Expose option to set kmer_probe_map_k parameter
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The two different tests mistakenly had the same name.
This provides varied values of the k-mer length used to construct a map of k-mers to probes. Each of these maps (for each k) is then used to test the probe.find_probe_covers_in_sequence() function.
This parameter specifies the k-mer length used when constructing a map of k-mers to probes. (In particular, CATCH tries to determine a suitable k-mer length using this value as a lower bound; if it cannot, it takes a randomized approach and uses this value as the k-mer length.) This is useful when designing short probes (e.g., meant to be primers), in which case the default k-mer length may be too short relative to the probe to find mappings of the probes to the target sequence.
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This adds a
--kmer-probe-map-kargument, which specifies the k-mer length used when constructing a map of k-mers to probes. (In particular, CATCH tries to determine a suitable k-mer length using this value as a lower bound; if it cannot, it takes a randomized approach and uses this value as the k-mer length.)This is useful when designing short probes (e.g., meant to be primers), in which case the default k-mer length may be too short relative to the probe to find mappings of the probes to the target sequence.