NAME
samtom4 - Convert a SAM file generated by blasr(1) to M4 format
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.
SEE ALSO
blasr(1) loadPulses(1) pls2fasta(1) samFilter(1) samtoh5(1) sawriter(1) sdpMatcher(1) toAfg(1)