File Changes for angie

v248_preview to v248_preview2 (2011-02-22 to 2011-03-01) v248

• src/ai/paraFlow/compiler/makefile
  • lines changed 1, 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/runAsm/makefile
  • lines changed 1, 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/runtime/makefile
  • lines changed 1, 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/aladdin/aladdin/makefile
  • lines changed 1, 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/cbAli/makefile
  • lines changed 1, 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/cdnaAli/ali2alx/makefile
  • lines changed 1, 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/cdnaAli/aliGlue/makefile
  • lines changed 1, 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/cdnaAli/binGood/makefile
  • lines changed 1, 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/cdnaAli/cdnaOff/makefile
  • lines changed 1, 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/cdnaAli/cluster/makefile
  • lines changed 2, 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/cdnaAli/exonAli/makefile
  • lines changed 3, 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/cdnaAli/introns/makefile
  • lines changed 1, 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/cdnaAli/pairClo/makefile
  • lines changed 1, 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/cdnaAli/patCount/makefile
  • lines changed 1, 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/cdnaAli/patSpace/makefile
  • lines changed 1, 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/cdnaAli/refineAli/makefile
  • lines changed 1, 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/cdnaAli/sortFilt/makefile
  • lines changed 1, 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/cdnaAli/stitchea/makefile
  • lines changed 1, 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/dnaDust/makefile
  • lines changed 1, 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/fuzzyFind/makefile
  • lines changed 1, 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/getgene/makefile
  • lines changed 1, 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/hg/affyGnf/makefile
  • lines changed 1, 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/hg/affyTransciptome/makefile
  • lines changed 1, 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/hg/altSplice/affySplice/makefile
  • lines changed 1, 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/hg/altSplice/axtCountBeds/makefile
  • lines changed 1, 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/hg/altSplice/exonWalk/makefile
  • lines changed 2, 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/hg/altSplice/filterEdges/makefile
  • lines changed 1, 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/hg/altSplice/spliceWalk/makefile
  • lines changed 2, 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/hg/autoXml/makefile
  • lines changed 1, 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/hg/blastToPsl/pslBuild.c
  • 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.h
  • 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/checkHgFindSpec/checkHgFindSpec.c
  • lines changed 5, 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/fakeOut/makefile
  • lines changed 1, 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/hg/gigAssembler/conJobs/patJobs/makefile
  • lines changed 1, 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/hg/gigAssembler/conJobs/repMaskJobs/makefile
  • lines changed 1, 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/hg/hgTracks/bamTrack.c
  • lines changed 7, context: html, text, full: html, text
    bamWigMethods was used but undefined in the absence of USE_BAM=1.
• src/hg/hgTracks/imageV2.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/inc/hgFindSpec.h
  • lines changed 11, 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/inc/knetUdc.h
  • lines changed 10, 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/hg/lib/customFactory.c
  • lines changed 8, 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/lib/hgFind.c
  • lines changed 12, 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/lib/hgFindSpecCustom.c
  • lines changed 66, 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/lib/knetUdc.c
  • lines changed 87, 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/hg/lib/makefile
  • lines changed 1, 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/hg/lib/pgSnp.c
  • lines changed 4, 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/makeDb/doc/hg17.txt
  • lines changed 11, context: html, text, full: html, text
    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/hg18.txt
  • lines changed 12, context: html, text, full: html, text
    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/hg19.txt
  • lines changed 11, context: html, text, full: html, text
    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/schema/all.joiner
  • lines changed 1, context: html, text, full: html, text
    Track #1684 (SNPS 132 (dbSNP)): Added snp132ExceptionDesc to tablesIgnored (thanks Brooke).
• src/hg/makeDb/trackDb/human/dgv.html
  • lines changed 6, context: html, text, full: html, text
    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/trackDb/snp132.html
  • lines changed 1, context: html, text, full: html, text
    Fixed tiny typo.
• src/hg/nci60/makefile
  • lines changed 1, 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/hg/splitFa/makefile
  • lines changed 1, 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/hg/utils/gtfToGenePred/makefile
  • lines changed 1, 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/idbQuery/makefile
  • lines changed 1, 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/inc/common.mk
  • lines changed 31, 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.
• src/inc/knetUdc.h
  • lines changed 10, 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/inc/linefile.h
  • lines changed 26, 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/inc/regexHelper.h
  • lines changed 29, 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/index/fofFa/makefile
  • lines changed 1, 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/index/indexRa/makefile
  • lines changed 1, 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/index/ixxenost/makefile
  • lines changed 1, 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/lib/knetUdc.c
  • lines changed 87, 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/lib/linefile.c
  • lines changed 122, 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/lib/makefile
  • lines changed 1, 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.
