af568c29d9e2d2ad91cea882a92c0a8991f7748c
aamp
  Fri Jul 8 16:11:15 2011 +0200
Separated BAM code into that which must compile into jkhgap.a (and be linked with mysql), and that which can go into jkweb.a (most of it).  Older BAM open, fetch, and exists functions call the new ones with the UDC fuse root parameter set to the hg.conf setting.  It is not yet clear to me if the UdcFuseRoot parameter can be set to NULL and used in a general way.
diff --git src/lib/makefile src/lib/makefile
index 1ab8292..3574bb1 100644
--- src/lib/makefile
+++ src/lib/makefile
@@ -1,58 +1,58 @@
 include ../inc/common.mk
 
 
-O = aliType.o apacheLog.o asParse.o axt.o axtAffine.o base64.o \
+O = aliType.o apacheLog.o asParse.o axt.o axtAffine.o bamUdc.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 dystring.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 \
     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 \
     jointalign.o jpegSize.o keys.o knetUdc.o kxTok.o linefile.o localmem.o log.o \
     maf.o mafFromAxt.o mafScore.o md5.o memalloc.o memgfx.o metaWig.o mgCircle.o \
     mgPolygon.o mime.o net.o nib.o nibTwo.o nt4.o numObscure.o \
     obscure.o oldGff.o oligoTm.o options.o osunix.o pairHmm.o peakCluster.o \
     phyloTree.o pipeline.o portimpl.o pngwrite.o psGfx.o psPoly.o pscmGfx.o \
     psl.o pslGenoShow.o pslShow.o pslTbl.o pslTransMap.o pthreadWrap.o \
     qa.o quickHeap.o quotedP.o \
     ra.o rainbow.o rbTree.o rangeTree.o regexHelper.o repMask.o \
     rle.o rnautil.o rqlEval.o rqlParse.o rudp.o \
     scoreWindow.o seg.o seqOut.o seqStats.o servBrcMcw.o servCrunx.o \
     servcis.o servcl.o servmsII.o servpws.o shaRes.o slog.o snof.o \
     snofmake.o snofsig.o spaceSaver.o spacedColumn.o spacedSeed.o \
     splatAli.o sqlList.o sqlNum.o subText.o sufa.o sufx.o synQueue.o \
     tabRow.o textOut.o tokenizer.o trix.o twoBit.o \
     udc.o vcf.o vGfx.o vPng.o verbose.o \
     wildcmp.o wormdna.o \
     xAli.o xa.o xap.o xenshow.o xmlEscape.o xp.o zlibFace.o
 
 $(MACHTYPE)/jkweb.a: $(O) $(MACHTYPE)
 	ar rcus $(MACHTYPE)/jkweb.a $(O)
 
 $(MACHTYPE):
 	mkdir $(MACHTYPE)
 
 test:
 	cd tests && ${MAKE} test
 
 clean:
 	rm -f ${O} $(MACHTYPE)/jkweb.a
 	cd tests && ${MAKE} clean
 
 tags:
 	etags ../inc/*.h ../lib/*.h ../lib/*.c  ../hg/inc/*.h ../hg/lib/*.h ../hg/lib/*.c ../hg/hgTracks/*.c ../hg/hgc/*.c ../hg/hgTrackUi/*.c