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/jkOwnLib/makefile src/jkOwnLib/makefile
index e8cd6e0..16f2cf5 100644
--- src/jkOwnLib/makefile
+++ src/jkOwnLib/makefile
@@ -1,19 +1,20 @@
+kentSrc = ..
 include ../inc/common.mk
 
 O = bandExt.o crudeali.o ffAliHelp.o ffSeedExtend.o fuzzyFind.o \
     genoFind.o gfBlatLib.o gfClientLib.o gfInternal.o gfOut.o gfPcrLib.o gfWebLib.o ooc.o \
     patSpace.o splix.o supStitch.o trans3.o xenbig.o xensmall.o 
 
 T = ../lib/$(MACHTYPE)/jkOwnLib.a
 
 $(T): $(O) ../lib/$(MACHTYPE)
 	ar rcus $(T) $(O)
 
 ../lib/$(MACHTYPE):
 	mkdir ../lib/$(MACHTYPE)
 
 clean:
 	rm -f ${O} ../lib/$(MACHTYPE)/jkOwnLib.a
 
 tags:
 	etags ../inc/*.h ../lib/*.h ../lib/*.c  ../hg/inc/*.h ../hg/lib/*.h ../hg/lib/*.c ../hg/hgTracks/hgTracks.c ../hg/hgc/hgc.c ../hg/hgTrackUi/hgTrackUi.c