samtom41
Convert a sam file generated by blasr(1) to m4 format
Usage
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.