/correlate.h 1.2 - lines changed: 4, context: html, text, full: html, text
  • src/lib/correlate.c 1.3 - lines changed: 16, context: html, text, full: html, text
• Reducing amount of zoom oversampling, which speeds up 100k views a fair bit.
  • src/lib/bbiRead.c 1.18 - lines changed: 2, context: html, text, full: html, text
• Moving some stuff from bwgCreate to bwgInternal.h where it can be shared a bit more. Tweaking things so first zoom level is a better size, which speeds up 100k views.
  • src/inc/bwgInternal.h 1.10 - lines changed: 71, context: html, text, full: html, text
  • src/lib/bwgCreate.c 1.25 - lines changed: 76, context: html, text, full: html, text
• SOme more timing measurements.
  • src/utils/wigTestMaker/timeNotes 1.2 - lines changed: 110, context: html, text, full: html, text
• Taking out span since it now defaults in one fixedStep line of test.
  • src/utils/wigToBigWig/testFixed.wig 1.2 - lines changed: 1, context: html, text, full: html, text
• adding test sets
  • src/hg/makeDb/hgLoadWiggle/test_data/testBedGraph.wig 1.1 - lines changed: 64, context: html, text, full: html, text
  • src/hg/makeDb/hgLoadWiggle/test_data/testFixed.wig 1.1 - lines changed: 106, context: html, text, full: html, text
  • src/hg/makeDb/hgLoadWiggle/test_data/testVar.wig 1.1 - lines changed: 77, context: html, text, full: html, text