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.\"     Title: compilesplicecands
.\"    Author: [see the "AUTHOR(S)" section]
.\" Generator: Asciidoctor 2.0.20
.\"      Date: 
.\"    Manual: \ \&
.\"    Source: \ \&
.\"  Language: English
.\"
.TH "COMPILESPLICECANDS" "1" "" "\ \&" "\ \&"
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.SH "NAME"
compileSpliceCands \- Find introns parsing a set of exon candidates in GFF format
.SH "SYNOPSIS"
.sp
\fBcompileSpliceCands\fP \-f <splice candidates filename> \-g <genome filename>
.SH "OPTIONS"
.SS "Parameters:"
.sp
\fB\-f\fP <filename>
.RS 4
potential splice sites in gff format
.RE
.sp
\fB\-g\fP <filename>
.RS 4
genome file in fasta format
.RE
.sp
\fB\-c\fP <integer>
.RS 4
defines the number of potential splice site every potential splice site itself is compared with
.RE
.sp
\fB\-t\fP <float>
.RS 4
has to be between 0 and 1 and  defines how much the average coverage may differ
.RE
.sp
\fB\-m\fP <integer>
.RS 4
defines how many bases around the splice site should be checked
.RE
.sp
\fB\-d\fP
.RS 4
enables debugging output
.RE
.sp
\fB\-i\fP <integer>
.RS 4
maximum length an Intron can be, default 500000 (human genome)
.RE
.SH "AUTHORS"
.sp
AUGUSTUS was written by M. Stanke, O. Keller, S. König, L. Gerischer and L. Romoth.
.SH "ADDITIONAL DOCUMENTATION"
.sp
An exhaustive documentation can be found in the file /usr/share/doc/augustus/README.md.gz.