Commits for kent
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v280_base to v281_preview (2013-03-05 to 2013-03-12) v281
- 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.
- src/kehayden/alphaAsm/alphaAsm.c - lines changed 59, context: html, text, full: html, text
- Improved label of submit button.
- src/hg/hgHubConnect/hgHubConnect.c - lines changed 1, context: html, text, full: html, text
- Exposing bwgCreate() function at Diane Trout at Caltech's request.
- Moving bwgCreate prototype to bwgInternal to fix compiler warning.
- Adding functions to extract a color component from a 32 bit color.
- Changing default value of aggregate to NONE rather than transparent.
- src/hg/lib/wiggleCart.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/imageV2.c - 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/hgTracks.h - lines changed 1, context: html, text, full: html, text
- src/hg/hgTracks/multiWig.c - lines changed 158, context: html, text, full: html, text
- src/hg/hgTracks/wigCommon.h - lines changed 24, context: html, text, full: html, text
- src/hg/hgTracks/wigTrack.c - lines changed 94, context: html, text, full: html, text
- Removing commented out debugging statement.
- src/hg/hgTracks/container.c - lines changed 1, context: html, text, full: html, text
- Making reverse work with new transparency code.
- src/hg/hgTracks/multiWig.c - lines changed 16, 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.
- Adding name index to bigBed files. The write side I _think_ is working. Still developing read side.
- src/utils/bedGraphToBigWig/bedGraphToBigWig.c - lines changed 3, context: html, text, full: html, text
- src/utils/bedToBigBed/bedToBigBed.c - lines changed 94, context: html, text, full: html, text
- src/utils/bedToBigBed/itemRgb.bed - lines changed 1, context: html, text, full: html, text
- src/utils/bigBedInfo/bigBedInfo.c - lines changed 1, context: html, text, full: html, text
- src/utils/bigBedNamedItems/bigBedNamedItems.c - lines changed 120, context: html, text, full: html, text
- src/utils/bigBedNamedItems/makefile - lines changed 18, context: html, text, full: html, text
- First cut at read side of named index seems to work. Still needs testing and polishing.
- src/utils/bigBedNamedItems/bigBedNamedItems.c - lines changed 47, context: html, text, full: html, text
- Fixing bug where it only finds item if it's in first part of block.
- src/utils/bigBedNamedItems/bigBedNamedItems.c - lines changed 9, context: html, text, full: html, text
- Removing some debugging uglyfs
- src/utils/bigBedNamedItems/bigBedNamedItems.c - lines changed 2, context: html, text, full: html, text
- Fixing a bug that caused crashes and error messages on beds with lots of blocks.
- Adding slRefFreeListAndVals utility routine.
- Adding support for multiple values with same key to bPlusTree.
- Making it so that multiple items can have same name, and all such items are found.
- src/utils/bigBedNamedItems/bigBedNamedItems.c - lines changed 59, context: html, text, full: html, text
- Adding chromId to bigBedInterval structure for item name based queries. Removing unused ppBed structure.
- Testing loadAndValidateBed.
- src/hg/oneShot/freen/freen.c - lines changed 14, context: html, text, full: html, text
- Adding bigBedNamedItems to utilities compilation.
- Refactoring in preparation for moving much of this to library.
- src/utils/bigBedNamedItems/bigBedNamedItems.c - lines changed 31, context: html, text, full: html, text
- Moving general purpose routines from bigBedNamedItems to appropriate library.
- src/utils/bigBedNamedItems/bigBedNamedItems.c - lines changed 151, context: html, text, full: html, text
- Fixing bug in rFindMulti that was making bigBed name index crash on uc021tvv.1 in ucscGenes.bb
- 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.
- src/utils/bigBedNamedItems/bigBedNamedItems.c - lines changed 16, context: html, text, full: html, text
- Reducing verbosity a bit.
- src/utils/bedToBigBed/bedToBigBed.c - lines changed 1, 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.
- Testing some C 1999 extensions.
- src/hg/oneShot/freen/freen.c - lines changed 17, context: html, text, full: html, text
- Renaming a local variable to be a bit more descriptive.
- 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/bedGraphToBigWig/bedGraphToBigWig.c - lines changed 2, context: html, text, full: html, text
- src/utils/bedToBigBed/bedToBigBed.c - lines changed 305, context: html, text, full: html, text
- Some more steps towards supporting multiple extra indexes in bigBed files.
- src/utils/bigBedInfo/bigBedInfo.c - lines changed 11, 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.
- src/utils/bedToBigBed/bedToBigBed.c - lines changed 35, context: html, text, full: html, text
- src/utils/bigBedNamedItems/bigBedNamedItems.c - lines changed 8, 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/bigBedNamedItems.c - lines changed 4, context: html, text, full: html, text
- Polishing code a little with no functional change.
- src/utils/bedToBigBed/bedToBigBed.c - lines changed 10, context: html, text, full: html, text
- Some refactoring in anticipation of expanding output if need be to accommodate full monomer diversity.
- src/kehayden/alphaAsm/alphaAsm.c - 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.
- src/kehayden/alphaAsm/alphaAsm.c - lines changed 68, context: html, text, full: html, text
- Fixed bug where the empty string was always making it look like one monomer was missing.
- src/kehayden/alphaAsm/alphaAsm.c - lines changed 1, context: html, text, full: html, text
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