TER

Transitive Edge Reduction

Transitive Edge Reduction (TER) is a tool that can be used to remove redundant edges. In order to properly use this module you need to install the dependencies. The README in the main SORA directory describes what is needed.

Build TER

The first step is building the package. This process is completed by sbt. Starting in the main SORA directory move to the 'TransitiveEdgeReduction' on the command line.

> cd TransitiveEdgeReduction

Second step is after you are in the TransitiveEdgeReduction folder you can run the sbt command. This builds the package into a single jar.

> sbt package

Once you have created the jar, confirm the jar is located in

target/scala-2.11/transitive-edge-reduction-module_2.11-1.0.jar

Run TRE

Finally you can call spark-submit to submit your program. Where the data.txt is your input data and the results_dir/ is the location where you want the results stored.

> {spark_home}/bin/spark-submit --class TransitiveEdgeReduction --master local[4] target/scala-2.11/transitive-edge-reduction-module_2.11-1.0.jar data.txt results_dir/

An example using a test dataset:

> {spark_home}/bin/spark-submit --class TransitiveEdgeReduction --master local[4] target/scala-2.11/transitive-edge-reduction-module_2.11-1.0.jar data/3reads_overlap_beforeTransitiveEdgeReduction_edge_list.txt ~/TERResults/