Merge pull request #8 from seqan/kmer_default

[FIX] If k-mer length not given explicitly then calculate from pigeonhole lemma
seqan · May 10, 2023 · 39f3e29 · 39f3e29
2 parents c4280f7 + 5e1c59c
commit 39f3e29
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diff --git a/include/stellar/options/index_options.hpp b/include/stellar/options/index_options.hpp
@@ -8,7 +8,7 @@ namespace stellar
 
 struct IndexOptions
 {
-    size_t qGram{32}; // length of the q-grams
+    size_t qGram{std::numeric_limits<size_t>::max()}; // length of the q-grams
     double qgramAbundanceCut{1};
 };
 

diff --git a/include/stellar/stellar_types.hpp b/include/stellar/stellar_types.hpp
@@ -72,7 +72,7 @@ struct StellarStatistics
         assert(options.epsilon.numerator() == 0 || StellarOptions::absoluteErrors(options.epsilon, n1) == e1);
 
         kMerLength = options.qGram;
-        kMerComputed = options.qGram == (unsigned)-1;
+        kMerComputed = options.qGram == (size_t)-1;
 
         if (kMerComputed)
             kMerLength = std::min(std::max(1u, smin), 32u);