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SAMTOM4(1) User Commands SAMTOM4(1)

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)
July 2015 samtom4 3ca7fe8