Commits for angie
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v248_preview to v248_preview2 (2011-02-22 to 2011-03-01) v248
- Bug #2917 (DGV colors need changing): following DGV's swap to newcoloring convention decided at ISCA, we're swapping red <-> blue.
While we're at it, since DGV now uses brown for 'both gain and loss',
switch green to brown.
- src/hg/makeDb/doc/hg17.txt - lines changed 11, context: html, text, full: html, text
- src/hg/makeDb/doc/hg18.txt - lines changed 12, context: html, text, full: html, text
- src/hg/makeDb/doc/hg19.txt - lines changed 11, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/dgv.html - lines changed 6, context: html, text, full: html, text
- bamWigMethods was used but undefined in the absence of USE_BAM=1.
- src/hg/hgTracks/bamTrack.c - lines changed 7, context: html, text, full: html, text
- Track #1684 (SNPS 132 (dbSNP)): Added snp132ExceptionDesc to tablesIgnored (thanks Brooke).
- src/hg/makeDb/schema/all.joiner - lines changed 1, context: html, text, full: html, text
- Fixed tiny typo.
- src/hg/makeDb/trackDb/snp132.html - lines changed 1, context: html, text, full: html, text
- Added initial values of a few new vars, to satisfy ubuntu's extra-Wall check. Due to the use of boolean firstTime, the values
would not be used uninitialized, this is just to satisfy gcc.
- src/utils/bigWigToBedGraph/bigWigToBedGraph.c - lines changed 2, context: html, text, full: html, text
- New src/inc/regexHelper.h module replaces the regex conveniencefunctions that were previously down in hg/lib/hgFindSpecCustom.c.
The primary motivation for this is so I can use regex functions in
the new src/lib/vcf.c for Feature #2821 (VCF parser), but I hope
this will make it easier in general to use regexes in any new code.
- src/hg/checkHgFindSpec/checkHgFindSpec.c - lines changed 5, context: html, text, full: html, text
- src/hg/hgTracks/imageV2.c - lines changed 2, context: html, text, full: html, text
- src/hg/inc/hgFindSpec.h - lines changed 11, context: html, text, full: html, text
- src/hg/lib/customFactory.c - lines changed 8, context: html, text, full: html, text
- src/hg/lib/hgFindSpecCustom.c - lines changed 66, context: html, text, full: html, text
- Feature #2820 (tabix: add as optional linked library in kent/src):added common.mk variables analogous to those for samtools:
TABIXDIR, USE_TABIX, TABIXINC, TABIXLIB. When compiling with
tabix, also set KNETFILE_HOOKS so tabix will use udc like samtools.
- Feature #2820 (tabix: add as optional linked library in kent/src):Updated src/product's sample environment config script with new
variables USE_TABIX etc.
- src/product/scripts/browserEnvironment.txt - lines changed 18, context: html, text, full: html, text
- Feature #2820 (tabix: add as optional linked library in kent/src):Added lineFile wrapper on tabix: lineFileOnTabix to open; then
lineFileNext and its derivatives work as usual.
lineFileSetTabixRegion seeks to the given position range, and
subsequent lineFileNext's return lines in that position range.
lineFileSeek is not supported -- tabix doesn't have linear offsets
but rather a block number and offset which are packed into 64 bits.
Line numbers are not known after calls to lineFileSetTabixRegion.
- src/oneShot/tabixFetch/makefile - lines changed 18, context: html, text, full: html, text
- src/oneShot/tabixFetch/tabixFetch.c - lines changed 114, context: html, text, full: html, text
- Feature #2820 (tabix: add as optional linked library in kent/src):Wow, adding an external lib dependency to linefile exposed the fact
that many makefiles did not include ${L} properly.
