File Changes for kent

v280_base to v281_preview (2013-03-05 to 2013-03-12) v281

• src/hg/hgHubConnect/hgHubConnect.c
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    Improved label of submit button.
• src/hg/hgTracks/container.c
  • lines changed 1, context: html, text, full: html, text
    Removing commented out debugging statement.
• src/hg/hgTracks/hgTracks.h
  • lines changed 1, context: html, text, full: html, text
    Changing way transparency is done so that it shows up in PDF, and also can be normalized when we add more cell lines.
• src/hg/hgTracks/imageV2.c
  • lines changed 1, context: html, text, full: html, text
    Changing 'ugly' in comment to 'unsightly' since like to use ugly as a keyword for debugging code.
• src/hg/hgTracks/multiWig.c
  • lines changed 158, context: html, text, full: html, text
    Changing way transparency is done so that it shows up in PDF, and also can be normalized when we add more cell lines.
  • lines changed 16, context: html, text, full: html, text
    Making reverse work with new transparency code.
• src/hg/hgTracks/wigCommon.h
  • lines changed 24, context: html, text, full: html, text
    Changing way transparency is done so that it shows up in PDF, and also can be normalized when we add more cell lines.
• src/hg/hgTracks/wigTrack.c
  • lines changed 94, context: html, text, full: html, text
    Changing way transparency is done so that it shows up in PDF, and also can be normalized when we add more cell lines.
• src/hg/lib/wiggleCart.c
  • lines changed 1, context: html, text, full: html, text
    Changing default value of aggregate to NONE rather than transparent.
• src/hg/oneShot/freen/freen.c
  • lines changed 14, context: html, text, full: html, text
    Testing loadAndValidateBed.
  • lines changed 17, context: html, text, full: html, text
    Testing some C 1999 extensions.
• src/inc/bPlusTree.h
  • lines changed 9, context: html, text, full: html, text
    Adding bptKeyAtPos and bptStringKeyAtPos methods so can go from a chromosome index back to a chromosome name quickly without loading all the chromosomes.
  • lines changed 4, context: html, text, full: html, text
    Adding support for multiple values with same key to bPlusTree.
• src/inc/bbiFile.h
  • lines changed 7, context: html, text, full: html, text
    Adding name index to bigBed files. The write side I _think_ is working. Still developing read side.
  • lines changed 8, context: html, text, full: html, text
    Moving general purpose routines from bigBedNamedItems to appropriate library.
  • lines changed 18, context: html, text, full: html, text
    Starting move from only one extra index (on the name field) being allowed to allowing multiple extra indexes. Also defining a header extension block for the file since the header is running out of space.
  • lines changed 23, context: html, text, full: html, text
    Some more steps towards supporting multiple extra indexes in bigBed files.
  • lines changed 6, context: html, text, full: html, text
    A little more progress on multiple extra index change. First time reader and writer have both worked in any small way together.
  • lines changed 5, context: html, text, full: html, text
    Big bed extra indexes seem to work now. Code still needs a little polish and testing.
  • lines changed 10, context: html, text, full: html, text
    Polishing code a little with no functional change.
• src/inc/bigBed.h
  • lines changed 11, context: html, text, full: html, text
    Adding chromId to bigBedInterval structure for item name based queries. Removing unused ppBed structure.
  • lines changed 30, context: html, text, full: html, text
    Moving general purpose routines from bigBedNamedItems to appropriate library.
  • lines changed 4, context: html, text, full: html, text
    Adding routine to do relatively efficient finding of multiple names in a bigBed name index, and giving bigBedNamedItems a command line option to do this.
  • lines changed 6, context: html, text, full: html, text
    Some more steps towards supporting multiple extra indexes in bigBed files.
  • lines changed 7, context: html, text, full: html, text
    A little more progress on multiple extra index change. First time reader and writer have both worked in any small way together.
  • lines changed 7, context: html, text, full: html, text
    Big bed extra indexes seem to work now. Code still needs a little polish and testing.
