Ability to mask regions; fixed several bugs; more transparency in output and in documentation

• able to restart set_test instead of having to remove the directory before restarting it
• Fixed vcfMerge.sh bug - looking for the wrong executable
• All MSA and SNP analysis is done on the matrix/bcftools level
• Masking the reference genome is possible through BED files.
  • There is a phage finder using the phast database, and it puts in masked regions
  • masking is done on the read-mapping level and so some reads will traverse the indicated 'bad regions'
• simulating reads is faster just by reducing the number of individual jobs
• Simulated reads are 100x instead of a fixed number. The number of reads is now more appropriate.
• fq and fq.gz extensions are now recognized
• Removed freebayes - it never calls invariant bases and so it is fundamentally wrong for this pipeline
• VarScan and future snp calling modules will be expected to have filtered output before the rest of the pipeline has seen it. See launch_varscan.pl for how it's done.
• More documentation like in FAQ.md
• Request in README.md for users to join Google Groups