new files:
    q.indel.scala
    Scala script for running RealignTargetCreator and IndelRealigner using Queue.jar.

    q.indel.sh
    Shell script that runs Queue.jar using the q.indel.scala script

    q.submit.sh
    Shell script that runs q.inde.sh in a for look for every .dd.bam file available;
     or files of interests, e.g. for in in $(ls *dd.bam)

modified: make.sjdb.sh, star.2pass.genome.slq, star.2pass.slq, star.cuffX.slq
    No code change. Changed file to executable with chmod +x