Switch to multi-context seeds hash function

src/arguments.hpp

@@ -26,10 +26,11 @@ struct SeedingArguments {
             "results with non default values.", {'s'}}
         , bits{parser, "INT", "No. of top bits of hash to use as bucket indices (8-31)"
             "[determined from reference size]", {'b'}}
+        , aux_len{parser, "INT", "No. of bits to use from secondary strobe hash [24]", {"aux-len"}}
     {
     }
     args::ArgumentParser& parser;
-    args::ValueFlag<int> r, m, k, l, u, c, s, bits;
+    args::ValueFlag<int> r, m, k, l, u, c, s, bits, aux_len;
 };
 
 #endif

src/cmdline.cpp

@@ -119,6 +119,7 @@ CommandLineOptions parse_command_line_arguments(int argc, char **argv) {
     if (seeding.s) { opt.s = args::get(seeding.s); opt.s_set = true; }
     if (seeding.c) { opt.c = args::get(seeding.c); opt.c_set = true; }
     if (seeding.bits) { opt.bits = args::get(seeding.bits); }
+    if (seeding.aux_len) { opt.aux_len = args::get(seeding.aux_len); }
 
     // Alignment
     // if (n) { n = args::get(n); }

src/cmdline.hpp

@@ -52,6 +52,7 @@ struct CommandLineOptions {
     int u { 7 };
     int s { 16 };
     int c { 8 };
+    int aux_len{24};
 
     // Alignment
     int A { 2 };

src/dumpstrobes.cpp

@@ -101,7 +101,7 @@ int run_dumpstrobes(int argc, char **argv) {
     }
 
     // Seeding
-    int r{150}, k{20}, s{16}, c{8}, l{1}, u{7};
+    int r{150}, k{20}, s{16}, c{8}, l{1}, u{7}, aux_len{24};
     int max_seed_len{};
 
     bool k_set{false}, s_set{false}, c_set{false}, max_seed_len_set{false}, l_set{false}, u_set{false};
@@ -125,7 +125,8 @@ int run_dumpstrobes(int argc, char **argv) {
         l_set ? l : IndexParameters::DEFAULT,
         u_set ? u : IndexParameters::DEFAULT,
         c_set ? c : IndexParameters::DEFAULT,
-        max_seed_len_set ? max_seed_len : IndexParameters::DEFAULT
+        max_seed_len_set ? max_seed_len : IndexParameters::DEFAULT,
+        aux_len ? aux_len : IndexParameters::DEFAULT
     );
 
     logger.info() << index_parameters << '\n';

src/index.cpp

@@ -21,7 +21,7 @@
 #include <sstream>
 
 static Logger& logger = Logger::get();
-static const uint32_t STI_FILE_FORMAT_VERSION = 2;
+static const uint32_t STI_FILE_FORMAT_VERSION = 3;
 
 
 namespace {
@@ -304,7 +304,7 @@ void StrobemerIndex::assign_randstrobes(size_t ref_index, size_t offset) {
             chunk.push_back(randstrobe);
         }
         for (auto randstrobe : chunk) {
-            RefRandstrobe::packed_t packed = ref_index << 8;
+            RefRandstrobe::packed_t packed = (ref_index << 9) | (randstrobe.main_is_first << 8);
             packed = packed + (randstrobe.strobe2_pos - randstrobe.strobe1_pos);
             randstrobes[offset++] = RefRandstrobe{randstrobe.hash, randstrobe.strobe1_pos, packed};
         }

src/indexparameters.cpp

@@ -18,7 +18,8 @@ bool RandstrobeParameters::operator==(const RandstrobeParameters& other) const {
         && this->q == other.q
         && this->max_dist == other.max_dist
         && this->w_min == other.w_min
-        && this->w_max == other.w_max;
+        && this->w_max == other.w_max
+        && this->aux_len == other.aux_len;
 }
 
 /* Pre-defined index parameters that work well for a certain
@@ -48,7 +49,7 @@ static std::vector<Profile> profiles = {
  * k, s, l, u, c and max_seed_len can be used to override determined parameters
  * by setting them to a value other than IndexParameters::DEFAULT.
  */
-IndexParameters IndexParameters::from_read_length(int read_length, int k, int s, int l, int u, int c, int max_seed_len) {
+IndexParameters IndexParameters::from_read_length(int read_length, int k, int s, int l, int u, int c, int max_seed_len, int aux_len) {
     const int default_c = 8;
     size_t canonical_read_length = 50;
     for (const auto& p : profiles) {
@@ -78,8 +79,11 @@ IndexParameters IndexParameters::from_read_length(int read_length, int k, int s,
         max_dist = max_seed_len - k; // convert to distance in start positions
     }
     int q = std::pow(2, c == DEFAULT ? default_c : c) - 1;
+    if (aux_len == DEFAULT) {
+        aux_len = 24;
+    }
 
