mkdir -p data/10xgenomics_PBMC_5k

# get fragment lenghts, taken on https://dbrg77.wordpress.com/2017/02/10/atac-seq-insert-size-plotting/
samtools view data/10xgenomics_PBMC_5k/atac_v1_pbmc_5k_possorted_filtered.bam | awk '$9>0' | cut -f 9 | sort | uniq -c | sort -k 2,2n | sed -e 's/^[ \t]*//' > data/10xgenomics_PBMC_5k/atac_v1_pbmc_5k_possorted_filtered_fragment_lengths.txt

# analyse the fragment lengths
python3.6 scripts/bam_tools/split_by_length.py -i data/10xgenomics_PBMC_5k/atac_v1_pbmc_5k_possorted_filtered.bam -o data/10xgenomics_PBMC_5k/atac_v1_pbmc_5k_possorted_filtered_30-149bp.bam --length 30-149

# based on fragment length analysis, separate the fragments as follows :
#  30 -  84bp : open chromatin fragments
# 133 - 266bp : mono-nucleosome fragments
# 341 - 500bp : di-nucleosome fragments
python3.6 scripts/bam_tools/split_by_length.py -i data/10xgenomics_PBMC_5k/atac_v1_pbmc_5k_possorted_filtered.bam -o data/10xgenomics_PBMC_5k/atac_v1_pbmc_5k_possorted_filtered_30-84bp.bam --length 30-84
python3.6 scripts/bam_tools/split_by_length.py -i data/10xgenomics_PBMC_5k/atac_v1_pbmc_5k_possorted_filtered.bam -o data/10xgenomics_PBMC_5k/atac_v1_pbmc_5k_possorted_filtered_133-266bp.bam --length 133-266
python3.6 scripts/bam_tools/split_by_length.py -i data/10xgenomics_PBMC_5k/atac_v1_pbmc_5k_possorted_filtered.bam -o data/10xgenomics_PBMC_5k/atac_v1_pbmc_5k_possorted_filtered_341-500bp.bam --length 341-500

# split di-nucleosome fragments into mononucleosome fragments
python3.6 scripts/bam_tools/split_in_two.py -i data/10xgenomics_PBMC_5k/atac_v1_pbmc_5k_possorted_filtered_341-500bp.bam -o data/10xgenomics_PBMC_5k/atac_v1_pbmc_5k_possorted_filtered_341-500bp_splitintwo.bam
samtools sort data/10xgenomics_PBMC_5k/atac_v1_pbmc_5k_possorted_filtered_341-500bp_splitintwo.bam > data/10xgenomics_PBMC_5k/atac_v1_pbmc_5k_possorted_filtered_341-500bp_splitintwo_sort.bam
mv data/10xgenomics_PBMC_5k/atac_v1_pbmc_5k_possorted_filtered_341-500bp_splitintwo_sort.bam data/10xgenomics_PBMC_5k/atac_v1_pbmc_5k_possorted_filtered_341-500bp_splitintwo.bam

# index all BAM files
samtools index data/10xgenomics_PBMC_5k/atac_v1_pbmc_5k_possorted_filtered_30-84bp.bam
samtools index data/10xgenomics_PBMC_5k/atac_v1_pbmc_5k_possorted_filtered_133-266bp.bam
samtools index data/10xgenomics_PBMC_5k/atac_v1_pbmc_5k_possorted_filtered_341-500bp.bam
samtools index data/10xgenomics_PBMC_5k/atac_v1_pbmc_5k_possorted_filtered_341-500bp_splitintwo.bam