Alignment mode changes #67
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-switch back to global alignment in snps module; makes program consistent with versions <= 1.2.2 -genes module has always used local alignment, so no changes here -added option `-m` in run_midas.py snps|genes to choose between global/local read alignment -updated help text and examples to reflect these changes
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-switch back to global alignment in snps module; makes program consistent with versions <= 1.2.2
-genes module has always used local alignment, so no changes here
-added option
-min run_midas.py snps|genes to choose between global/local read alignment-updated help text and examples to reflect these changes