11e45667d4e291b3038ccda729a1cdf5bcaf004a
braney
  Mon Jul 11 15:46:54 2016 -0700
incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
defines, modify a bunch of makefiles to include kentSrc variable
pointing to top of the tree.

diff --git src/hg/lib/makefile src/hg/lib/makefile
index 14eefb4..1f0c670 100644
--- src/hg/lib/makefile
+++ src/hg/lib/makefile
@@ -1,15 +1,16 @@
+kentSrc = ../..
 include ../../inc/localEnvironment.mk
 include ../../inc/common.mk
 XINC = -I$(MYSQLINC)
 
 O = acemblyClass.o adjacency.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 \
     annoFormatVep.o annoGratorGpVar.o annoGrateWigDb.o \
     annoStreamDb.o annoStreamDbFactorSource.o annoStreamWig.o \
     api.o atomDb.o autoUpgrade.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 bigBedFind.o \
     bigGenePred.o bigPsl.o bioImage.o \
     blastTab.o blastzNet.o blatServers.o borf.o borkPseudoHom.o botDelay.o\