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)