Index: src/inc/common.mk
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/inc/common.mk,v
retrieving revision 1.60
retrieving revision 1.61
diff -b -B -U 4 -r1.60 -r1.61
--- src/inc/common.mk	6 Apr 2009 22:19:09 -0000	1.60
+++ src/inc/common.mk	24 Jun 2009 19:14:27 -0000	1.61
@@ -20,8 +20,19 @@
 endif
 
 HG_INC=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc
 
+#default to not using bam
+ifeq (${USE_BAM},)
+    USE_BAM=0
+endif
+
+ifeq (${USE_BAM},1)
+    SAMPATH = /hive/data/outside/samtools/samtools
+    HG_INC += -I${SAMPATH}
+    HG_DEFS+=-DUSE_BAM
+endif
+
 ifeq (${HG_WARN},)
   ifeq (darwin,$(findstring darwin,${OSTYPE}))
       HG_WARN = -Wall -Wno-unused-variable -Wno-long-double
       HG_WARN_UNINIT=

