.TH SDPMATCHER "1" "July 2015" "sdpMatcher 3ca7fe8" "User Commands"
.SH NAME
sdpMatcher \- nucleotide sequence matching using sparse dynamic programming
.SH SYNOPSIS
.B sdpMatcher
.I query
.I target
.I k
.RB [ \-indelRate
.IR delta ]
.RB [ \-showalign ]
.RB [ \-printsw ]
.RB [ \-noRefine ]
.RB [ \-indel
.IR i ]
.RB [ \-local ]
.RB [ \-match
.IR m ]
.RB [ \-sdpIndel
.IR i ]
.SH DESCRIPTION
Performs sparse dynamic programming (SDP) between pairs of sequences as they 
are given in two FASTA files, called \fIquery\fR and \fItarget\fR for
convenience. \fIk\fR is the size of the k-mer used for the SDP algorithm.
.SH SEE ALSO
.BR blasr (1)
.BR loadPulses (1)
.BR pls2fasta (1)
.BR samFilter (1)
.BR samtoh5 (1)
.BR samtom4 (1)
.BR sawriter (1)
.BR toAfg (1)