First commit.
Add note on advantages of SAM format.
Add script and functions to parse SAM output into reads file.

Should be far faster than parsing standard bowtie output.
Could also add specialized read-to-count script for this; will
consider.
Ignore swap files.
Add time code to processSAMOutput.
Fix indentation in getReadLengthDist.
Document randomize and seed options. Fix indentation.
Fix indentation in readsToCounts.py
Fix rmdup handling in wrapper script.
Fix bugs in rmdup. Make sorting and rmdup filename-aware.

Skip sorted if extension is .sorted.bam.
Skip rmdup if extension is .unique.bam.
Code formatting and clean up.
Merge branch 'master' of github.com:awblocker/paired-end-pipeline