# Java implementation for LocusTree_v1
# binT_v1 -Lacks structure creation and filling optimisation  

# Setup & compile - download binT_v1 folder

cd binT_v1
mkdir classes 
javac -d classes/ -cp classes/ src/bint_v1/*.java

# Example

# Create structure using bottom binsize 1000 and number children 2, using chr_file.txt (only chr1) 
java -cp classes/ bint_v1.Main -m 1 -f test/chr1Test.txt -o test/mydata.dat -c test/chr_file.txt -r 1000 -n 2

# Search structure using chr, start and stop positions
java -cp classes/ bint_v1.Main -m 0 -f test/chr1Test.txt -o test/mydata.dat -c test/chr_file.txt -r 1000 -n 2 -s 1 -chr 1 -sta 2840453 -sto 2940453

# Search Structure using level and node number
java -cp classes/ bint_v1.Main -m 0 -f test/chr1Test.txt -o test/mydata.dat -c test/chr_file.txt -r 1000 -n 2 -s 0 -chr 1 -level 17 -node 2845