kent: changes by file

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

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