The files used for testing were obtained by downloading the following:
* NC_045512.2.fasta from https://www.ncbi.nlm.nih.gov/nuccore/NC_045512.2?report=fasta
* SRR11728627.fastq from https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR11728627

And applying the following operations:

bwa index -p sars-cov-2 -a bwtsw NC_045512.2.fasta    
bwa aln sars-cov-2 SRR11728627.fastq > SRR11728627.sai
bwa samse sars-cov-2 SRR11728627.sai SRR11728627.fastq > SRR11728627.sam
samtools view -b SRR11728627.sam > SRR11728627.bam 
samtools sort SRR11728627.bam > SRR11728627.sorted.bam 
samtools index SRR11728627.sorted.bam
