e2ec5ef77645a662ba31c7cfbd7499794975275a angie Fri Mar 23 16:44:07 2012 -0700 Feature #6152 (Variant Annotation Tool): Initial work, squashed infrom origin/annoGrator branch. Superclasses annoColumn, annoFilter, annoRow, annoStreamer, annoGrator, and annoFormatter define the core interfaces for passing data and configuration to and from components. The annoGrator superclass can join annoRows on position and pass forward all rows of secondary source. The annoGratorQuery module orchestrates the passing of annoRows between the primary source, annoGrator(s) and annoFormatter(s). The subclasses annoStreamDb and annoFormatTab, together with hg/lib/tests/annoGratorTester.c, can join columns of two database tables such as hg19's pgNA12878 and knownGene into tab-separated output. diff --git src/hg/lib/makefile src/hg/lib/makefile index b4ea4ea..ebbfcfa 100644 --- src/hg/lib/makefile +++ src/hg/lib/makefile @@ -1,21 +1,21 @@ include ../../inc/common.mk XINC = -I$(MYSQLINC) O = acemblyClass.o affyAllExonProbe.o affyAtlas.o affy10KDetails.o affy120KDetails.o \ affyOffset.o affyPairs.o agp.o agpFrag.o agpGap.o alignSeqSizes.o altGraph.o \ - altGraphX.o ancientRref.o atomDb.o axtInfo.o \ + altGraphX.o ancientRref.o annoStreamDb.o atomDb.o axtInfo.o \ axtLib.o bactigPos.o hgBam.o baseMaskCommon.o bdgpExprLink.o bdgpGeneInfo.o \ bed.o bed5FloatScore.o bed5Pval.o bed6FloatScore.o bed8Attrs.o bed12Source.o \ bed12wSeq.o bedCart.o bgiGeneInfo.o bgiGeneSnp.o bgiSnp.o bioImage.o \ blastTab.o blastzNet.o blatServers.o borf.o borkPseudoHom.o botDelay.o\ cart.o cartDb.o cdsEvidence.o cdsOrtho.o cdsPick.o cdsSpec.o \ ccdsInfo.o ccdsNotes.o ccdsGeneMap.o celeraCoverage.o \ celeraDupPositive.o cgapSage/cgapSage.o cgapSage/cgapSageLib.o cgh.o chainCart.o \ chainDb.o chainLink.o chainNet.o chainNetDbLoad.o \ chicken13kInfo.o chromBins.o chr18deletions.o \ chromGraph.o chromGraphFactory.o chromInfo.o chromInserts.o chromKeeper.o \ clonePos.o codeBlast.o codeBlastScore.o cogs.o cogsxra.o columnInfo.o \ contigAcc.o coordConv.o \ cnpIafrate.o cnpIafrate2.o cnpLocke.o cnpRedon.o cnpSebat.o cnpSebat2.o \ cnpSharp2.o cnpSharpCutoff.o cnpSharpSample.o cnpSharp.o \ cpgIsland.o cpgIslandExt.o ctgPos.o ctgPos2.o \