src/inc/common.mk 1.61

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 1000000 -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
@@ -1,83 +1,94 @@
 CC=gcc
 # to build on sundance: CC=gcc -mcpu=v9 -m64
 ifeq (${COPT},)
     COPT=-O
 endif
 CFLAGS=
 HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE}
 
 #global external libraries 
 L=
 
 #default to not using ssl
 ifeq (${USE_SSL},)
     USE_SSL=0
 endif
 
 ifeq (${USE_SSL},1)
     L+=-lssl
     HG_DEFS+=-DUSE_SSL
 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=
   else
     ifeq (solaris,$(findstring solaris,${OSTYPE}))
       HG_WARN = -Wall -Wformat -Wimplicit -Wreturn-type
       HG_WARN_UNINIT=-Wuninitialized
     else
       HG_WARN = -Wall -Werror -Wformat -Wimplicit -Wreturn-type
       HG_WARN_UNINIT=-Wuninitialized
     endif
   endif
   # -Wuninitialized generates a warning without optimization
   ifeq ($(findstring -O,${COPT}),-O)
      HG_WARN += ${HG_WARN_UNINIT}
   endif
 endif
 
 # this is to hack around many make files not including HG_WARN in
 # the link line
 CFLAGS += ${HG_WARN}
 
 ifeq (${SCRIPTS},)
     SCRIPTS=/cluster/bin/scripts
 endif
 ifeq (${CGI_BIN},)
     CGI_BIN=/usr/local/apache/cgi-bin
 endif
 ifeq (${DOCUMENTROOT},)
     DOCUMENTROOT=/usr/local/apache/htdocs
 endif
 ifeq (${BINDIR},)
     BINDIR = ${HOME}/bin/${MACHTYPE}
 endif
 ifeq (${ENCODE_PIPELINE_BIN},)
     ENCODE_PIPELINE_BIN=/cluster/data/encode/pipeline/bin
 endif
 
 MKDIR=mkdir -p
 ifeq (${STRIP},)
    STRIP=strip
 endif
 CVS=cvs
 
 # portable naming of compiled executables: add ".exe" if compiled on 
 # Windows (with cygwin).
 ifeq (${OS}, Windows_NT)
   AOUT=a.exe
   EXE=.exe
 else
   AOUT=a.out
   EXE=
 endif
 
 # location of stringify program
 STRINGIFY = ${BINDIR}/stringify
 
 %.o: %.c
 	${CC} ${COPT} ${CFLAGS} ${HG_DEFS} ${HG_WARN} ${HG_INC} ${XINC} -o $@ -c $<