how to execute the program?
1. put bam file generated from tophat in subdirectory xxx.
2. type the following command. if you have more memory, please change the parameter -Xms and -Xmx, it will be faster.
java -jar -Xms9000m -Xmx9000m HPC_wiggleGenerator.jar xxx/accepted_hits.bam
3. the wiggle files will be generated under the subdirectory xxx with extension "wiggle".