-    return IndexParameters(canonical_read_length, k, s, l, u, q, max_dist);
+    return IndexParameters(canonical_read_length, k, s, l, u, q, max_dist, aux_len);
 }
 
 void IndexParameters::write(std::ostream& os) const {
@@ -90,6 +94,7 @@ void IndexParameters::write(std::ostream& os) const {
     write_int_to_ostream(os, randstrobe.u);
     write_int_to_ostream(os, randstrobe.q);
     write_int_to_ostream(os, randstrobe.max_dist);
+    write_int_to_ostream(os, randstrobe.aux_len);
 }
 
 IndexParameters IndexParameters::read(std::istream& is) {
@@ -100,7 +105,8 @@ IndexParameters IndexParameters::read(std::istream& is) {
     int u = read_int_from_istream(is);
     int q = read_int_from_istream(is);
     int max_dist = read_int_from_istream(is);
-    return IndexParameters(canonical_read_length, k, s, l, u, q, max_dist);
+    int aux_len = read_int_from_istream(is);
+    return IndexParameters(canonical_read_length, k, s, l, u, q, max_dist, aux_len);
 }
 
 bool IndexParameters::operator==(const IndexParameters& other) const {

src/indexparameters.hpp

@@ -43,14 +43,16 @@ struct RandstrobeParameters {
     const int max_dist;
     const unsigned w_min;
     const unsigned w_max;
+    const unsigned aux_len;
 
-    RandstrobeParameters(int l, int u, uint64_t q, int max_dist, unsigned w_min, unsigned w_max)
+    RandstrobeParameters(int l, int u, uint64_t q, int max_dist, unsigned w_min, unsigned w_max, unsigned aux_len)
         : l(l)
         , u(u)
         , q(q)
         , max_dist(max_dist)
         , w_min(w_min)
         , w_max(w_max)
+        , aux_len(aux_len)
     {
         verify();
     }
@@ -65,6 +67,9 @@ struct RandstrobeParameters {
         if (w_min > w_max) {
             throw BadParameter("w_min is greater than w_max (choose different -l/-u parameters)");
         }
+        if (aux_len > 63) {
+            throw BadParameter("aux_len is larger than 63");
+        }
     }
 };
 
@@ -77,16 +82,15 @@ class IndexParameters {
 
     static const int DEFAULT = std::numeric_limits<int>::min();
 
-    IndexParameters(size_t canonical_read_length, int k, int s, int l, int u, int q, int max_dist)
+    IndexParameters(size_t canonical_read_length, int k, int s, int l, int u, int q, int max_dist, int aux_len)
         : canonical_read_length(canonical_read_length)
         , syncmer(k, s)
-        , randstrobe(l, u, q, max_dist, std::max(0, k / (k - s + 1) + l), k / (k - s + 1) + u)
+        , randstrobe(l, u, q, max_dist, std::max(0, k / (k - s + 1) + l), k / (k - s + 1) + u, aux_len)
     {
     }
 
     static IndexParameters from_read_length(
-        int read_length, int k = DEFAULT, int s = DEFAULT, int l = DEFAULT, int u = DEFAULT, int c = DEFAULT, int max_seed_len = DEFAULT
-    );
+        int read_length, int k = DEFAULT, int s = DEFAULT, int l = DEFAULT, int u = DEFAULT, int c = DEFAULT, int max_seed_len = DEFAULT, int aux_len = DEFAULT);
     static IndexParameters read(std::istream& os);
     std::string filename_extension() const;
     void write(std::ostream& os) const;

src/main.cpp

@@ -179,7 +179,8 @@ int run_strobealign(int argc, char **argv) {
         opt.l_set ? opt.l : IndexParameters::DEFAULT,
         opt.u_set ? opt.u : IndexParameters::DEFAULT,
         opt.c_set ? opt.c : IndexParameters::DEFAULT,
-        opt.max_seed_len_set ? opt.max_seed_len : IndexParameters::DEFAULT
+        opt.max_seed_len_set ? opt.max_seed_len : IndexParameters::DEFAULT,
+        opt.aux_len ? opt.aux_len : IndexParameters::DEFAULT
     );
     logger.debug() << index_parameters << '\n';
     AlignmentParameters aln_params;
@@ -228,6 +229,7 @@ int run_strobealign(int argc, char **argv) {
         throw InvalidFasta("Too many reference sequences. Current maximum is " + std::to_string(RefRandstrobe::max_number_of_references));
     }
 
+    logger.debug() << "Auxiliary hash length: " << index_parameters.randstrobe.aux_len << "\n";
     StrobemerIndex index(references, index_parameters, opt.bits);
     if (opt.use_index) {
         // Read the index from a file

src/randstrobes.cpp

@@ -45,8 +45,12 @@ static inline syncmer_hash_t syncmer_smer_hash(uint64_t packed) {
     return xxh64(packed);
 }
 
