.TH EXONPAIRS "1" "October 2013" "exonpairs 2010-07-28" "User Commands"
.SH NAME
exonpairs \- SNAP module exonpairs
.SH SYNOPSIS
.B exonpairs
[\fIoptions\fR] <\fBHMM file\fR> <\fBFASTA file\fR> [\fIoptions\fR]
.SH OPTIONS
.TP
\fB\-min\-intron\fR <int>
minimum Intron length [30]
.TP
\fB\-max\-intron\fR <int>
maximum Intron length [10000]
.TP
\fB\-einit\-length\fR <int>
minimum Einit length in bp [10]
.TP
\fB\-eterm\-length\fR <int>
minimum Eterm length in bp [10]
.TP
\fB\-exon\-length\fR <int>
minimum Exon length in bp [30]
.HP
\fB\-intron\-score\fR <float> minimum Intron score in bits [\-5]
.TP
\fB\-einit\-score\fR <float>
minimum Einit score in bits [\-5]
.TP
\fB\-eterm\-score\fR <float>
minimum Eterm score in bits [\-5]
.TP
\fB\-exon\-score\fR <float>
minimum Exon score in bits [\-5]
.TP
\fB\-pair\-score\fR <float>
minimum pair score (exon\-intron\-exon) [10]
.TP
\fB\-flank\-length\fR <int>
length of flanking sequence per exon [20]
.TP
\fB\-lcmask\fR
treat lowercase as N