Fix #98 QC check for mixed subtypes

[peterk87]

• Fixes QC module not failing samples where positive and negative kmers are detected for the same genome position #98 QC check for component subtype positive and negative kmers are present at the same position
• Added unit tests for QC utility functions

[peterk87]

Hi @glabbe

With the changes in this pull request I am able to get the proper QC messages using the schema you linked to in #98

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For ERR163996, I now get a QC FAIL with the message:

FAIL: Mixed subtype; the positive and negative kmers were found for the same target site 62657 for subtype "4.1.2".

Command-line:

$ hansel -s tb_speciation_scheme_v1.0.5.fasta -p ERR163996_* -O output.tsv --min-kmer-freq 8

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For ERR182041, I now get a QC FAIL with the message:

FAIL: Mixed subtype; the positive and negative kmers were found for the same target site 4260268 for subtype ""4.6.1.1"".

Command-line

$ hansel -v -s tb_speciation_scheme_v1.0.5.fasta -p ERR182041_*.fastq.gz --min-kmer-freq 8 --force

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I'll continue testing the other genomes next week!

[glabbe]

Great! Thanks a lot @peterk87

[DarianHole]

Looks good and fixes the QC issue!

All of the datasets tested are consistent with what they were before and the ones that should fail QC due to the new QC check do so.