385aff5f901d24ed7e077566a312ae34d11f3422
kate
  Wed Jul 13 09:52:42 2011 -0700
Removing junk
diff --git src/inc/sav/common.mk src/inc/sav/common.mk
deleted file mode 100644
index 3eb5597..0000000
--- src/inc/sav/common.mk
+++ /dev/null
@@ -1,201 +0,0 @@
-CC=gcc
-# to build on sundance: CC=gcc -mcpu=v9 -m64
-ifeq (${COPT},)
-    COPT=-O -g
-endif
-CFLAGS=
-HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE}
-HG_INC=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc
-
-#global external libraries 
-L=
-
-# autodetect if openssl is installed
-ifeq (${SSLDIR},)
-  SSLDIR = /usr/include/openssl
-endif
-ifeq (${USE_SSL},)
-  ifneq ($(wildcard ${SSLDIR}),)
-     USE_SSL=1
-  endif
-endif
-
-
-# libssl: disabled by default
-ifeq (${USE_SSL},1)
-    L+=-lssl -lcrypto
-    HG_DEFS+=-DUSE_SSL
-endif
-
-# autodetect where png is installed
-ifeq (${PNGLIB},)
-  ifneq ($(wildcard /usr/lib64/libpng.a),)
-      PNGLIB=/usr/lib64/libpng.a
-  endif
-endif
-ifeq (${PNGLIB},)
-  ifneq ($(wildcard /usr/lib/libpng.a),)
-      PNGLIB=/usr/lib/libpng.a
-  endif
-endif
-ifeq (${PNGLIB},)
-  PNGLIB=-lpng
-endif
-
-L+=${PNGLIB}
-HG_INC+=${PNGINCL}
-
-# 32-bit color enabled by default
-ifneq (${COLOR32},0)
-    HG_DEFS+=-DCOLOR32
-endif
-
-# autodetect local installation of samtools:
-ifeq (${SAMDIR},)
-  SAMDIR = /hive/data/outside/samtools/svn_${MACHTYPE}/samtools
-  ifneq ($(wildcard ${SAMDIR}),)
-     KNETFILE_HOOKS=1
-  endif
-endif
-ifeq (${USE_BAM},)
-  ifneq ($(wildcard ${SAMDIR}),)
-     USE_BAM=1
-  endif
-endif
-
-# libbam (samtools, and Angie's KNETFILE_HOOKS extension to it): disabled by default
-ifeq (${USE_BAM},1)
-    ifeq (${SAMINC},)
-        SAMINC = ${SAMDIR}
-    endif
-    ifeq (${SAMLIB},)
-        SAMLIB = ${SAMDIR}/libbam.a
-    endif
-    HG_INC += -I${SAMINC}
-    L+=${SAMLIB}
-    HG_DEFS+=-DUSE_BAM
-    ifeq (${KNETFILE_HOOKS},1)
-	HG_DEFS+=-DKNETFILE_HOOKS
-    endif
-endif
-
-# As we do for bam/samtools, so do for tabix.  autodetect local installation:
-ifeq (${TABIXDIR},)
-  TABIXDIR = /hive/data/outside/tabix/tabix-0.2.3/${MACHTYPE}
-  ifneq ($(wildcard ${TABIXDIR}),)
-     KNETFILE_HOOKS=1
-  endif
-endif
-ifeq (${USE_TABIX},)
-  ifneq ($(wildcard ${TABIXDIR}),)
-     USE_TABIX=1
-  endif
-endif
-
-# libtabix and Angie's KNETFILE_HOOKS extension to it: disabled by default
-ifeq (${USE_TABIX},1)
-    ifeq (${TABIXINC},)
-        TABIXINC = ${TABIXDIR}
-    endif
-    ifeq (${TABIXLIB},)
-        TABIXLIB = ${TABIXDIR}/libtabix.a
-    endif
-    HG_INC += -I${TABIXINC}
-    L+=${TABIXLIB} -lz
-    HG_DEFS+=-DUSE_TABIX
-    ifeq (${KNETFILE_HOOKS},1)
-	HG_DEFS+=-DKNETFILE_HOOKS
-    endif
-endif
-
-
-SYS = $(shell uname -s)
-
-ifeq (${HG_WARN},)
-  ifeq (${SYS},Darwin)
-      HG_WARN = -Wall -Wno-unused-variable
-      HG_WARN_UNINIT=
-  else
-    ifeq (${SYS},SunOS)
-      HG_WARN = -Wall -Wformat -Wimplicit -Wreturn-type
-      HG_WARN_UNINIT=-Wuninitialized
-    else
-      #HG_WARN = -Wall -Werror -Wformat -Wimplicit -Wreturn-type
-      HG_WARN = -Wall -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=${HOME}/bin/scripts
-endif
-ifeq (${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
-GIT=git
-
-# portable naming of compiled executables: add ".exe" if compiled on 
-# Windows (with cygwin).
-ifeq (${OS}, Windows_NT)
-  AOUT=a
-  EXE=.exe
-else
-  AOUT=a.out
-  EXE=
-endif
-
-# location of stringify program
-STRINGIFY = ${DESTDIR}${BINDIR}/stringify
-
-#Lowelab defines
-#The lowelab specific code will be included in compilation if the following conditions are satistied
-LOWELAB_WIKI_DEF=
-LOWELAB_DEF=
-ifdef LOWELAB
-    LOWELAB_WIKI=1
-    LOWELAB_DEF=-DLOWELAB
-endif
-ifdef LOWELAB_WIKI
-    LOWELAB_WIKI_DEF=-DLOWELAB_WIKI
-endif
-LOWELAB_DEFS=${LOWELAB_DEF} ${LOWELAB_WIKI_DEF}
-
-ifdef LOWELAB
-    ifeq (${SCRIPTS},/cluster/bin/scripts)
-        SCRIPTS=${HOME}/scripts
-    endif
-    ifeq (${CGI_BIN},/usr/local/apache/cgi-bin)
-        CGI_BIN=/www/cgi-bin
-    endif
-    ifeq (${DOCUMENTROOT},/usr/local/apache/htdocs)
-        DOCUMENTROOT=/www/browser-docs
-    endif
-endif
-
-%.o: %.c
-	${CC} ${COPT} ${CFLAGS} ${HG_DEFS} ${LOWELAB_DEFS} ${HG_WARN} ${HG_INC} ${XINC} -o $@ -c $<
-