#!/usr/bin/env bash

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

SAMPLE_ID=$1
WORKDIR=$2
HET_OUT=$3
MATRIX_OUT=$4
ASE_RESULT_MARKER=$5
ASE_RESULT_GENE=$6

THRESH_AI=0.3
THRESH_PVALUE_ASE=0.05

GENE_MODEL=$CIS_X_HOME/refs/external/hg19_refGene

WGS_RNA_COUNT="$WORKDIR/$SAMPLE_ID.combine.WGS.RNAseq.goodmarkers.txt"
GENE_MODEL_Temp1="$WORKDIR/$SAMPLE_ID.combine.WGS.RNAseq.goodmarkers.binom.genemodel.summary.txt"
GENE_MODEL_Temp2="$WORKDIR/$SAMPLE_ID.combine.WGS.RNAseq.goodmarkers.binom.genemodel.summary.merged.txt"

perl $CIS_X_CORE_HOME/src/02.add.count.pl $SAMPLE_ID $HET_OUT $MATRIX_OUT $WGS_RNA_COUNT
Rscript $CIS_X_CORE_HOME/src/binom.R $WGS_RNA_COUNT $ASE_RESULT_MARKER

perl $CIS_X_CORE_HOME/src/07.gene.model.Oct2017.pl \
    $SAMPLE_ID \
    $ASE_RESULT_MARKER \
    $GENE_MODEL \
    $THRESH_AI \
    $THRESH_PVALUE_ASE \
    $GENE_MODEL_Temp1

perl $CIS_X_CORE_HOME/src/05.merge.pl $GENE_MODEL_Temp1 $GENE_MODEL_Temp2
Rscript $CIS_X_CORE_HOME/src/fdr.R $GENE_MODEL_Temp2 $ASE_RESULT_GENE
