.TH FORGE "1" "October 2013" "forge 2010-07-28" "User Commands"
.SH NAME
forge \- training program for SNAP
.SH SYNOPSIS
.B forge
[\fIoptions\fR] <\fBann\fR> <\fBdna\fR> [\fIoptions\fR]
.SH OPTIONS
.HP
\fB\-help\fR
.HP
\fB\-verbose\fR
.TP
\fB\-pseudocount\fR <float>
[1]   (absolute number for all models)
.HP
\fB\-pseudoCoding\fR <float> [0.0] (eg. 0.05)
.HP
\fB\-pseudoIntron\fR <float> [0.0]
.TP
\fB\-pseudoInter\fR <float>
[0.0]
.TP
\fB\-min\-counts\fR
[0]
.HP
\fB\-lcmask\fR [\-fragmentN]
.TP
\fB\-utr5\-length\fR <int>
[50]
.TP
\fB\-utr5\-offset\fR <int>
[10]
.TP
\fB\-utr3\-length\fR <int>
[50]
.TP
\fB\-utr3\-offset\fR <int>
[10]
.TP
\fB\-explicit\fR <int>
[250]
.TP
\fB\-min\-intron\fR <int>
[30]
.TP
\fB\-boost\fR <file>
(file of ID <int>)