#!/bin/ksh
#
# Description:
#   Tests calling Dotter on a long sequence versus itself. Transcripts are 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: since the two sequences match exactly, 
#   there will be a diagonal line from the top-left to the bottom-right corner. Any other matching
#   regions (i.e. internal repeats) will also display as diagonal lines.
#
#   Transcripts from the features file should be shown along both axes.
#

RC=0

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

dotter -q 246634 -s 246634 -f $data_dir/chr4_dna_align.gff $data_dir/chr4_ref_seq.fasta $data_dir/chr4_ref_seq.fasta

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

exit $RC