can `trim-left` and `trunc-len` be made optional and default to no trimming/truncation?

[gregcaporaso]

can `trim-left` and `trunc-len` be made optional and default to no trimming/truncation?

[benjjneb]

I pushed variable-length support to the main devel-branch of dada2 today (cddce98a98894e4a621f6767e61fe9aaed638e06) so this feature will definitely be in the upcoming 1.4 release.

Another consequence, dada2 now works for ITS data, since trimming to a fixed length is no longer required.

[benjjneb]

Making trim-left optional with a default of 0 would be appropriate right now.

Making trunc-len optional is trickier to do automatically, especially for sequencing techs that don't always have the same number of bases.

[gregcaporaso]

Making trunc-len optional is trickier to do automatically, especially for sequencing techs that don't always have the same number of bases.

I was thinking that it would default to not trimming.

[benjjneb]

The dada2 code currently requires all input sequences to be the same length, although if all goes well that requirement will be removed in our next release (1.4, March/April).

[gregcaporaso]

OK, we can hold off on this until then.

[ebolyen]

FYI: trim-left is already set to default to 0 (in the 2017.2 release).

[ebolyen]

This was resolved in #66.