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/getallpep/makefile src/hg/getallpep/makefile
index de57c51..4ebeb54 100644
--- src/hg/getallpep/makefile
+++ src/hg/getallpep/makefile
@@ -1,37 +1,38 @@
+kentSrc = ../..
 
 include ../../inc/common.mk
 
 L += -lm $(MYSQLLIBS)
 MYLIBDIR = ../../lib/$(MACHTYPE)
 MYLIBS =  $(MYLIBDIR)/jkhgap.a $(MYLIBDIR)/jkweb.a
 
 A = getallpep
 
 O = $A.o
 
 my: compile
 	mv $A${EXE} $(HOME)/bin/i386/$A
 
 mgsc: compile
 	mv $A${EXE} /usr/local/apache/cgi-bin-mgsc/$A
 
 alpha: compile
 	mv $A${EXE} /usr/local/apache/cgi-bin/$A
 
 beta: compile
 	mv $A${EXE} /usr/local/apache/cgi-bin-beta/$A
 
 compile: $O 
 	${CC} ${COPT} ${CFLAGS} $O $(MYLIBS) $(L) 
 	mv ${AOUT} $A${EXE}
 #	${STRIP} $A${EXE}
 	chmod a+rx $A${EXE}
 
 lib:
 	cd ../../lib && ${MAKE}
 
 tags: 
 	ctags *.h *.c ../lib/*.c ../inc/*.h ../../lib/*.c ../../inc/*.h
 
 clean::
 	rm -f $A $A.o $A${EXE}