- src/ai/paraFlow/compiler/makefile - lines changed 1, context: html, text, full: html, text
- src/ai/paraFlow/runAsm/makefile - lines changed 1, context: html, text, full: html, text
- src/ai/paraFlow/runtime/makefile - lines changed 1, context: html, text, full: html, text
- src/aladdin/aladdin/makefile - lines changed 1, context: html, text, full: html, text
- src/cdnaAli/ali2alx/makefile - lines changed 1, context: html, text, full: html, text
- src/cdnaAli/aliGlue/makefile - lines changed 1, context: html, text, full: html, text
- src/cdnaAli/binGood/makefile - lines changed 1, context: html, text, full: html, text
- src/cdnaAli/cdnaOff/makefile - lines changed 1, context: html, text, full: html, text
- src/cdnaAli/cluster/makefile - lines changed 2, context: html, text, full: html, text
- src/cdnaAli/exonAli/makefile - lines changed 3, context: html, text, full: html, text
- src/cdnaAli/introns/makefile - lines changed 1, context: html, text, full: html, text
- src/cdnaAli/pairClo/makefile - lines changed 1, context: html, text, full: html, text
- src/cdnaAli/patCount/makefile - lines changed 1, context: html, text, full: html, text
- src/cdnaAli/patSpace/makefile - lines changed 1, context: html, text, full: html, text
- src/cdnaAli/refineAli/makefile - lines changed 1, context: html, text, full: html, text
- src/cdnaAli/sortFilt/makefile - lines changed 1, context: html, text, full: html, text
- src/cdnaAli/stitchea/makefile - lines changed 1, context: html, text, full: html, text
- src/hg/affyGnf/makefile - lines changed 1, context: html, text, full: html, text
- src/hg/affyTransciptome/makefile - lines changed 1, context: html, text, full: html, text
- src/hg/altSplice/affySplice/makefile - lines changed 1, context: html, text, full: html, text
- src/hg/altSplice/axtCountBeds/makefile - lines changed 1, context: html, text, full: html, text
- src/hg/altSplice/exonWalk/makefile - lines changed 2, context: html, text, full: html, text
- src/hg/altSplice/filterEdges/makefile - lines changed 1, context: html, text, full: html, text
- src/hg/altSplice/spliceWalk/makefile - lines changed 2, context: html, text, full: html, text
- src/hg/autoXml/makefile - lines changed 1, context: html, text, full: html, text
- src/hg/fakeOut/makefile - lines changed 1, context: html, text, full: html, text
- src/hg/gigAssembler/conJobs/patJobs/makefile - lines changed 1, context: html, text, full: html, text
- src/hg/gigAssembler/conJobs/repMaskJobs/makefile - lines changed 1, context: html, text, full: html, text
- src/hg/splitFa/makefile - lines changed 1, context: html, text, full: html, text
- src/hg/utils/gtfToGenePred/makefile - lines changed 1, context: html, text, full: html, text
- src/index/fofFa/makefile - lines changed 1, context: html, text, full: html, text
- src/index/indexRa/makefile - lines changed 1, context: html, text, full: html, text
- src/index/ixxenost/makefile - lines changed 1, context: html, text, full: html, text
- src/oneShot/checkLayout/makefile - lines changed 1, context: html, text, full: html, text
- src/oneShot/chkGlue/makefile - lines changed 1, context: html, text, full: html, text
- src/oneShot/cntGlue/makefile - lines changed 1, context: html, text, full: html, text
- src/oneShot/coverage/makefile - lines changed 1, context: html, text, full: html, text
- src/oneShot/deEns/makefile - lines changed 1, context: html, text, full: html, text
- src/oneShot/dynAlign/makefile - lines changed 1, context: html, text, full: html, text
- src/oneShot/fixInfo/makefile - lines changed 1, context: html, text, full: html, text
- src/oneShot/grokGff/makefile - lines changed 1, context: html, text, full: html, text
- src/oneShot/invert/makefile - lines changed 1, context: html, text, full: html, text
- src/oneShot/m22dirs/makefile - lines changed 1, context: html, text, full: html, text
- src/oneShot/ooRev/makefile - lines changed 1, context: html, text, full: html, text
- src/oneShot/passHi/makefile - lines changed 1, context: html, text, full: html, text
- src/oneShot/patJobs/makefile - lines changed 1, context: html, text, full: html, text
- src/oneShot/shorten/makefile - lines changed 1, context: html, text, full: html, text
- src/oneShot/sources/makefile - lines changed 1, context: html, text, full: html, text
- src/oneShot/splitSql/makefile - lines changed 1, context: html, text, full: html, text
- src/oneShot/uniqSize/makefile - lines changed 1, context: html, text, full: html, text
- src/oneShot/unmasked/makefile - lines changed 1, context: html, text, full: html, text
- src/oneShot/unwrap/makefile - lines changed 1, context: html, text, full: html, text
- src/parasol/netC/makefile - lines changed 1, context: html, text, full: html, text
- src/parasol/netS/makefile - lines changed 1, context: html, text, full: html, text
- src/parasol/para/makefile - lines changed 1, context: html, text, full: html, text
- src/parasol/paraHubStop/makefile - lines changed 1, context: html, text, full: html, text
- src/parasol/paraNode/makefile - lines changed 1, context: html, text, full: html, text
- src/parasol/paraNodeStart/makefile - lines changed 1, context: html, text, full: html, text
- src/parasol/paraNodeStatus/makefile - lines changed 1, context: html, text, full: html, text
- src/parasol/paraNodeStop/makefile - lines changed 1, context: html, text, full: html, text
- src/parasol/parasol/makefile - lines changed 1, context: html, text, full: html, text
- src/parasol/simpleC/makefile - lines changed 1, context: html, text, full: html, text
- src/parasol/simpleS/makefile - lines changed 1, context: html, text, full: html, text
- src/reformat/fa4blast/makefile - lines changed 1, context: html, text, full: html, text
