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/shortReads/makefile src/shortReads/makefile
index 84e1dc1..e0d757f 100644
--- src/shortReads/makefile
+++ src/shortReads/makefile
@@ -1,40 +1,41 @@
+kentSrc = ..
 include ../inc/common.mk
 
 # List of directories to build
 USE_DIRS = $(DIRS)
 
 DIRS = \
 	bfastMafFix \
 	bwtFind \
 	bwtMake \
 	bwtReverse \
 	elandToSpl \
 	i16Find \
 	itsaDump \
 	itsaFind \
 	itsaMake \
 	shortRepeatFind \
 	shortRepeatMerge \
 	splat \
 	splatCheck1 \
 	splatCheck2 \
 	splatMerge \
 	splatTestSet \
 	splatToEland \
 	splixMake \
 	sufaFind \
 	sufaMake \
 	sufaRepeatFind \
 	sufxDump \
 	sufxFind \
 	sufxMake
 
 all: $(USE_DIRS:%=%.all)
 
 %.all:
 	( cd $* && echo $* && $(MAKE) )
 
 clean:: $(USE_DIRS:%=%.clean)
 
 %.clean::
 	( cd $* && echo $* && $(MAKE) clean )