#!/bin/sh
# Configure script for R package with htslib integration

# Exit on any error
set -e

HTSLIB_DIR="src/htslib-1.21"
echo "Configuring HTSlib in $HTSLIB_DIR"
cd $HTSLIB_DIR
## copy file instead of symbolic linking
cp htscodecs_bundled.mk htscodecs.mk 
./configure CFLAGS="-O2 -fPIC" 
    
make libhts.a