  • lines changed 1, 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/lib/regexHelper.c
  • lines changed 80, 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/lib/tests/makefile
  • lines changed 4, 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/oneShot/checkLayout/makefile
  • lines changed 1, 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/oneShot/chkGlue/makefile
  • lines changed 1, 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/oneShot/cntGlue/makefile
  • lines changed 1, 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/oneShot/coverage/makefile
  • lines changed 1, 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/oneShot/deEns/makefile
  • lines changed 1, 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/oneShot/dynAlign/makefile
  • lines changed 1, 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/oneShot/fixInfo/makefile
  • lines changed 1, 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/oneShot/grokGff/makefile
  • lines changed 1, 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/oneShot/invert/makefile
  • lines changed 1, 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/oneShot/m22dirs/makefile
  • lines changed 1, 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/oneShot/ooRev/makefile
  • lines changed 1, 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/oneShot/passHi/makefile
  • lines changed 1, 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/oneShot/patJobs/makefile
  • lines changed 1, 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/oneShot/shorten/makefile
  • lines changed 1, 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/oneShot/sources/makefile
  • lines changed 1, 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/oneShot/splitSql/makefile
  • lines changed 1, 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/oneShot/tabixFetch/makefile
  • 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/tabixFetch.c
  • lines changed 114, 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/uniqSize/makefile
  • lines changed 1, 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/oneShot/unmasked/makefile
  • lines changed 1, 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/oneShot/unwrap/makefile
  • lines changed 1, 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/parasol/netC/makefile
  • lines changed 1, 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/parasol/netS/makefile
  • lines changed 1, 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/parasol/para/makefile
  • lines changed 1, 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/parasol/paraHubStop/makefile
  • lines changed 1, 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/parasol/paraNode/makefile
  • lines changed 1, 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/parasol/paraNodeStart/makefile
  • lines changed 1, 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/parasol/paraNodeStatus/makefile
  • lines changed 1, 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/parasol/paraNodeStop/makefile
  • lines changed 1, 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/parasol/parasol/makefile
  • lines changed 1, 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/parasol/simpleC/makefile
  • lines changed 1, 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/parasol/simpleS/makefile
  • lines changed 1, 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/primeMate/makefile
  • lines changed 1, 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/product/scripts/browserEnvironment.txt
  • lines changed 18, context: html, text, full: html, text
    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/protDust/makefile
  • lines changed 1, 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/reformat/fa4blast/makefile
  • lines changed 1, 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/reformat/fatont4/makefile
  • lines changed 1, 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/reformat/fsg/makefile
  • lines changed 1, 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/reformat/gb2cdi/makefile
  • lines changed 1, 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/reformat/gbToFaRa/makefile
  • lines changed 1, 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/reformat/gbtofa/makefile
  • lines changed 1, 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/reformat/geniegff/makefile
  • lines changed 1, 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/reformat/gffgenes/makefile
  • lines changed 1, 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/reformat/makeOrf2gene/makefile
  • lines changed 1, 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/reformat/makec2c/makefile
  • lines changed 1, 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/reformat/moresyn/makefile
  • lines changed 1, 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/reformat/wabToSt/makefile
  • lines changed 1, 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/scanIntrons/makefile
  • lines changed 1, 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/test/makefile
  • lines changed 4, 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/utils/addCols/makefile
  • lines changed 1, 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/utils/aveCols/makefile
  • lines changed 1, 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/utils/bigWigToBedGraph/bigWigToBedGraph.c
  • lines changed 2, 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/cCp/makefile
  • lines changed 1, 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/utils/catUncomment/makefile
  • lines changed 1, 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/utils/ccCp/makefile
  • lines changed 2, 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/utils/ccCpLock/makefile
  • lines changed 2, 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/utils/colCount/makefile
  • lines changed 1, 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/utils/countChars/makefile
  • lines changed 1, 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/utils/faGapLocs/makefile
  • lines changed 1, 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/utils/faGapSizes/makefile
  • lines changed 1, 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/utils/faNoise/makefile
  • lines changed 1, 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/utils/faOneRecord/makefile
  • lines changed 1, 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/utils/faRandomize/makefile
  • lines changed 1, 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/utils/faSplit/makefile
  • lines changed 2, 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/utils/fixCr/makefile
  • lines changed 1, 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/utils/htmlPics/makefile
  • lines changed 1, 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/utils/jkUniq/makefile
  • lines changed 1, 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/utils/newProg/makefile
  • lines changed 1, 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/utils/nibCheck/makefile
  • lines changed 1, 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/utils/nibFrag/makefile
  • lines changed 1, 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/utils/nibSize/makefile
  • lines changed 1, 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/utils/rmFaDups/makefile
  • lines changed 1, 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/utils/scaffoldFaToAgp/makefile
  • lines changed 1, 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/utils/scrambleFa/makefile
  • lines changed 1, 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/utils/sortFa/makefile
  • lines changed 1, 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/utils/subChar/makefile
  • lines changed 1, 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/utils/subs/makefile
  • lines changed 1, 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/utils/tailLines/makefile
  • lines changed 2, 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/utils/toLower/makefile
  • lines changed 1, 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/utils/toUpper/makefile
  • lines changed 1, 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/utils/undupFa/makefile
  • lines changed 1, 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/utils/upper/makefile
  • lines changed 1, 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/utils/wordLine/makefile
  • lines changed 1, 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/webBlat/makefile
  • lines changed 1, 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/weblet/bottleneck/makefile
  • lines changed 1, 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/weblet/hitreport/makefile
  • lines changed 1, 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/wormAli/makefile
  • lines changed 1, 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/xenoAli/aliStats/makefile
  • lines changed 1, 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/xenoAli/blastStats/makefile
  • lines changed 1, 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/xenoAli/bwana/makefile
  • lines changed 1, 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/xenoAli/cbAli/makefile
  • lines changed 1, 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/xenoAli/dynAlign/makefile
  • lines changed 0, 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/xenoAli/newIntron/makefile
  • lines changed 1, 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/xenoAli/smithWat/makefile
  • lines changed 1, 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/xenoAli/stitcher/makefile
  • lines changed 1, 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/xenoAli/waba/makefile
  • lines changed 1, 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/xenoAli/xaShow/makefile
  • lines changed 1, 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/xenoAli/xenWorm/makefile
  • lines changed 1, 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.