new features. bug fixes.

* Changed name of BOWTIE output BAM to be sampleID.bowtie.sorted.bam
* Changed BOWTIE minInsertSize default from 100 to 250.
* Added error checking to make sure BOWTIE output file exists.
* Fixed typo in BOWTIE argument list.
* Allow user to set amount of (or disable) polyAT trimming in TRIM
* Allow user to disable removing of Ns from the ends of the reads in
TRIM
* Added error checking for TRIM output files.
* Fixed type in trimReads.py docs.