Marcel Martin
Marcel Martin
This code: ```python # fmt: off #nospace # twospaces # fmt: on ``` is changed to: ```python # fmt: off # nospace # twospaces # fmt: on ``` I expected...
We should precompute the maximum possible score for all the adapters and if a match with that maximal score was found, we can exit the loop iterating over all adapters...
As discussed in #620 and https://github.com/marcelm/cutadapt/issues/620#issuecomment-1112196925, it may be interesting to add a step that ensures that trimmed reads do not contain any further matches to other adapters. When demultiplexing...
The option would change Cutadapt’s behavior such that one 5' adapter and one 3' adapter is removed from each read. Somewhat like `--times=2`, but in the first round, only 5'...
Given a sequence with 5' adapter, eg **ALONGADAPTOR**sequence, if sequence is low quality in the end, or has polyG, cutadapt will trim this sequence into **ALONGADAPTOR**seq (*1st case*) or **ALONGADAP**...
The error handling needs to be improved when running on multiple cores. Motivated by the attempted fix for #525 in commit 7aa04206196c29f4988f57ccdc01ad89f978f8b3, which does not quite work. - An error...
Reverse-complementing a paired-end read means to swap R1 and R2. See also #560
If read modifications are done before adapter trimming (such as quality trimming), the info file does not contain the correct offsets and sequences. - The offsets are relative to the...