fix compilation errors

include/buckets.hpp

@@ -215,7 +215,7 @@ struct buckets {
                 m_clear = false;
                 m_read_kmer.drop_char();
                 m_last_char = m_bv_it.get_next_char();
-                read_kmer.kth_char_or(m_k - 1, m_last_char);
+                m_read_kmer.kth_char_or(m_k - 1, m_last_char);
                 ++m_begin_kmer_id;
                 ++m_offset;
                 return m_ret;

include/kmer.hpp

@@ -93,8 +93,8 @@ constexpr char nucleotides[] = "ACTG";
 #endif
 
 template <typename Kmer>
-struct dna_uint_kmer_t : alpha_kmer_t<Kmer, 2, dna_alphabet> {
-    using base = alpha_kmer_t<Kmer, 2, dna_alphabet>;
+struct dna_uint_kmer_t : alpha_kmer_t<Kmer, 2, nucleotides> {
+    using base = alpha_kmer_t<Kmer, 2, nucleotides>;
     using base::uint_kmer_bits;
     using base::bits_per_char;
     using base::max_k;
@@ -149,7 +149,7 @@ struct dna_uint_kmer_t : alpha_kmer_t<Kmer, 2, dna_alphabet> {
     g    103     01100111 -> 10
     t    116     01110100 -> 11
     */
-    static inline uint64_t char_to_uint(char c) { return (((c >> 1) ^ (c >> 2)) & 3); }
+    static uint64_t char_to_uint(char c) { return (((c >> 1) ^ (c >> 2)) & 3); }
 #else
     /*
     char decimal  binary

src/check_utils.hpp

@@ -434,7 +434,8 @@ bool check_correctness_kmer_iterator(dictionary<kmer_t> const& dict) {
     return true;
 }
 
-bool check_correctness_contig_iterator(dictionary const& dict) {
+template<class kmer_t>
+bool check_correctness_contig_iterator(dictionary<kmer_t> const& dict) {
     std::cout << "checking correctness of contig iterator..." << std::endl;
     std::string expected_kmer(dict.k(), 0);
     for (uint64_t contig_id = 0; contig_id != dict.num_contigs(); ++contig_id) {

test/test_alphabet.cpp

@@ -25,8 +25,8 @@ int main(int argc, char** argv) {
         return 1;
     }
     uint64_t k = std::stoull(argv[1]);
-    if (k > constants::max_k) {
-        std::cerr << "k must be less <= " << constants::max_k << " but got k = " << k << '\n';
+    if (k > kmer_t::max_k) {
+        std::cerr << "k must be less <= " << kmer_t::max_k << " but got k = " << k << '\n';
         return 1;
     }
     std::string read(
@@ -54,23 +54,23 @@ int main(int argc, char** argv) {
     /****/
 
 #ifdef SSHASH_USE_TRADITIONAL_NUCLEOTIDE_ENCODING
-    expect(kmer_t::char_to_int('A'), kmer_t(0));
-    expect(kmer_t::char_to_int('a'), kmer_t(0));
-    expect(kmer_t::char_to_int('C'), kmer_t(1));
-    expect(kmer_t::char_to_int('c'), kmer_t(1));
-    expect(kmer_t::char_to_int('G'), kmer_t(2));
-    expect(kmer_t::char_to_int('g'), kmer_t(2));
-    expect(kmer_t::char_to_int('T'), kmer_t(3));
-    expect(kmer_t::char_to_int('t'), kmer_t(3));
+    expect(kmer_t::char_to_uint('A'), 0);
+    expect(kmer_t::char_to_uint('a'), 0);
+    expect(kmer_t::char_to_uint('C'), 1);
+    expect(kmer_t::char_to_uint('c'), 1);
+    expect(kmer_t::char_to_uint('G'), 2);
+    expect(kmer_t::char_to_uint('g'), 2);
+    expect(kmer_t::char_to_uint('T'), 3);
+    expect(kmer_t::char_to_uint('t'), 3);
 #else
-    expect(kmer_t::char_to_int('A'), kmer_t(0));
-    expect(kmer_t::char_to_int('a'), kmer_t(0));
-    expect(kmer_t::char_to_int('C'), kmer_t(1));
-    expect(kmer_t::char_to_int('c'), kmer_t(1));
-    expect(kmer_t::char_to_int('T'), kmer_t(2));
-    expect(kmer_t::char_to_int('t'), kmer_t(2));
-    expect(kmer_t::char_to_int('G'), kmer_t(3));
-    expect(kmer_t::char_to_int('g'), kmer_t(3));
+    expect(kmer_t::char_to_uint('A'), 0);
+    expect(kmer_t::char_to_uint('a'), 0);
+    expect(kmer_t::char_to_uint('C'), 1);
+    expect(kmer_t::char_to_uint('c'), 1);
+    expect(kmer_t::char_to_uint('T'), 2);
+    expect(kmer_t::char_to_uint('t'), 2);
+    expect(kmer_t::char_to_uint('G'), 3);
+    expect(kmer_t::char_to_uint('g'), 3);
 #endif
 
     for (uint64_t kmer_len = 1; kmer_len <= k; ++kmer_len) {
@@ -80,10 +80,10 @@ int main(int argc, char** argv) {
         for (uint64_t i = 0; i != 1000; ++i) {
             // generate a random kmer of length kmer_len
             random_kmer(kmer.data(), kmer_len);
-            kmer_t::compute_reverse_complement(kmer.data(), rc.data(), kmer_len);
-            kmer_t uint_kmer = kmer_t::string_to_uint_kmer(kmer.data(), kmer_len);
-            uint_kmer = kmer_t::compute_reverse_complement(uint_kmer, kmer_len);
-            expect(kmer_t::uint_kmer_to_string(uint_kmer, kmer_len), rc);
+            util::compute_reverse_complement(kmer.data(), rc.data(), kmer_len);
+            kmer_t uint_kmer = util::string_to_uint_kmer<kmer_t>(kmer.data(), kmer_len);
+            uint_kmer = uint_kmer.reverse_complement(kmer_len);
+            expect(util::uint_kmer_to_string(uint_kmer, kmer_len), rc);
         }
     }