#!/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
ASE_RESULT_RUN=$7
CNV_LOH_ACTION=$8
COVG_RNA=$9

#THRESH_AI=0.3
THRESH_AI_DI=0.3
THRESH_AI_CNV=0.2
THRESH_PVALUE_ASE=0.05

GENE_MODEL=$CIS_X_HOME/refs/external/hg19_refGene
GENE_MODEL_BED=$CIS_X_HOME/refs/external/hg19_refGene.bed

WGS_RNA_COUNT="$WORKDIR/$SAMPLE_ID.combine.WGS.RNAseq.goodmarkers.txt"
ASE_RUNS="$WORKDIR/$SAMPLE_ID.ase.runs.txt"
ASE_RUNS_BED="$WORKDIR/$SAMPLE_ID.ase.runs.bed"
ASE_RUNS_GENE="$WORKDIR/$SAMPLE_ID.ase.runs.genes.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 $COVG_RNA
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_DI \
    $THRESH_AI_CNV \
    $THRESH_PVALUE_ASE \
    $CNV_LOH_ACTION \
    $GENE_MODEL_Temp1 \
    $COVG_RNA

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

#perl $CIS_X_CORE_HOME/src/ase_runs.pl $ASE_RESULT_MARKER $THRESH_AI_DI $THRESH_AI_CNV $ASE_RUNS1 $ASE_RUNS_BED1 15 0.8 200000
perl $CIS_X_CORE_HOME/src/ase_runs.pl $ASE_RESULT_MARKER $THRESH_AI_DI $THRESH_AI_CNV $ASE_RUNS $ASE_RUNS_BED 4 0.6 500000000
#bedtools intersect -a $ASE_RUNS_BED1 -b $GENE_MODEL_BED -F 0.8 -wao > $ASE_RUNS_GENE1
bedtools intersect -a $ASE_RUNS_BED -b $GENE_MODEL_BED -wao > $ASE_RUNS_GENE
perl $CIS_X_CORE_HOME/src/proc_ase_runs.pl $ASE_RUNS $ASE_RUNS_GENE $ASE_RESULT_RUN
