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/affyTransciptome/makefile src/hg/affyTransciptome/makefile
index af95c42..8419268 100644
--- src/hg/affyTransciptome/makefile
+++ src/hg/affyTransciptome/makefile
@@ -1,15 +1,16 @@
+kentSrc = ../..
 include ../../inc/common.mk
 
 L += -lz -lm $(MYSQLLIBS)
 MYLIBDIR = ../../lib/$(MACHTYPE)
 MYLIBS =  $(MYLIBDIR)/jkhgap.a $(MYLIBDIR)/jkweb.a $(L)
 
 O = affyPairsToSample normalizeSampleFile avgTranscriptomeExps maxTranscriptomeExps scaleSampleFiles averageZoomLevels \
 	groupSamples
 
 %: %.c 
 	${CC} ${COPT} ${CFLAGS} -Wimplicit  -I../inc -I../../inc  -o ${DESTDIR}${BINDIR}/$@ $(addsuffix .c,$@) $(MYLIBS) ${L}
 
 all : $(O)
 
 clean::