#!/usr/bin/env bash

set -e

CIS_X_CORE_HOME=$(realpath $(dirname $0)/../../core)
PATH=$CIS_X_CORE_HOME/bin:$PATH

SAMPLE_ID=$1
ROOTDIR=$2
HIGH20=$3
RNABAM=$4
CNV_LOH=$5

if [ $# -lt 5 ]; then
    basename $0
    echo
    echo "USAGE:"
    echo "    cis-X ref-exp preprocess <sample-id> <results-dir> <markers> <bam> <cnv-loh>"
    exit 1
fi

WORKDIR=$ROOTDIR/$SAMPLE_ID/working_space
mkdir -p $WORKDIR
cd $WORKDIR

SNV4_OUT="$WORKDIR/$SAMPLE_ID.snv4.txt"
HET_OUT="$WORKDIR/$SAMPLE_ID.heterozygous.markers.txt"
cis-X-mark $SAMPLE_ID $HIGH20 $CNV_LOH $SNV4_OUT $HET_OUT

MATRIX_OUT="$WORKDIR/matrix_combined_matrix_simple.tab"
cis-X-build-matrix $RNABAM $SNV4_OUT $WORKDIR $MATRIX_OUT

ASE_RESULT_MARKER="$WORKDIR/$SAMPLE_ID.ase.combine.WGS.RNAseq.goodmarkers.binom.txt"
ASE_RESULT_GENE="$WORKDIR/$SAMPLE_ID.ase.gene.model.fdr.txt"
cis-X-ase $SAMPLE_ID $WORKDIR $HET_OUT $MATRIX_OUT $ASE_RESULT_MARKER $ASE_RESULT_GENE
