#!/bin/bash --login

module load apps/gcc/R/4.1.2

script_dir=${1}
tumour_set=${2}
input_dir=${3}
output_dir=${4}
chr_file=${5}
centro_file=${6}
subclones_dir=${7}
sample_list=${8}
remove_acrocentric=${9}

if [ "${remove_acrocentric}" = "" ]; then
  remove_acrocentric=TRUE
fi

# Performs binomial probability to assign p-values (and values adjusted with Bonferroni/FDR correction)
#  indicating probability of each CNA occurring in as many samples as observed by chance
Rscript ${script_dir}/Binomial.R ${tumour_set} input_dir=${input_dir} output_dir=${output_dir} subclones_dir=${subclones_dir} sample_list=${sample_list}

# Find enriched regions and filter out those at loci prone to artefacts e.g. acrocentric regions
Rscript ${script_dir}/TM_postFDR_1_enriched_CW.R ${tumour_set} input_dir=${input_dir} output_dir=${output_dir} chr_file=${chr_file} centro_file=${centro_file} remove_acrocentric=${remove_acrocentric}

# Merge overlapping enriched regions
Rscript ${script_dir}/TM_postFDR_2_merging_CW.R ${tumour_set} input_dir=${input_dir} output_dir=${output_dir} chr_file=${chr_file}

# Check for new breakpoints
Rscript ${script_dir}/TM_postFDR_3_multiPCF_CW.R ${tumour_set} input_dir=${input_dir} output_dir=${output_dir}

# Convert regions into ...[CNA]_mergedsegs.txt files ready for ordering
Rscript ${script_dir}/TM_postFDR_4_prepare_input_CNA_table_CW.R ${tumour_set} input_dir=${input_dir} output_dir=${output_dir} chr_file=${chr_file}