Allow adding lowercase sequences (#480)

sourmash-bio · May 27, 2018 · 06ffeac · 06ffeac
1 parent 26cafa1
commit 06ffeac
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Showing 2 changed files with 16 additions and 1 deletion.
diff --git a/sourmash/kmer_min_hash.hh b/sourmash/kmer_min_hash.hh
@@ -122,7 +122,9 @@ public:
         if (strlen(sequence) < ksize) {
             return;
         }
-        const std::string seq = sequence;
+        std::string seq = sequence;
+        transform(seq.begin(), seq.end(), seq.begin(), ::toupper);
+
         if (!is_protein) {
             for (unsigned int i = 0; i < seq.length() - ksize + 1; i++) {
                 const std::string kmer = seq.substr(i, ksize);

diff --git a/tests/test__minhash.py b/tests/test__minhash.py
@@ -233,6 +233,19 @@ def test_basic_dna_bad_force_2(track_abundance):
     assert len(mh.get_mins()) == 2       # (only 2 hashes should be there)
 
 
+def test_consume_lowercase(track_abundance):
+    a = MinHash(20, 10, track_abundance=track_abundance)
+    b = MinHash(20, 10, track_abundance=track_abundance)
+
+    a.add_sequence('TGCCGCCCAGCACCGGGTGACTAGGTTGAGCCATGATTAACCTGCAATGA'.lower())
+    b.add_sequence('TGCCGCCCAGCACCGGGTGACTAGGTTGAGCCATGATTAACCTGCAATGA')
+
+    assert a.compare(b) == 1.0
+    assert b.compare(b) == 1.0
+    assert b.compare(a) == 1.0
+    assert a.compare(a) == 1.0
+
+
 def test_compare_1(track_abundance):
     a = MinHash(20, 10, track_abundance=track_abundance)
     b = MinHash(20, 10, track_abundance=track_abundance)