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/splignToPsl/makefile src/hg/splignToPsl/makefile
index 7b4a89b..3bed1c1 100644
--- src/hg/splignToPsl/makefile
+++ src/hg/splignToPsl/makefile
@@ -1,23 +1,24 @@
+kentSrc = ../..
 include ../../inc/common.mk
 
 
 L += -lm ${MYSQLLIBS}
 MYLIBDIR = ../../lib/${MACHTYPE}
 MYLIBS =  ${MYLIBDIR}/jkhgap.a ${MYLIBDIR}/jkweb.a
 
 A = splignToPsl
 
 O = $A.o
 
 include ../../inc/cgi_build_rules.mk
 
 mgsc: compile
 	cp $A ${CGI_BIN}-${USER}/$A
 
 test: compile
 	cp $A ${CGI_BIN}-${USER}/$A
 compile: $O 
 	${CC} $O ${F64} ${MYLIBS} ${L} #/cse/grads/markd/lib/libefence.a -lpthread 
 	#${CC} $O ${F64} ${MYLIBS} ${L}	
 	mv ${AOUT} $A${EXE}
 	chmod a+rx $A