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
@@ -1,15 +1,16 @@
+kentSrc = ..
 include ../inc/common.mk
 
 # List of directories to build
 USE_DIRS = $(DIRS)
 
 DIRS = \
 	bfastMafFix \
 	bwtFind \
 	bwtMake \
 	bwtReverse \
 	elandToSpl \
 	i16Find \
 	itsaDump \
 	itsaFind \
 	itsaMake \