Add dumpstrobes --seeds option for writing out the full seed vector

src/dumpstrobes.cpp

@@ -78,12 +78,17 @@ int run_dumpstrobes(int argc, char **argv) {
 
     args::HelpFlag help(parser, "help", "Print help and exit", {'h', "help"});
     args::Flag syncmers(parser, "syncmers", "Dump syncmers instead of randstrobes", {"syncmers"});
+    args::Flag seeds(parser, "seeds", "Dump sorted seed vector (format: hash, position, ref_index, strobe2_offset)", {"seeds"});
     args::Flag count(parser, "count", "Count only", {"count"});
+    args::ValueFlag<int> threads(parser, "INT", "Number of threads [8]", {'t', "threads"});
     auto seeding = SeedingArguments{parser};
     args::Positional<std::string> ref_filename(parser, "reference", "Reference in FASTA format", args::Options::Required);
 
     try {
         parser.ParseCLI(argc, argv);
+        if ((seeds && syncmers) || (seeds && count)) {
+            throw args::Error("Cannot combine --seeds with --syncmers or --count");
+        }
     }
     catch (const args::Help&) {
         std::cout << parser;
@@ -148,6 +153,16 @@ int run_dumpstrobes(int argc, char **argv) {
             }
         }
         std::cout << n << std::endl;
+    } else if (seeds) {
+        float top_filter_fraction = 0.0002;
+        int bits = -1;  // autodetermine
+        int n_threads = threads ? args::get(threads) : 8;
+        StrobemerIndex index(references, index_parameters, bits);
+        index.populate(top_filter_fraction, n_threads);
+        for (size_t i = 0; i < index.size(); ++i) {
+            auto rs = index.get_randstrobe(i);
+            std::cout << rs.hash << "," << rs.position << "," << rs.reference_index() << "," << rs.strobe2_offset() << '\n';
+        }
     } else {
         for (size_t i = 0; i < references.size(); ++i) {
             auto& seq = references.sequences[i];

src/index.cpp

@@ -22,6 +22,54 @@
 static Logger& logger = Logger::get();
 static const uint32_t STI_FILE_FORMAT_VERSION = 2;
 
+
+namespace {
+
+uint64_t count_randstrobes(const std::string& seq, const IndexParameters& parameters) {
+    uint64_t n_syncmers = 0;
+    SyncmerIterator syncmer_iterator(seq, parameters.syncmer);
+    Syncmer syncmer;
+    while (!(syncmer = syncmer_iterator.next()).is_end()) {
+        n_syncmers++;
+    }
+    // The last w_min syncmers do not result in a randstrobe
+    if (n_syncmers < parameters.randstrobe.w_min) {
+        return 0;
+    } else {
+        return n_syncmers - parameters.randstrobe.w_min;
+    }
+}
+
+std::vector<uint64_t> count_all_randstrobes(const References& references, const IndexParameters& parameters, size_t n_threads) {
+    std::vector<std::thread> workers;
+    std::atomic_size_t ref_index{0};
+
+    std::vector<uint64_t> counts;
+    counts.assign(references.size(), 0);
+
+    for (size_t i = 0; i < n_threads; ++i) {
+        workers.push_back(
+            std::thread(
+                [&ref_index](const References& references, const IndexParameters& parameters, std::vector<uint64_t>& counts) {
+                    while (true) {
+                        size_t j = ref_index.fetch_add(1);
+                        if (j >= references.size()) {
+                            break;
+                        }
+                        counts[j] = count_randstrobes(references.sequences[j], parameters);
+                    }
+                }, std::ref(references), std::ref(parameters), std::ref(counts))
+        );
+    }
+    for (auto& worker : workers) {
+        worker.join();
+    }
+
+    return counts;
+}
+
+}
+
 void StrobemerIndex::write(const std::string& filename) const {
     std::ofstream ofs(filename, std::ios::binary);
 
@@ -90,49 +138,6 @@ int StrobemerIndex::pick_bits(size_t size) const {
     return std::clamp(static_cast<int>(log2(estimated_number_of_randstrobes)) - 1, 8, 31);
 }
 
-uint64_t count_randstrobes(const std::string& seq, const IndexParameters& parameters) {
-    uint64_t n_syncmers = 0;
-    SyncmerIterator syncmer_iterator(seq, parameters.syncmer);
-    Syncmer syncmer;
-    while (!(syncmer = syncmer_iterator.next()).is_end()) {
-        n_syncmers++;
-    }
-    // The last w_min syncmers do not result in a randstrobe
-    if (n_syncmers < parameters.randstrobe.w_min) {
-        return 0;
-    } else {
-        return n_syncmers - parameters.randstrobe.w_min;
-    }
-}
-
-std::vector<uint64_t> count_all_randstrobes(const References& references, const IndexParameters& parameters, size_t n_threads) {
-    std::vector<std::thread> workers;
-    std::atomic_size_t ref_index{0};
-
-    std::vector<uint64_t> counts;
-    counts.assign(references.size(), 0);
-
-    for (size_t i = 0; i < n_threads; ++i) {
-        workers.push_back(
-            std::thread(
-                [&ref_index](const References& references, const IndexParameters& parameters, std::vector<uint64_t>& counts) {
-                    while (true) {
-                        size_t j = ref_index.fetch_add(1);
-                        if (j >= references.size()) {
-                            break;
-                        }
-                        counts[j] = count_randstrobes(references.sequences[j], parameters);
-                    }
-                }, std::ref(references), std::ref(parameters), std::ref(counts))
-        );
-    }
-    for (auto& worker : workers) {
-        worker.join();
-    }
-
-    return counts;
-}
-
 void StrobemerIndex::populate(float f, size_t n_threads) {
     Timer count_hash;
     auto randstrobe_counts = count_all_randstrobes(references, parameters, n_threads);

src/index.hpp

@@ -104,6 +104,14 @@ struct StrobemerIndex {
         return randstrobes[position].reference_index();
     }
 
+    RefRandstrobe get_randstrobe(bucket_index_t position) const {
+        return randstrobes[position];
+    }
+
+    size_t size() const {
+        return randstrobes.size();
+    }
+
     unsigned int get_count(bucket_index_t position) const {
         // For 95% of cases, the result will be small and a brute force search
         // is the best option. Once, we go over MAX_LINEAR_SEARCH, though, we