*.fai
bin/
out.vcf
.classpath
.settings/
*java.util*
*java.io*
src/org.junit.Assert.assertEquals
.project
*.class
*.in
*.out
*.ngm
*.region.fa
*.log
update.sh
test/*/*refined*
test/bigsimtest/bigaln_sorted.bam
test/bigsimtest/bigaln_sorted.bam.bai
test/bigsimtest/bigreads.fastq
test/bigsimtest/bigsim.bed
test/bigsimtest/bigsim.fasta
test/bigsimtest/bigsim.insertions.fa
test/bigsimtest/bigsim.vcf
test/bigsimtest/bigsniffles.vcf
resultsstore.txt
results.tsv
rebuilt_external_scripts/
test/*
test/*/*
external_scripts/*
canu
htslib
samtools
*.png
*.txt
*.py
