#!/usr/bin/env bash

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

SAMPLE_ID=$1
DISEASE=$2
FPKM_MATRIX=$3
OHE_RESULT=$4

# Ensure reference expression matrices exist for the given disease ID.
BILIST=$CIS_X_HOME/refs/diseases/$DISEASE/exp.ref.bi.txt
WHITELIST=$CIS_X_HOME/refs/diseases/$DISEASE/exp.ref.white.txt
WHOLELIST=$CIS_X_HOME/refs/diseases/$DISEASE/exp.ref.entire.txt

if [ ! -f $BILIST ] || [ ! -f $WHITELIST ] || [ ! -f $WHOLELIST ]; then
    echo "ERROR: $(date): cis-X-test-outliers: reference expression matrices missing for $DISEASE"
    exit 1
fi

Rscript $CIS_X_CORE_HOME/src/exp.check.R \
    $SAMPLE_ID \
    $FPKM_MATRIX \
    $BILIST \
    $WHOLELIST \
    $WHITELIST \
    $OHE_RESULT
