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Detect index switch + reverse complemented index #86

@matrulda

Description

@matrulda

I encountered a case where CheckQC couldn't tell the whole story behind incorrectly specified indexes:

Index in sample sheet:

ACATAGCG+CTAGCTTG

Index found in undetermined indexes:

CAAGCTAG+ACATAGCG

Reported by CheckQC:

Index: CAAGCTAG+ACATAGCG on lane: 1 was significantly overrepresented (5.9%) at significance threshold of: 1%.
We found a possible match for the reverse complement of tag: CAAGCTAG, on: Lane: 1, for sample: Sample_A
The tag we found was: CTAGCTTG.
This originated from the dual index tag: CAAGCTAG+ACATAGCG

It would have been helpful if it also was reported that ACATAGCG was find among index 1 in the sample sheet.

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