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broadinstitute / catch

A package for designing compact and comprehensive capture probe sets.
MIT License
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Expose option to set `kmer_probe_map_k` parameter #16

Closed haydenm closed 6 years ago

haydenm commented 6 years ago

This adds a --kmer-probe-map-k argument, 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.

coveralls commented 6 years ago

Coverage Status

Coverage increased (+0.05%) to 94.787% when pulling f8b5a6c657e16f4d51a07e6161b35f8a38db101b on expose-kmer-probe-map-k into af7929e8d7c8155ae1e1aa2bf75115f7239dc22d on master.