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)