#File with reads that passed WASP filtering

cd WASP_Runs

for sample in HG00731  NA12878_Nucleus_nonPolyA      NA12878_Nucleus_PolyA_Rep  NA12878_RAMPAGE      NA12878_Total      NA19239 HG00512           HG00732  NA12878_Nucleus_nonPolyA_Rep  NA12878_PolyA              NA12878_RAMPAGE_Rep  NA12878_Total_Rep  NA19240 HG00513           HG00733  NA12878_Nucleus_PolyA         NA12878_PolyA_Rep          NA12878_Small        NA19238


do
	#echo $sample
	cd /home/asiimwe/projects/run_env/alpha_star_wasp_benchmarking/WASP/WASP_Runs/$sample
	echo $sample >> /home/asiimwe/projects/run_env/alpha_star_wasp_benchmarking/WASP/comparison_tables.txt
	grep vW:i:1 /home/asiimwe/projects/run_env/alpha_star_wasp_benchmarking/WASP/WASP_Runs/$sample/32threads/STAR_WASP_vW_Tagged_Reads_Unique > /home/asiimwe/projects/run_env/alpha_star_wasp_benchmarking/WASP/WASP_Runs/$sample/32threads/passed_WASP_filtering_vW_1
	echo passed wasp filtering: >> /home/asiimwe/projects/run_env/alpha_star_wasp_benchmarking/WASP/comparison_tables.txt 
	wc -l /home/asiimwe/projects/run_env/alpha_star_wasp_benchmarking/WASP/WASP_Runs/$sample/32threads/passed_WASP_filtering_vW_1 >> /home/asiimwe/projects/run_env/alpha_star_wasp_benchmarking/WASP/comparison_tables.txt

	#Vw tagged reads:
	echo VW_Tagged reads: >> /home/asiimwe/projects/run_env/alpha_star_wasp_benchmarking/WASP/comparison_tables.txt 
	wc -l /home/asiimwe/projects/run_env/alpha_star_wasp_benchmarking/WASP/WASP_Runs/$sample/32threads/STAR_WASP_vW_Tagged_Reads_Unique >> /home/asiimwe/projects/run_env/alpha_star_wasp_benchmarking/WASP/comparison_tables.txt 

	#vw=1:
	echo vw=1: >> /home/asiimwe/projects/run_env/alpha_star_wasp_benchmarking/WASP/comparison_tables.txt 
	grep -r "vW:i:1" /home/asiimwe/projects/run_env/alpha_star_wasp_benchmarking/WASP/WASP_Runs/$sample/32threads/STAR_WASP_vW_Tagged_Reads_Unique | wc -l  >> /home/asiimwe/projects/run_env/alpha_star_wasp_benchmarking/WASP/comparison_tables.txt


	#Reads to remap:
	echo reads to remap: /home/asiimwe/projects/run_env/alpha_star_wasp_benchmarking/WASP/comparison_tables.txt 
	wc - l /home/asiimwe/projects/run_env/alpha_star_wasp_benchmarking/WASP/WASP_Runs/$sample/32threads/reads_to_remap_unique >> /home/asiimwe/projects/run_env/alpha_star_wasp_benchmarking/WASP/comparison_tables.txt

	#Reads to keep:
	echo reads to keep: /home/asiimwe/projects/run_env/alpha_star_wasp_benchmarking/WASP/comparison_tables.txt 
	wc - l  /home/asiimwe/projects/run_env/alpha_star_wasp_benchmarking/WASP/WASP_Runs/$sample/32threads/reads_to_keep_unique >> /home/asiimwe/projects/run_env/alpha_star_wasp_benchmarking/WASP/comparison_tables.txt


	#-----------------------------------------

	#Overlapped variants (Files to compare: STAR_WASP_vW_Tagged_Reads_Unique (all vW_Tagged reads) Vs WASP reads_to_remap):
	#Common to both files:
	echo Reads overlapping variants - common to both STAR_WASP and WASP: >> /home/asiimwe/projects/run_env/alpha_star_wasp_benchmarking/WASP/comparison_tables.txt 
	awk 'FNR==NR{a[$1]++;next}a[$1]' /home/asiimwe/projects/run_env/alpha_star_wasp_benchmarking/WASP/WASP_Runs/$sample/32threads/STAR_WASP_vW_Tagged_Reads_Unique  /home/asiimwe/projects/run_env/alpha_star_wasp_benchmarking/WASP/WASP_Runs/$sample/32threads/reads_to_remap_unique | wc -l >> /home/asiimwe/projects/run_env/alpha_star_wasp_benchmarking/WASP/comparison_tables.txt