- src/reformat/fatont4/makefile - lines changed 1, context: html, text, full: html, text
- src/reformat/fsg/makefile - lines changed 1, context: html, text, full: html, text
- src/reformat/gb2cdi/makefile - lines changed 1, context: html, text, full: html, text
- src/reformat/gbToFaRa/makefile - lines changed 1, context: html, text, full: html, text
- src/reformat/gbtofa/makefile - lines changed 1, context: html, text, full: html, text
- src/reformat/geniegff/makefile - lines changed 1, context: html, text, full: html, text
- src/reformat/gffgenes/makefile - lines changed 1, context: html, text, full: html, text
- src/reformat/makeOrf2gene/makefile - lines changed 1, context: html, text, full: html, text
- src/reformat/makec2c/makefile - lines changed 1, context: html, text, full: html, text
- src/reformat/moresyn/makefile - lines changed 1, context: html, text, full: html, text
- src/reformat/wabToSt/makefile - lines changed 1, context: html, text, full: html, text
- src/scanIntrons/makefile - lines changed 1, context: html, text, full: html, text
- src/utils/addCols/makefile - lines changed 1, context: html, text, full: html, text
- src/utils/aveCols/makefile - lines changed 1, context: html, text, full: html, text
- src/utils/catUncomment/makefile - lines changed 1, context: html, text, full: html, text
- src/utils/ccCp/makefile - lines changed 2, context: html, text, full: html, text
- src/utils/ccCpLock/makefile - lines changed 2, context: html, text, full: html, text
- src/utils/colCount/makefile - lines changed 1, context: html, text, full: html, text
- src/utils/countChars/makefile - lines changed 1, context: html, text, full: html, text
- src/utils/faGapLocs/makefile - lines changed 1, context: html, text, full: html, text
- src/utils/faGapSizes/makefile - lines changed 1, context: html, text, full: html, text
- src/utils/faNoise/makefile - lines changed 1, context: html, text, full: html, text
- src/utils/faOneRecord/makefile - lines changed 1, context: html, text, full: html, text
- src/utils/faRandomize/makefile - lines changed 1, context: html, text, full: html, text
- src/utils/faSplit/makefile - lines changed 2, context: html, text, full: html, text
- src/utils/fixCr/makefile - lines changed 1, context: html, text, full: html, text
- src/utils/htmlPics/makefile - lines changed 1, context: html, text, full: html, text
- src/utils/jkUniq/makefile - lines changed 1, context: html, text, full: html, text
- src/utils/newProg/makefile - lines changed 1, context: html, text, full: html, text
- src/utils/nibCheck/makefile - lines changed 1, context: html, text, full: html, text
- src/utils/nibFrag/makefile - lines changed 1, context: html, text, full: html, text
- src/utils/nibSize/makefile - lines changed 1, context: html, text, full: html, text
- src/utils/rmFaDups/makefile - lines changed 1, context: html, text, full: html, text
- src/utils/scaffoldFaToAgp/makefile - lines changed 1, context: html, text, full: html, text
- src/utils/scrambleFa/makefile - lines changed 1, context: html, text, full: html, text
- src/utils/sortFa/makefile - lines changed 1, context: html, text, full: html, text
- src/utils/subChar/makefile - lines changed 1, context: html, text, full: html, text
- src/utils/subs/makefile - lines changed 1, context: html, text, full: html, text
- src/utils/tailLines/makefile - lines changed 2, context: html, text, full: html, text
- src/utils/toLower/makefile - lines changed 1, context: html, text, full: html, text
- src/utils/toUpper/makefile - lines changed 1, context: html, text, full: html, text
- src/utils/undupFa/makefile - lines changed 1, context: html, text, full: html, text
- src/utils/upper/makefile - lines changed 1, context: html, text, full: html, text
- src/utils/wordLine/makefile - lines changed 1, context: html, text, full: html, text
- src/weblet/bottleneck/makefile - lines changed 1, context: html, text, full: html, text
- src/weblet/hitreport/makefile - lines changed 1, context: html, text, full: html, text
- src/xenoAli/aliStats/makefile - lines changed 1, context: html, text, full: html, text
- src/xenoAli/blastStats/makefile - lines changed 1, context: html, text, full: html, text
- src/xenoAli/bwana/makefile - lines changed 1, context: html, text, full: html, text
- src/xenoAli/cbAli/makefile - lines changed 1, context: html, text, full: html, text
- src/xenoAli/dynAlign/makefile - lines changed 0, context: html, text, full: html, text
- src/xenoAli/newIntron/makefile - lines changed 1, context: html, text, full: html, text
- src/xenoAli/smithWat/makefile - lines changed 1, context: html, text, full: html, text
- src/xenoAli/stitcher/makefile - lines changed 1, context: html, text, full: html, text
- src/xenoAli/waba/makefile - lines changed 1, context: html, text, full: html, text
- src/xenoAli/xaShow/makefile - lines changed 1, context: html, text, full: html, text
- src/xenoAli/xenWorm/makefile - lines changed 1, context: html, text, full: html, text
- Feature #2820 (tabix: add as optional linked library in kent/src):This is a total mystery to me, but for some reason when tabix.h is
included via linefile.h, the compiler complains about the
redefinition of pslBuildScoresOpen when bool is used... fortunately
boolean is OK. I have no idea why using bool would be OK in the
rest of the tree but not here. ??? Anyway, since using boolean
allows it to compile, I'll just go with that.
- src/hg/blastToPsl/pslBuild.c - lines changed 1, context: html, text, full: html, text
- src/hg/blastToPsl/pslBuild.h - lines changed 1, context: html, text, full: html, text
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