#!/bin/sh

# Exit on any error
set -e

HTSLIB_DIR="htslib-1.21"

echo "Configuring HTSlib in $HTSLIB_DIR"
cd src/$HTSLIB_DIR
## copy file instead of symbolic linking
cp htscodecs_bundled.mk htscodecs.mk
./configure CFLAGS="-g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -DNDEBUG"

hasdeflate="no"
if grep -wq "#define HAVE_LIBDEFLATE 1" config.h;then
    hasdeflate="yes"
fi
    
make libhts.a

echo "Create Makevar file"
cd ../../
SRC_MAKEVAR="src/Makevars"
echo "PKG_CPPFLAGS=-I${HTSLIB_DIR} -I../inst/include" >$SRC_MAKEVAR

if [ $hasdeflate = "no" ]; then
    echo "PKG_LIBS=${HTSLIB_DIR}/libhts.a -lz -lm -lbz2 -llzma -lcurl" >>$SRC_MAKEVAR
else
    echo "PKG_LIBS=${HTSLIB_DIR}/libhts.a -ldeflate -lz -lm -lbz2 -llzma -lcurl" >>$SRC_MAKEVAR
fi    
