xenial (1) samtom4.1.gz

Provided by: blasr_0~20151014+git8e668be-1_amd64 bug

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)