Clearer output; -s singled-ended option; -p <profile.fq>; -v as tlen proportion

0. Clearer output
1. Added singled-ended option -s
2. Re-size to longest profile read
3. Multiple profile files with -p option
4. Handles adding Ns to reads
5. -v <tlenstddev> is now a proportion of -t <tlen> [default: 0.1]