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/pslPseudo/makefile src/hg/pslPseudo/makefile
index cc49890..7b5d244 100644
--- src/hg/pslPseudo/makefile
+++ src/hg/pslPseudo/makefile
@@ -1,15 +1,16 @@
+kentSrc = ../..
 include ../../inc/common.mk
 
 
 L += -lm $(MYSQLLIBS)
 MYLIBDIR = ../../lib/$(MACHTYPE)
 MYLIBS =  $(MYLIBDIR)/jkhgap.a $(MYLIBDIR)/jkweb.a 
 DEBUGOPTIONS = -skipExciseRepeats -minAli=0.98 -nearTop=0.005 
 OPTIONS = -minAli=0.98 -nearTop=0.005 -verbose=3 -stripVersion
 #MARKDEBUG = /cse/grads/markd/compbio/dbgmalloc/debug-malloc.o
 MARKDEBUG =
 DB = hg17
 MRNA = mrnaHg17.2bit 
 DBDIR = /cluster/data/$(DB)
 BED = $(DBDIR)/bed
 PSEUDO = $(DBDIR)/bed/pseudo