Changes to read alignment mode for snps and genes

• Switched back to global Bowtie2 read alignment in run_midas.py snps. This makes the program consistent with versions <= 1.2.2.
• run_midas.py genes module has always used local alignment, so there are no changes here
• Added option -m in run_midas.py to choose between global and local read alignment. For example, you can now runs the snps module using local alignment: run_midas.py snps /path/to/indir -1 /path/to/fastq -m local --aln_cov 0.75. This command will recapitulate the behavior of v1.3.0.
• Addresses issue #66