• src/inc/bigWig.h
  • lines changed 5, context: html, text, full: html, text
    Exposing bwgCreate() function at Diane Trout at Caltech's request.
  • lines changed 5, context: html, text, full: html, text
    Moving bwgCreate prototype to bwgInternal to fix compiler warning.
• src/inc/bwgInternal.h
  • lines changed 5, context: html, text, full: html, text
    Moving bwgCreate prototype to bwgInternal to fix compiler warning.
• src/inc/common.h
  • lines changed 3, context: html, text, full: html, text
    Adding slRefFreeListAndVals utility routine.
• src/inc/memgfx.h
  • lines changed 9, context: html, text, full: html, text
    Adding functions to extract a color component from a 32 bit color.
• src/kehayden/alphaAsm/alphaAsm.c
  • lines changed 59, context: html, text, full: html, text
    Rearranging logging levels so verbose(2) prints a handful of status messages one for each major phase. Some of the logging leaks memory, so put in a test to avoid this unless logging level is high.
  • lines changed 68, context: html, text, full: html, text
    Some refactoring in anticipation of expanding output if need be to accommodate full monomer diversity.
  • lines changed 68, context: html, text, full: html, text
    Adding maxToMiss and maxOutSize parameters to let program expand output size if need be to get in all monomers, or to miss a few monomers.
  • lines changed 1, context: html, text, full: html, text
    Fixed bug where the empty string was always making it look like one monomer was missing.
• src/lib/bPlusTree.c
  • lines changed 68, context: html, text, full: html, text
    Adding bptKeyAtPos and bptStringKeyAtPos methods so can go from a chromosome index back to a chromosome name quickly without loading all the chromosomes.
  • lines changed 94, context: html, text, full: html, text
    Adding support for multiple values with same key to bPlusTree.
  • lines changed 4, context: html, text, full: html, text
    Fixing bug in rFindMulti that was making bigBed name index crash on uc021tvv.1 in ucscGenes.bb
  • lines changed 16, context: html, text, full: html, text
    Making a lot of the arithmetic 64-bit so that it doesn't overflow on files with lots of items.
  • lines changed 2, context: html, text, full: html, text
    Starting move from only one extra index (on the name field) being allowed to allowing multiple extra indexes. Also defining a header extension block for the file since the header is running out of space.
• src/lib/basicBed.c
  • lines changed 14, context: html, text, full: html, text
    Fixing a bug that caused crashes and error messages on beds with lots of blocks.
  • lines changed 14, context: html, text, full: html, text
    Renaming a local variable to be a bit more descriptive.
• src/lib/bbiRead.c
  • lines changed 2, context: html, text, full: html, text
    Adding name index to bigBed files. The write side I _think_ is working. Still developing read side.
  • lines changed 14, context: html, text, full: html, text
    Moving general purpose routines from bigBedNamedItems to appropriate library.
  • lines changed 13, context: html, text, full: html, text
    Some more steps towards supporting multiple extra indexes in bigBed files.
• src/lib/bbiWrite.c
  • lines changed 16, context: html, text, full: html, text
    Adding name index to bigBed files. The write side I _think_ is working. Still developing read side.
  • lines changed 42, context: html, text, full: html, text
    Starting move from only one extra index (on the name field) being allowed to allowing multiple extra indexes. Also defining a header extension block for the file since the header is running out of space.
• src/lib/bigBed.c
  • lines changed 1, context: html, text, full: html, text
    Adding chromId to bigBedInterval structure for item name based queries. Removing unused ppBed structure.
  • lines changed 164, context: html, text, full: html, text
    Moving general purpose routines from bigBedNamedItems to appropriate library.
  • lines changed 122, context: html, text, full: html, text
    Adding routine to do relatively efficient finding of multiple names in a bigBed name index, and giving bigBedNamedItems a command line option to do this.
  • lines changed 69, context: html, text, full: html, text
    Some more steps towards supporting multiple extra indexes in bigBed files.
