#!/bin/ksh
#
# Description:
#   Test Dotter in nucleotide->nucleotide mode. Tests the dot-matrix calculation as well
#   as the display of transcripts and HSPs supplied via a features file.
#
# Results:
#   Dotter's graphical display should start up, showing a dot-plot where strong matching regions
#   between the two sequences are shown as diagonal lines. The greyramp tool can be used to adjust
#   the contrast of the dot plot. Transcripts from the features file should be shown along the
#   horizontal axis and HSPs from the features file can be displayed by enabling the relevant
#   option in the View menu. Note that the pixelmap and HSPs will show matches against both strands
#   of the reference sequence.
#

RC=0

test_name=`basename $0`
test_dir=`dirname $0`
data_dir=$test_dir/../../../data

dotter -q 246634 -f $data_dir/chr4_dna_align.gff $data_dir/chr4_ref_seq_short.fasta $data_dir/DA730641.fasta

# If there was an error, set RC
if [ $? -ne 0 ] 
then
  RC=1
fi

exit $RC