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@diff
Feature: Variant calling (filters) - diffing nucleotide counts
Basic filtering happens on the command line with the --filter switch. To
support somewhat more advanced features the following features are
included.
When diffing nucleotide counts we want to find out which nucleotide defines
the tumor. The difference has to be larger than 0 and the relative difference
is the max. When a threshold is set only those nucleotides are included which
pass the threshold (i.e., no more than x supporting nucleotides in the
reference).
The advantage is that filtering is possible without actually looking at
the rec.alt and rec.ref values, i.e., no assumptions are being made
about the underlying nucleotides.
Scenario: Diffing nucleotide counts
Given normal and tumor counts [0,25,0,1] and [0,40,0,12]
When I look for the difference
Then I expect the diff to be [0,15,0,11]
And I expect the defining tumor nucleotide to be "T"
And I expect the tumor count to be 12
When I set an inclusion threshold for the reference
Then I expect the diff for threshold 2 to be [0,0,0,11]
And the relative diff to be [0,0,0,0.85]
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