-static inline randstrobe_hash_t randstrobe_hash(syncmer_hash_t hash1, syncmer_hash_t hash2) {
-    return hash1 + hash2;
+static inline randstrobe_hash_t randstrobe_hash(syncmer_hash_t hash1, syncmer_hash_t hash2, size_t aux_len) {
+    // Make the function symmetric
+    if (hash1 > hash2) {
+        std::swap(hash1, hash2);
+    }
+    return ((hash1 >> aux_len) << aux_len) ^ (hash2 >> (64 - aux_len));
 }
 
 std::ostream& operator<<(std::ostream& os, const Syncmer& syncmer) {
@@ -131,7 +135,8 @@ std::vector<Syncmer> canonical_syncmers(
 }
 
 std::ostream& operator<<(std::ostream& os, const Randstrobe& randstrobe) {
-    os << "Randstrobe(hash=" << randstrobe.hash << ", strobe1_pos=" << randstrobe.strobe1_pos << ", strobe2_pos=" << randstrobe.strobe2_pos << ")";
+    os << "Randstrobe(hash=" << randstrobe.hash << ", strobe1_pos=" << randstrobe.strobe1_pos << ", strobe2_pos="
+       << randstrobe.strobe2_pos << ", main_is_first=" << randstrobe.main_is_first << ")";
     return os;
 }
 
@@ -145,11 +150,13 @@ std::ostream& operator<<(std::ostream& os, const QueryRandstrobe& randstrobe) {
     return os;
 }
 
-Randstrobe make_randstrobe(Syncmer strobe1, Syncmer strobe2) {
+Randstrobe make_randstrobe(Syncmer strobe1, Syncmer strobe2, int aux_len) {
+    bool main_is_first = strobe1.hash < strobe2.hash;
     return Randstrobe{
-        randstrobe_hash(strobe1.hash, strobe2.hash),
+        randstrobe_hash(strobe1.hash, strobe2.hash, aux_len),
         static_cast<uint32_t>(strobe1.position),
-        static_cast<uint32_t>(strobe2.position)
+        static_cast<uint32_t>(strobe2.position),
+        main_is_first
     };
 }
 
@@ -175,7 +182,7 @@ Randstrobe RandstrobeIterator::get(unsigned int strobe1_index) const {
         }
     }
 
-    return make_randstrobe(strobe1, strobe2);
+    return make_randstrobe(strobe1, strobe2, aux_len);
 }
 
 Randstrobe RandstrobeGenerator::next() {
@@ -207,7 +214,7 @@ Randstrobe RandstrobeGenerator::next() {
     }
     syncmers.pop_front();
 
-    return make_randstrobe(strobe1, strobe2);
+    return make_randstrobe(strobe1, strobe2, aux_len);
 }
 
 /*

src/randstrobes.hpp

@@ -39,8 +39,12 @@ struct RefRandstrobe {
         return lhs < rhs;
     }
 
+    bool main_is_first() const {
+        return (m_packed >> bit_alloc) & 1;
+    }
+
     int reference_index() const {
-        return m_packed >> bit_alloc;
+        return m_packed >> (bit_alloc + 1);
     }
 
     int strobe2_offset() const {
@@ -54,7 +58,7 @@ struct RefRandstrobe {
     packed_t m_packed; // packed representation of ref_index and strobe offset
 
 public:
-    static constexpr uint32_t max_number_of_references = (1 << (32 - bit_alloc)) - 1;
+    static constexpr uint32_t max_number_of_references = (1 << (32 - bit_alloc - 1)) - 1; // bit_alloc - 1 because 1 bit to main_is_first()
 };
 
 struct QueryRandstrobe {
@@ -74,6 +78,7 @@ struct Randstrobe {
     randstrobe_hash_t hash;
     unsigned int strobe1_pos;
     unsigned int strobe2_pos;
+    bool main_is_first;
 
     bool operator==(const Randstrobe& other) const {
         return hash == other.hash && strobe1_pos == other.strobe1_pos && strobe2_pos == other.strobe2_pos;
@@ -107,6 +112,7 @@ class RandstrobeIterator {
       , w_max(parameters.w_max)
       , q(parameters.q)
       , max_dist(parameters.max_dist)
+      , aux_len(parameters.aux_len)
     {
         if (w_min > w_max) {
             throw std::invalid_argument("w_min is greater than w_max");
@@ -128,7 +134,8 @@ class RandstrobeIterator {
     const unsigned w_max;
     const uint64_t q;
     const unsigned int max_dist;
-    unsigned int strobe1_index = 0;
+    const unsigned int aux_len;
+    unsigned strobe1_index = 0;
 };
 
 std::ostream& operator<<(std::ostream& os, const Syncmer& syncmer);
@@ -176,17 +183,19 @@ class RandstrobeGenerator {
       , w_max(randstrobe_parameters.w_max)
       , q(randstrobe_parameters.q)
       , max_dist(randstrobe_parameters.max_dist)
+      , aux_len(randstrobe_parameters.aux_len)
     { }
 
     Randstrobe next();
-    Randstrobe end() const { return Randstrobe{0, 0, 0}; }
+    Randstrobe end() const { return Randstrobe{0, 0, 0, false}; }
 
 private:
     SyncmerIterator syncmer_iterator;
     const unsigned w_min;
     const unsigned w_max;
     const uint64_t q;
     const unsigned int max_dist;
+    const unsigned int aux_len;
     std::deque<Syncmer> syncmers;
 };