Checkqc

Latest version: v4.0.5

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3.1.0

This release introduces the `UnidentifiedIndexHandler`. This will aid in identifying indexes which end up as unidentified after demultiplexing. This is a nifty feature since often when there is a high amount of unidentified reads, this is cased by errors in the samplesheet. For example, when using dual indexes index one and index two may have swapped places.

The new handler will look for in indexes found in undetermined at a frequency compared to the number of reads on the lane above what is specified by `significance_threshold` (default: 1%) in the config and compare them to the samplesheet to decide if:
- dual indexes have been swapped
- the index has been reversed
- the index is the reverse complement
- the index is the complementary index
- the index is present in another lane

An example of that the output you will get could look like is:

WARNING QC warning: Index: TTCGAT on lane: 8 was significantly over represented (10.0%) at significance threshold of: 1%.
WARNING QC warning: We found a possible match for the reverse of tag: TTCGAT, on: Lane: 2, for sample: SampleA. The tag we found was: TAGCTT

The first line will warn that the index is represented over the configured threshold, and the second line will suggest what might be wrong (based on the scenarios listed above).

3.0.1

3.0.0

The `UndeterminedPercentageHandler` will now take the amount of PhiX on the lane into account. The reason for this is that all PhiX will count as undetermined indexes. This will cause runfolders for which a user may not want an error to count as one, especially since the amount of PhiX spiked in can vary a lot. The configuration thresholds in the configuration are now specified as: `<% PhiX> + <configuration value>`

3.0.0rc1

2.0.1

Bugfixes:
- Updated interop dependency for iSeq support
- iSeq support is now mentioned in README and docs

2.0.0

Major changes:

New definition of reads per sample
Reads per sample are now counted per `sample name` instead of `sample ID`. It allows a sample to have multiple libraries in the same lane and still be counted as one sample. For example, in a run with the following sample sheet:

Sample_ID,Sample_Name
Pool1_1,Pool1
Pool1_2,Pool1
Pool2_1,Pool2
Pool2_2,Pool2

the sum of reads for **Pool1_1** and **Pool1_2** will be defined as the reads for **Pool1**. This was not the case in previous versions of CheckQC, where each unique `sample ID` was considered a sample.

Minor changes:
- Support for iSeq
- Improved error handling

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