#!/usr/bin/env bash

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

COMMAND=$1

usage() {
    basename $0
    echo
    echo "USAGE:"
    echo "    cis-X ref-exp <SUBCOMMAND> [args...]"
    echo
    echo "SUBCOMMANDS:"
    echo "    generate    Generate a biallelic reference expression matrix"
    echo "    prepare     Create a batch script for preprocessing inputs"
    echo "    preprocess  Runs allelic specific expression (ASE) tests on inputs"
    exit 1
}

case $COMMAND in
    generate) $CIS_X_REF_EXP_HOME/bin/cis-X-ref-exp-generate "${@:2}" ;;
    prepare) $CIS_X_REF_EXP_HOME/bin/cis-X-ref-exp-prepare "${@:2}" ;;
    preprocess) $CIS_X_REF_EXP_HOME/bin/cis-X-ref-exp-preprocess "${@:2}" ;;
    *) usage ;;
esac
