7580a364f0819e5ab6244b2b1ff685980b93c188
kent
  Fri Jul 1 18:25:00 2022 -0700
First cut at cacheTwoBit system - which will cache pieces of two bit files we've read.  System has some sense about only loading what it hasn't seen already, and only loading the part it needs to see. Could be improved, but better than storing all of each sequence.

diff --git src/lib/makefile src/lib/makefile
index 2fe5aef..647f519 100644
--- src/lib/makefile
+++ src/lib/makefile
@@ -1,26 +1,26 @@
 kentSrc = ..
 include ../inc/localEnvironment.mk
 include ../inc/common.mk
 
 O = aliType.o annoAssembly.o annoFilter.o annoFormatter.o annoFormatTab.o \
     annoGrator.o annoGrateWig.o annoGratorQuery.o annoOption.o annoRow.o annoStreamer.o \
     annoStreamBigBed.o annoStreamBigWig.o annoStreamTab.o annoStreamLongTabix.o annoStreamVcf.o \
     apacheLog.o asParse.o aveStats.o axt.o axtAffine.o bamFile.o base64.o \
     basicBed.o bbiAlias.o bbiRead.o bbiWrite.o bedTabix.o bigBed.o binRange.o bits.o \
-    blastOut.o blastParse.o boxClump.o boxLump.o bPlusTree.o \
-    bwgCreate.o bwgQuery.o bwgValsOnChrom.o \
+    blastOut.o blastParse.o boxClump.o boxLump.o bPlusTree.o cacheTwoBit.o \
+    bwgCreate.o bwgQuery.o bwgValsOnChrom.o cacheTwoBit.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  csv.o \
     dgRange.o diGraph.o dlist.o dnaLoad.o dnaMarkov.o dnaMotif.o dnaseq.o \
     dnautil.o dtdParse.o dyOut.o dystring.o elmTree.o \
     emblParse.o errCatch.o errAbort.o \
     fa.o ffAli.o ffScore.o fieldedTable.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 \
     fq.o freeType.o fuzzyShow.o \