Convert alignments in SAM format to a human-readable, BLAST-like format.
Options
The SAM filename to convert is
specified following -sam2aln.
A FASTA filename for the reference genome is specified by the -ref option (required).
The output filename is specified by the -output option. To send output to a pipe, use /dev/stdout as the filename.
Example
urmap -sam2aln reads.sam -ref hg38.fasta -output reads.aln