  • lines changed 78, context: html, text, full: html, text
    A little more progress on multiple extra index change. First time reader and writer have both worked in any small way together.
  • lines changed 79, context: html, text, full: html, text
    Big bed extra indexes seem to work now. Code still needs a little polish and testing.
• src/lib/bwgCreate.c
  • lines changed 1, context: html, text, full: html, text
    Exposing bwgCreate() function at Diane Trout at Caltech's request.
  • lines changed 2, context: html, text, full: html, text
    Adding name index to bigBed files. The write side I _think_ is working. Still developing read side.
• src/lib/common.c
  • lines changed 14, context: html, text, full: html, text
    Adding slRefFreeListAndVals utility routine.
• src/utils/bedGraphToBigWig/bedGraphToBigWig.c
  • lines changed 3, context: html, text, full: html, text
    Adding name index to bigBed files. The write side I _think_ is working. Still developing read side.
  • lines changed 2, context: html, text, full: html, text
    Starting move from only one extra index (on the name field) being allowed to allowing multiple extra indexes. Also defining a header extension block for the file since the header is running out of space.
• src/utils/bedToBigBed/bedToBigBed.c
  • lines changed 94, context: html, text, full: html, text
    Adding name index to bigBed files. The write side I _think_ is working. Still developing read side.
  • lines changed 1, context: html, text, full: html, text
    Reducing verbosity a bit.
  • lines changed 305, context: html, text, full: html, text
    Starting move from only one extra index (on the name field) being allowed to allowing multiple extra indexes. Also defining a header extension block for the file since the header is running out of space.
  • lines changed 35, context: html, text, full: html, text
    A little more progress on multiple extra index change. First time reader and writer have both worked in any small way together.
  • lines changed 10, context: html, text, full: html, text
    Polishing code a little with no functional change.
• src/utils/bedToBigBed/itemRgb.bed
  • lines changed 1, context: html, text, full: html, text
    Adding name index to bigBed files. The write side I _think_ is working. Still developing read side.
• src/utils/bigBedInfo/bigBedInfo.c
  • lines changed 1, context: html, text, full: html, text
    Adding name index to bigBed files. The write side I _think_ is working. Still developing read side.
  • lines changed 11, context: html, text, full: html, text
    Some more steps towards supporting multiple extra indexes in bigBed files.
• src/utils/bigBedNamedItems/bigBedNamedItems.c
  • lines changed 120, context: html, text, full: html, text
    Adding name index to bigBed files. The write side I _think_ is working. Still developing read side.
  • lines changed 47, context: html, text, full: html, text
    First cut at read side of named index seems to work. Still needs testing and polishing.
  • lines changed 9, context: html, text, full: html, text
    Fixing bug where it only finds item if it's in first part of block.
  • lines changed 2, context: html, text, full: html, text
    Removing some debugging uglyfs
  • lines changed 59, context: html, text, full: html, text
    Making it so that multiple items can have same name, and all such items are found.
  • lines changed 31, context: html, text, full: html, text
    Refactoring in preparation for moving much of this to library.
  • lines changed 151, context: html, text, full: html, text
    Moving general purpose routines from bigBedNamedItems to appropriate library.
  • lines changed 16, context: html, text, full: html, text
    Adding routine to do relatively efficient finding of multiple names in a bigBed name index, and giving bigBedNamedItems a command line option to do this.
  • lines changed 8, context: html, text, full: html, text
    A little more progress on multiple extra index change. First time reader and writer have both worked in any small way together.
  • lines changed 4, context: html, text, full: html, text
    Big bed extra indexes seem to work now. Code still needs a little polish and testing.
• src/utils/bigBedNamedItems/makefile
  • lines changed 18, context: html, text, full: html, text
    Adding name index to bigBed files. The write side I _think_ is working. Still developing read side.
• src/utils/makefile
  • lines changed 1, context: html, text, full: html, text
    Adding bigBedNamedItems to utilities compilation.