rule sam_to_bam:
	input: "03_sam_files/{sample}.sam"
	output: "04_bam_files/{sample}.bam"
	log: "00_logs/{sample}_sam_to_bam.log"
	shell: "samtools view -@ THREADS -Sb '{input}' > '{output}' 2> '{log}'"

rule sam_fixmate:
	input: "04_bam_files/{sample}.bam"
	output: "04_bam_files/{sample}.fixmate.bam"
	log: "00_logs/{sample}_sam_fixmate.log"
	shell: "samtools fixmate -@ THREADS -rcm -O bam '{input}' '{output}' 2> '{log}'"
		
rule sam_sort:
	input: "04_bam_files/{sample}.fixmate.bam"
	output: "04_bam_files/{sample}.sorted.fixmate.bam"
	log: "00_logs/{sample}_sam_sort.log"
	shell: "samtools sort -@ THREADS -O bam '{input}' > '{output}' 2> '{log}'"