	#Unique to STAR_WASP
	echo Reads unique to STAR_WASP: >> /home/asiimwe/projects/run_env/alpha_star_wasp_benchmarking/WASP/comparison_tables.txt 
	diff /home/asiimwe/projects/run_env/alpha_star_wasp_benchmarking/WASP/WASP_Runs/$sample/32threads/reads_to_remap_unique /home/asiimwe/projects/run_env/alpha_star_wasp_benchmarking/WASP/WASP_Runs/$sample/32threads/STAR_WASP_vW_Tagged_Reads_Unique | grep "^>" | wc -l >> /home/asiimwe/projects/run_env/alpha_star_wasp_benchmarking/WASP/comparison_tables.txt


	#Unique to WASP
	echo Reads unique to WASP: >> /home/asiimwe/projects/run_env/alpha_star_wasp_benchmarking/WASP/comparison_tables.txt 
	diff /home/asiimwe/projects/run_env/alpha_star_wasp_benchmarking/WASP/WASP_Runs/$sample/32threads/STAR_WASP_vW_Tagged_Reads_Unique /home/asiimwe/projects/run_env/alpha_star_wasp_benchmarking/WASP/WASP_Runs/$sample/32threads/reads_to_remap_unique | grep "^>" | wc -l >> /home/asiimwe/projects/run_env/alpha_star_wasp_benchmarking/WASP/comparison_tables.txt

	#-----------------------------------------

	#Passed WASP filtering (Files to compare: passed_WASP_filtering_vW_1 Vs WASP reads_to_keep)
	#Common to both files:
	echo Reads that passed WASP filtering - common to both STAR_WASP and WASP  >> /home/asiimwe/projects/run_env/alpha_star_wasp_benchmarking/WASP/comparison_tables.txt 
	awk 'FNR==NR{a[$1]++;next}a[$1]' /home/asiimwe/projects/run_env/alpha_star_wasp_benchmarking/WASP/WASP_Runs/$sample/32threads/passed_WASP_filtering_vW_1  /home/asiimwe/projects/run_env/alpha_star_wasp_benchmarking/WASP/WASP_Runs/$sample/32threads/reads_to_keep_unique | wc -l >> /home/asiimwe/projects/run_env/alpha_star_wasp_benchmarking/WASP/comparison_tables.txt
	
	#Unique to STAR_WASP	
	echo Reads unique to STAR_WAP: >> /home/asiimwe/projects/run_env/alpha_star_wasp_benchmarking/WASP/comparison_tables.txt 
	diff /home/asiimwe/projects/run_env/alpha_star_wasp_benchmarking/WASP/WASP_Runs/$sample/32threads/reads_to_keep_unique /home/asiimwe/projects/run_env/alpha_star_wasp_benchmarking/WASP/WASP_Runs/$sample/32threads/passed_WASP_filtering_vW_1 | grep "^>" | wc -l >> /home/asiimwe/projects/run_env/alpha_star_wasp_benchmarking/WASP/comparison_tables.txt


	#Unique to WASP
	echo Reads unique to WASP: >> /home/asiimwe/projects/run_env/alpha_star_wasp_benchmarking/WASP/comparison_tables.txt 
	diff /home/asiimwe/projects/run_env/alpha_star_wasp_benchmarking/WASP/WASP_Runs/$sample/32threads/passed_WASP_filtering_vW_1 /home/asiimwe/projects/run_env/alpha_star_wasp_benchmarking/WASP/WASP_Runs/$sample/32threads/reads_to_keep_unique | grep "^>" | wc -l >> /home/asiimwe/projects/run_env/alpha_star_wasp_benchmarking/WASP/comparison_tables.txt
done