config.mk

MACH = $(shell uname -m)
SYS = $(shell uname -s)
SHELL = /bin/bash

# edit to set to UCSC browser kent/src
KENTDIR = ${HOME}/kent/src

KENTINC = -I${KENTDIR}/inc -I${KENTDIR}/hg/inc
KENTLIBDIR = ${KENTDIR}/lib/${MACH}
KENTLIBS = ${KENTLIBDIR}/jkhgap.a ${KENTLIBDIR}/jkweb.a
LIBS = -lssl -lcrypto -lz -lpthread

# autodetect UCSC installation of htslib:
ifeq (${HTSDIR},)
    HTSDIR = /hive/groups/browser/htslib
    ifneq ($(wildcard ${HTSDIR}),)
        ifeq (${USE_HTS},)
            USE_HTS=1
            USE_TABIX=1
            USE_SAMTABIX=1
            SAMTABIXDIR = /hive/groups/browser/htslib
            SAMTABIXLIB=/hive/groups/browser/htslib/libhts.a
            HG_DEFS+=-DUSE_HTS
        endif
    endif
endif
ifneq (${SAMTABIXDIR},)
    LIBS += ${SAMTABIXLIB}
endif


ifeq (${SYS},Darwin)
    CXX = g++-mp-4.9
    CXXFLAGS = -std=c++11 -Wall -Werror -Wno-sign-compare
    CXXDEBUG = -g -O0 -fno-default-inline -fno-inline
else ifneq ($(wildcard /opt/rh/devtoolset-2/root/usr/bin/g++),)
    CXX = /opt/rh/devtoolset-2/root/usr/bin/g++
else
    CXX = g++
endif
CXXFLAGS = -std=c++11 -Wall -Werror -Wno-sign-compare 
CXXDEBUG = -g -gdwarf-3 -O0 -fno-default-inline -fno-inline
#CXXDEBUG += -pg

CXXFLAGS += ${KENTINC} ${CXXDEBUG}

BINDIR = ${ROOT}/bin
OBJDIR = ${ROOT}/objs
gencode_backmap = ${BINDIR}/gencode-backmap
gencodeAttrsStats = ${BINDIR}/gencodeAttrsStats