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/pslCDnaGenomeMatch/makefile src/hg/pslCDnaGenomeMatch/makefile
index 7554c6d..f4c7a90 100644
--- src/hg/pslCDnaGenomeMatch/makefile
+++ src/hg/pslCDnaGenomeMatch/makefile
@@ -1,15 +1,16 @@
+kentSrc = ../..
 include ../../inc/common.mk
 
 L += -lm $(MYSQLLIBS)
 MYLIBDIR = ../../lib/$(MACHTYPE)
 MYLIBS =  $(MYLIBDIR)/jkhgap.a $(MYLIBDIR)/jkweb.a 
 
 M = pslCDnaGenomeMatch.o  
 DB=hg18
 
 O = pslMismatch.o misMatch.o 
 pslCDnaGenomeMatch: $M $(MYLIBS)
 	gcc -ggdb -o ${BINDIR}/pslCDnaGenomeMatch $M $(MARKDEBUG) $(MYLIBS) $L 
 #${STRIP} ${BINDIR}/pslCDnaGenomeMatch${EXE}
 
 misMatch: $O $(MYLIBS)