I'm trying to give the user of my program the option to run bwa aln or bwa bwasw.
But from reading the documentation I don't understand what the output from running bwasw is.
That's ideally what I'd like so that the rest of the pipeline can run without modification.
I found this cached version of the documentation. It shows this usage example:
bwa index -a bwtsw database.fasta bwa aln database.fasta short_read.fastq > aln_sa.sai bwa samse database.fasta aln_sa.sai short_read.fastq > aln.sam bwa sampe database.fasta aln_sa1.sai aln_sa2.sai read1.fq read2.fq > aln.sam bwa bwasw database.fasta long_read.fastq > aln.sam