#!/bin/bash

CURR_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )
EXTERNAL_DIR=${CURR_DIR}/../external
INSTALL_DIR=${CURR_DIR}/../external/install

if [ -d ${EXTERNAL_DIR}/RapMap ] ; then
    rm -fr ${EXTERNAL_DIR}/RapMap
fi

if [ -d ${INSTALL_DIR}/include/rapmap ] ; then
    rm -fr ${INSTALL_DIR}/include/rapmap
fi

if [ -d ${INSTALL_DIR}/src/rapmap ] ; then
    rm -fr ${INSTALL_DIR}/src/rapmap
fi

mkdir -p ${EXTERNAL_DIR}
curl -k -L https://github.com/COMBINE-lab/RapMap/archive/sf-v0.10.1.zip -o ${EXTERNAL_DIR}/rapmap.zip

rm -fr ${EXTERNAL_DIR}/RapMap 
unzip ${EXTERNAL_DIR}/rapmap.zip -d ${EXTERNAL_DIR}
mv ${EXTERNAL_DIR}/RapMap-sf-v0.10.1 ${EXTERNAL_DIR}/RapMap

mkdir -p ${INSTALL_DIR}/include/rapmap 
mkdir -p ${INSTALL_DIR}/src/rapmap

rm ${EXTERNAL_DIR}/RapMap/src/xxhash.c
rm ${EXTERNAL_DIR}/RapMap/include/xxhash.h

cp -r ${EXTERNAL_DIR}/RapMap/external/libdivsufsort.zip ${EXTERNAL_DIR}
cp -r ${EXTERNAL_DIR}/RapMap/src/*.c ${INSTALL_DIR}/src/rapmap 
cp -r ${EXTERNAL_DIR}/RapMap/src/*.cpp ${INSTALL_DIR}/src/rapmap 
cp -r ${EXTERNAL_DIR}/RapMap/include/tclap ${INSTALL_DIR}/include/rapmap
cp -r ${EXTERNAL_DIR}/RapMap/include/*.h ${INSTALL_DIR}/include/rapmap
cp -r ${EXTERNAL_DIR}/RapMap/include/*.hpp ${INSTALL_DIR}/include/rapmap 



