all: SRR1972917_aligned_sorted.bam

SRR1972917_aligned_sorted.bam: SRR1972917_aligned.sam
	# Convert SAM file to BAM file
	bwa.kit/samtools view -bS SRR1972917_aligned.sam > SRR1972917_aligned.bam

	# Sort BAM file
	bwa.kit/samtools sort SRR1972917_aligned.bam SRR1972917_aligned_sorted

	# Index BAM file
	bwa.kit/samtools index SRR1972917_aligned_sorted.bam

SRR1972917_aligned.sam: bwa.kit/bwa KJ660346.fa SRR1972917_1.fastq
	# Align FASTQ data to reference genome and save to SAM file
	bwa.kit/bwa mem  KJ660346.fa SRR1972917_1.fastq SRR1972917_1.fastq > SRR1972917_aligned.sam

bwa.kit/bwa:
	# Download and unpack BWA software
	wget http://downloads.sourceforge.net/project/bio-bwa/bwakit/bwakit-0.7.12_x64-linux.tar.bz2
	tar -jxvf bwakit-0.7.12_x64-linux.tar.bz2

KJ660346.fa:
	# Download and unzip reference genome
	wget -O refGenomeFiles.zip https://ndownloader.figshare.com/files/4841809
	unzip refGenomeFiles.zip

SRR1972917_1.fastq:
	# Download and unzip FASTQ files
	wget -O FASTQ.zip https://ndownloader.figshare.com/articles/3114454/versions/1
	unzip FASTQ.zip

clean:
	rm -rfv KJ660346.fa* FASTQ.zip refGenomeFiles.zip bwa.kit* bwakit-0.7.12_x64-linux.tar.bz2 SRR1972917*