SYNOPSIS
samtom4 in.sam reference.fasta out.m4 [options]OPTIONS
- in.sam
- Input SAM file, which is produced by blasr.
- reference.fasta
- Reference used to generate file.sam.
- out.m4
- Output in blasr(1) M4 format.
- -header
- Print M4 header.
- -useShortRefName
- Use abbreviated reference names obtained from file.sam instead of using full names from reference.fasta.