modified:   bwa.map.slq
	    Removed additional comment lines in the SLURM resource request header, and added minor code comments

modified:   gatk.pp.slq
	    Removed additional comment lines in the SLURM resource request header, and added minor code comments

modified:   idx_htseq.slq
	    Removed additional comment lines in the SLURM resource request header, and added minor code comments

modified:   star.2pass.genome.slq
	    Commented on what the single chunk of code does, and what is needed to run it.
	    Removed additional comment lines in the SLURM resource request header

modified:   star.2pass.slq
	    Added an explanation of what the code chunks do.
	    Removed additional comment lines in the SLURM resource request header.

modified:   star.cuffX.slq
	    Activated lines of code that were previously commented out.
	    Removed additional comment lines in the SLURM resource request header.

modified:   star.htseq.slq
	    Removed additional comment lines in the SLURM resource request header.
	    Deactivated the picard/CollectRnaSeqMetrics.jar code. Doesn't always work as it requires
	      that chromosomes in the reference genome are in the same order as the file.  After
	      sorting, this is not always the case, thus to avoid jobs getting erros, we removed the
	      code until further notice.

modified:   star.map.slq
	    Removed empty lines and unused echo messages

modified:   tophat.map.slq
	    Removed additional comment lines in the SLURM resource request header, and added minor comments
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)