ShotMCF

ShotMCF - sources of ShotMCF tool

To run it u supposed to have java CPLEX interface file in the folder lib near your ShotMCF.jar

Content of your folder should be:

path_to/ShotMCF.jar

path_to/lib/cplex.jar 

Before running ShotMCF ViSpA should be ran.

Usage:

first argument the path to file with aligned reads (extended output reads from ViSpA)

second argument path to file with quasispecies (extended output from ViSpA) 

Also to run this program CPLEX Optimization toolkit is required

Also path to CPLEX libraries should be specified in command line to run

-Djava.library.path=<path_to_shared_library>

For example:

java -jar -Djava.library=/opt/ibm/ILOG/CPLEX_Studio125/cplex/bin/x86-64_sles10_4.1 ShotMCF.jar reads.txt qusispecies.txt