#!/usr/bin/env bash

CIS_X_HOME=$(realpath $(dirname $0)/..)

COMMAND=$1

usage() {
    basename $0
    echo
    echo "USAGE:"
    echo "    cis-X <SUBCOMMAND> [args...]"
    echo ""
    echo "SUBCOMMANDS:"
    echo "    ref-exp  Generate reference expression matrices"
    echo "    run      Search for activating regulatory variants in the tumor genome"
    echo "    seed     Download and generate a set of common references"
    exit 1
}

case $COMMAND in
    ref-exp) $CIS_X_HOME/src/ref-exp/bin/cis-X-ref-exp "${@:2}" ;;
    run) $CIS_X_HOME/src/core/bin/cis-X-run "${@:2}" ;;
    seed) $CIS_X_HOME/src/seed/bin/cis-X-seed "${@:2}" ;;
    *) usage ;;
esac
