Crash on empty string

[jnalanko]

Hi, thank you for writing this very useful tool!

I'm getting the crash below. It seems to me that maybe trimming somehow produced an empty sequence, which is a problem for SeqAn. Unfortunately I can't yet share the data that produces this crash.

1,459,740 / 1,474,724 reads had adapters trimmed from their start (83,331,249 bp removed)
1,343,331 / 1,474,724 reads had adapters trimmed from their end (66,351,271 bp removed)
Splitting reads containing middle adapters
440 / 1,474,724 (0.0%)porechop_abi/include/seqan/align/dp_setup.h:283 Assertion failed : length(seqH) >= 1u was: 0 < 1

[qbonenfant]

Hi,
You do not need to share the data, this is kind of a known bug that exists in the original Porechop code.
There is in fact a closed issue on this repo (see #3) explaining the problem.
In short: your reads are trimmed completly by the end trimming, and results in an empty sequences, like you suggested.

There is two outcome frome here:

• Either you remove read shorter than a pair of adapters + a safety margin. It's not really a great solution, but it is easy.
• Or I do what I should have done back in 2019 and replace this assert by a warning.

I will try to push a fix next week, and will notify you.