'\" t
.\"     Title: gthgetseq
.\"    Author: [see the "AUTHOR(S)" section]
.\" Generator: Asciidoctor 2.0.12
.\"      Date: 
.\"    Manual: \ \&
.\"    Source: \ \&
.\"  Language: English
.\"
.TH "GTHGETSEQ" "1" "" "\ \&" "\ \&"
.ie \n(.g .ds Aq \(aq
.el       .ds Aq '
.ss \n[.ss] 0
.nh
.ad l
.de URL
\fI\\$2\fP <\\$1>\\$3
..
.als MTO URL
.if \n[.g] \{\
.  mso www.tmac
.  am URL
.    ad l
.  .
.  am MTO
.    ad l
.  .
.  LINKSTYLE blue R < >
.\}
.SH "NAME"
gthgetseq \- get FASTA sequences from GenomeThreader files
.SH "SYNOPSIS"
.sp
\fBgthgetseq\fP \-getcdna | \-getprotein | \-getgenomic [option ...] [file ...]
.SH "DESCRIPTION"
.sp
Get FASTA sequences from GenomeThreader files containing intermediate results.
The sequences are shown on stdout.
.SH "OPTIONS"
.sp
\fB\-getcdna\fP
.RS 4
get cDNA/EST sequences
default: no
.RE
.sp
\fB\-getcdnacomp\fP
.RS 4
get complement of cDNA/EST sequences
default: no
.RE
.sp
\fB\-getprotein\fP
.RS 4
get protein sequences
default: no
.RE
.sp
\fB\-getproteincomp\fP
.RS 4
get complement of protein sequences
default: no
.RE
.sp
\fB\-getgenomic\fP
.RS 4
get genomic sequences
default: no
.RE
.sp
\fB\-getgenomiccomp\fP
.RS 4
get complement of genomic sequences
default: no
.RE
.sp
\fB\-minalignmentscore\fP
.RS 4
set the minimum alignment score for spliced alignments to be
included into the set of spliced alignments
default: 0.00
.RE
.sp
\fB\-maxalignmentscore\fP
.RS 4
set the maximum alignment score for spliced alignments to be
included into the set of spliced alignments
default: 1.00
.RE
.sp
\fB\-mincoverage\fP
.RS 4
set the minimum coverage for spliced alignments to be
included into the set of spliced alignments
default: 0.00
.RE
.sp
\fB\-maxcoverage\fP
.RS 4
set the maximum coverage for spliced alignments to be
included into the set of spliced alignments
default: 9999.99
.RE
.sp
\fB\-gzip\fP
.RS 4
gzip compressed input file(s)
default: no
.RE
.sp
\fB\-bzip2\fP
.RS 4
bzip2 compressed input file(s)
default: no
.RE
.sp
\fB\-help\fP
.RS 4
display help and exit
.RE
.sp
\fB\-version\fP
.RS 4
display version information and exit
.RE