#!/bin/bash -e

if [ $# != 4 ] ; then
    echo "wrong # args: query queryChrom target outPsl " >&2
    exit 1
fi
query=$1
queryChrom=$2
target=$3
outPsl=$4

tmpOutPsl=${outPsl}.$(hostname).$$.tmp
mkdir -p $(dirname ${outPsl})

resolution=1000000
../../../bin/halSynteny --minBlockSize $resolution --maxAnchorDistance $resolution --targetGenome ${target} --queryGenome ${query} --queryChromosome ${queryChrom} ../../../data/primates_eichler.hal ${tmpOutPsl}
mv -f ${tmpOutPsl} ${outPsl}