Mask poorly aligned bases at beginning or end of input alignment!

[seanmcallister]

Have ZH remove lower case bases from SINA aligned input at the beginnings and ends of sequences so that bases that poorly align to the SILVA database are removed. These are likely adaptors/vector and should be removed anyway.

¡Important!

[mooreryan]

Should these be permanently removed at the beginning of the pipeline?

[seanmcallister]

Yes, I think so. Both beginning and end of the alignments. I wouldn't worry too much about the lowercase in the middle. Although, if there are a lot, I suppose that the sequence should be flagged. (although it will likely be called as a chimera).