# some paths
## directories
data_dir='data/10xgenomics_PBMC_5k'
seq_dir='data/genomes'
results_dir='data/10xgenomics_PBMC_5k_peaks'
## input
file_bed_rmsk=$data_dir/'atac_v1_pbmc_5k_peaks_rmsk.bed'
file_bam_open="$data_dir/atac_v1_pbmc_5k_possorted_filtered_30-84bp.bam"
file_bai_open="$data_dir/atac_v1_pbmc_5k_possorted_filtered_30-84bp.bam.bai"
file_bam_nucl="$data_dir/atac_v1_pbmc_5k_possorted_filtered_nucleosomes.bam"
file_bai_nucl="$data_dir/atac_v1_pbmc_5k_possorted_filtered_nucleosomes.bam.bai"
file_seq="$seq_dir/hg19.fasta"

mkdir -p $results_dir

# matrix creation
## 1kb sequences
file_mat_seq_1kb="$results_dir/peaks_rmsk_sequences_1kb.mat"
bin/SequenceMatrixCreator --bed $file_bed_rmsk --fasta $file_seq --from -500 --to 500 > $file_mat_seq_1kb

## open chromatin around peaks
for method in 'read_atac'
do
	file_mat_open_1kb="$results_dir/peaks_rmsk_openchromatin_1kb_$method.mat"
	bin/CorrelationMatrixCreator --bed $file_bed_rmsk --bam $file_bam_open --bai $file_bai_open --from -500 --to 500   --binSize 1 --method $method > $file_mat_open_1kb
done

## all nucleosomes around peaks
for method in 'fragment_center'
do
	file_mat_nucl_1kb="$results_dir/peaks_rmsk_nucleosomes_1kb_$method.mat"
	bin/CorrelationMatrixCreator --bed $file_bed_rmsk --bam $file_bam_nucl --bai $file_bai_nucl --from -500 --to 500   --binSize 1 --method $method > $file_mat_nucl_1kb
done