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Adapter trimming order should be the same as on the command line #401

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marcelm opened this issue Sep 9, 2019 · 0 comments

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@marcelm
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@marcelm marcelm commented Sep 9, 2019

When multiple adapters are given on the command line, they are first grouped by type and then searched in this order: 5', 3', anywhere. This behavior should be changed such that adapters are searched in the same order as they are provided on the command line, irrespective of type.

The actual order used for adapter trimming can be seen in the report. Currently, even if the command line contains -g AAA -a CCC, the CCC adapter will be listed first, and it will also be searched first.

The order is relevant and can sometimes lead to different results. For example, trimming the read AAACCGGG using options -g ^AAACC -a CCGGG will currently result in AAA because the 3' (-a) adapter is always searched first, no matter the order of options on the command line.

This should be changed such that the -g adapter is searched first in the above example, which will then result in GGG. Then the command line -a CCGGG -g ^AAACC could be used to get AAA as before.

@marcelm marcelm closed this in 2959a00 Sep 9, 2019
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