TODO

- May 20, 2014
* Need to fix: bamFileList returns a bam file list that may not be unique. 
  (done)

- Sep 5, 2013
* Add sanity check for BED file. (done)

- July 9, 2013
* Use bin avg. instead of spline? (done)
* Add font size control (done).

- July 8, 2013
* Turn off legend option (done).

- June 27, 2013
* Custom avg. profile colors. (done)
* Label clusters by colors and numbers.

- June 4, 2013
* Consider biologial replicates?

- June 3, 2013
* Custom heatmap color scale (done).

- May 9, 2013
* Use gene list to subset in replot?

- Mar 7, 2013
* Color key for heatmaps. (DONE)
* Add K-means for gene ranking. (DONE)
* Implement replot as a dynamic visulization program.
* Add gene symbols/IDs to output. (DONE)

- Nov 12, 2012
* Turn off std error when there is one gene. (DONE)
* Add example data, gene lists. (DONE)

- May 8, 2012
* Make sure read and process paired-end reads correctly.
* Make sure read and process gapped alignment correctly.
* When a mate pair overlaps, make sure the overlapped region is not 
  double-counted.
* Automatically recognize Bowtie/Tophat alignment and convert all NA's to a 
  proper number. (DONE DIRTY)
* Check index file for BAM, generate one if not present. (DONE)
* Read short reads chromosome by chromosome as implemented by SHAO. This 
  should be the default. (DONE)
* Parallelize both reading and coverage-calculating. (DONE)