#!/bin/bash

echo "Downloading files and software"
echo

wget http://faculty.washington.edu/browning/beagle/beagle.jar
wget bochet.gcc.biostat.washington.edu/beagle/beagle3_examples/ref.markers
wget bochet.gcc.biostat.washington.edu/beagle/beagle3_examples/ref.bgl.gz
wget bochet.gcc.biostat.washington.edu/beagle/beagle3_examples/sparse.target.bgl.gz

echo
echo "Example 1a: phasing the reference panel"
echo
java -Xmx1000m -jar beagle.jar unphased=ref.bgl.gz missing=N out=ex1a lowmem=true gprobs=false verbose=true

echo
echo "Example 1b: phasing the reference panel AND perform fastIBD analysis"
echo "  -- setting ibdscale parameter to sqrt[ (# samples) / 100 ]  (current best practice)"
echo
java -Xmx1000m -jar beagle.jar unphased=ref.bgl.gz missing=N out=ex1b lowmem=true gprobs=false verbose=true fastibd=true ibdscale=2.3

echo
echo "Example 2: imputation of ungenotyped markers using a phased reference panel"
echo
java -Xmx1000m -jar beagle.jar markers=ref.markers phased=ex1b.ref.bgl.gz.phased.gz unphased=sparse.target.bgl.gz missing=N out=ex2 lowmem=true verbose=true

echo
echo "Finished examples"