run_big_sim.sh

./build.sh
cd test/bigsimtest
./big_sim.sh
cd ../../
java -cp src Iris genome_in=test/base.fa reads_in=test/bigsimtest/bigaln_sorted.bam vcf_in=test/bigsimtest/bigsniffles.vcf vcf_out=test/bigsimtest/bigngmlrraconrefined.vcf --ngmlr threads=2 out_dir=output --also_deletions
java -cp src Iris genome_in=test/base.fa reads_in=test/bigsimtest/bigaln_sorted.bam vcf_in=test/bigsimtest/bigsniffles.vcf vcf_out=test/bigsimtest/bigminimapraconrefined.vcf threads=2 out_dir=output --also_deletions
java -cp src Iris genome_in=test/base.fa reads_in=test/bigsimtest/bigaln_sorted.bam vcf_in=test/bigsimtest/bigsniffles.vcf vcf_out=test/bigsimtest/bigminimapracon2refined.vcf threads=2 --rerun_racon out_dir=output --also_deletions
java -cp src Iris genome_in=test/base.fa reads_in=test/bigsimtest/bigaln_sorted.bam vcf_in=test/bigsimtest/bigsniffles.vcf vcf_out=test/bigsimtest/bigminimapracon10refined.vcf threads=2 racon_iters=10 out_dir=output --also_deletions
java -cp src Iris genome_in=test/base.fa reads_in=test/bigsimtest/bigaln_sorted.bam vcf_in=test/bigsimtest/bigsniffles.vcf vcf_out=test/bigsimtest/bigngmlrfalconsenserefined.vcf --ngmlr --falconsense threads=2 out_dir=output --also_deletions
java -cp src Iris genome_in=test/base.fa reads_in=test/bigsimtest/bigaln_sorted.bam vcf_in=test/bigsimtest/bigsniffles.vcf vcf_out=test/bigsimtest/bigminimapfalconsenserefined.vcf --falconsense threads=2 out_dir=output --also_deletions

echo 'Sniffles accuracy results'
echo '-----------------------------------'
java -cp src EvaluateSimulatedAccuracy ground_truth=test/bigsimtest/bigsim.insertions.fa iris_calls=test/bigsimtest/bigsniffles.vcf
echo ''
echo 'minimap2/racon refined accuracy results'
echo '-----------------------------------'
java -cp src EvaluateSimulatedAccuracy ground_truth=test/bigsimtest/bigsim.insertions.fa iris_calls=test/bigsimtest/bigminimapraconrefined.vcf
echo ''
echo 'minimap2/racon_twice refined accuracy results'
echo '-----------------------------------'
java -cp src EvaluateSimulatedAccuracy ground_truth=test/bigsimtest/bigsim.insertions.fa iris_calls=test/bigsimtest/bigminimapracon2refined.vcf
echo ''
echo 'minimap2/racon_ten refined accuracy results'
echo '-----------------------------------'
java -cp src EvaluateSimulatedAccuracy ground_truth=test/bigsimtest/bigsim.insertions.fa iris_calls=test/bigsimtest/bigminimapracon10refined.vcf
echo ''