752bae9723eeeabb02d950157ab0f9512fd689b3
tdreszer
  Mon Jan 28 15:05:59 2013 -0800
Checking in 'elmTree' which uses neighbor joining to build a tree in local memory.  Also checking in 2 sets of changes to vcf.  First, added support for a 'reuse' local memory pool which aid traversing giant files.  Second, added routines for bitmap based analysis of variants.
diff --git src/lib/makefile src/lib/makefile
index f2ad4bc..fc2e902 100644
--- src/lib/makefile
+++ src/lib/makefile
@@ -1,29 +1,29 @@
 include ../inc/common.mk
 
 
 O = aliType.o annoColumn.o annoFilter.o annoFormatter.o annoFormatTab.o \
     annoGrator.o annoGrateWig.o annoGratorQuery.o annoOption.o annoRow.o \
     annoStreamer.o annoStreamBigBed.o annoStreamBigWig.o annoStreamVcf.o \
     apacheLog.o asParse.o axt.o axtAffine.o bamFile.o base64.o \
     basicBed.o bbiRead.o bbiWrite.o bigBed.o binRange.o bits.o \
     blastOut.o blastParse.o boxClump.o boxLump.o bPlusTree.o \
     bwgCreate.o bwgQuery.o bwgValsOnChrom.o \
     cda.o chain.o chainBlock.o chainConnect.o chainToAxt.o chainToPsl.o \
     cheapcgi.o cirTree.o codebias.o colHash.o common.o correlate.o crTree.o \
     dgRange.o diGraph.o dlist.o dnaLoad.o dnaMarkov.o dnaMotif.o dnaseq.o \
-    dnautil.o dtdParse.o dyOut.o dystring.o \
+    dnautil.o dtdParse.o dyOut.o dystring.o elmTree.o \
     emblParse.o errCatch.o errabort.o \
     fa.o ffAli.o ffScore.o filePath.o fixColor.o flydna.o fof.o \
     font/mgCourier10.o font/mgCourier12.o font/mgCourier14.o font/mgCourier18.o \
     font/mgCourier24.o font/mgCourier34.o font/mgCourier8.o font/mgHelvetica10.o \
     font/mgHelvetica12.o font/mgHelvetica14.o font/mgHelvetica18.o font/mgHelvetica24.o \
     font/mgHelvetica34.o font/mgHelvetica8.o font/mgHelveticaBold10.o font/mgHelveticaBold12.o \
     font/mgHelveticaBold14.o font/mgHelveticaBold18.o font/mgHelveticaBold24.o \
     font/mgHelveticaBold34.o font/mgHelveticaBold8.o font/mgSixhi6.o font/mgSail8.o \
     font/mgTimes10.o font/mgTimes12.o font/mgTimes14.o font/mgTimes18.o \
     font/mgTimes24.o font/mgTimes34.o font/mgTimes8.o font/mgMenlo12.o \
     fuzzyShow.o \
     gapCalc.o gdf.o gemfont.o genomeRangeTree.o \
     gfNet.o gff.o gff3.o gfxPoly.o gifLabel.o \
     hacTree.o hash.o histogram.o hmmPfamParse.o hmmstats.o htmlPage.o htmshell.o \
     https.o intExp.o intValTree.o internet.o itsa.o iupac.o \