Add option for 0 mismatch with bowtie1

[joncahn]

Hi Mike,

Would you consider adding an option for allowing 0 mismatch with bowtie1 (-v 0)?
I would be interested in studying heterozygous plants so I believe this option would enable a more precise identification of the allele of origin. Do you think it could indeed be valuable or am I missing something?

Thank you,

Jon

[MikeAxtell]

Yeah seems reasonable. Not sure when next time I will make a release is. In the meantime, just edit line 1097:

bt_args = (['bowtie', input_option, '-p', str(args.threads), '-v', '1',

to

bt_args = (['bowtie', input_option, '-p', str(args.threads), '-v', '0',

Notice the last entry on the line is changed from 1 to 0. This is the -v option for bowtie which sets the max number of allowed mismatches for a valid hit.