sshash with checking for cfseg supported

jermp · Jul 26, 2024 · a5b662a · a5b662a
1 parent 691e26a
commit a5b662a
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Showing 2 changed files with 14 additions and 16 deletions.
diff --git a/src/build.cpp b/src/build.cpp
@@ -99,11 +99,11 @@ int build(int argc, char** argv) {
     bool check = parser.get<bool>("check");
     if (check) {
         check_correctness_lookup_access(dict, input_filename, fmt);
-        // check_correctness_navigational_kmer_query(dict, input_filename, fmt);
-        // check_correctness_navigational_contig_query(dict);
-        // if (build_config.weighted) check_correctness_weights(dict, input_filename);
-        // check_correctness_kmer_iterator(dict);
-        // check_correctness_contig_iterator(dict);
+        check_correctness_navigational_kmer_query(dict, input_filename, fmt);
+        check_correctness_navigational_contig_query(dict);
+        if (build_config.weighted) check_correctness_weights(dict, input_filename);
+        check_correctness_kmer_iterator(dict);
+        check_correctness_contig_iterator(dict);
     }
     bool bench = parser.get<bool>("bench");
     if (bench) {

diff --git a/src/check_utils.hpp b/src/check_utils.hpp
@@ -38,10 +38,10 @@ bool check_correctness_lookup_access(std::istream& is, dictionary const& dict, s
     std::string expected_kmer_str(k, 0);
 
     std::cout << "checking correctness of access and positive lookup..." << std::endl;
+
     while (appendline(is, line)) {
-        // std::getline(is, line);
+        sequence.clear();
         if (fmt == "fasta") {
-            std::cout << "pos " << line[0] << std::endl;
             if (line.size() == pos || line[pos] == '>' || line[pos] == ';') {
             // comment or empty line restart the term buffer
                 line.clear();
@@ -62,7 +62,6 @@ bool check_correctness_lookup_access(std::istream& is, dictionary const& dict, s
                            [](char c) { return std::tolower(c); });
         }
         ++num_lines;
-        std::cout << "seq " << sequence << std::endl;
         for (uint64_t i = 0; i + k <= sequence.size(); ++i) {
             assert(util::is_valid(sequence.data() + i, k));
 
@@ -172,9 +171,9 @@ bool check_correctness_lookup_access(std::istream& is, dictionary const& dict, s
             ++num_kmers;
     }
         if (sequence.size() > k - 1) {
-            std::copy(sequence.data() + sequence.size() - (k - 1), sequence.data() + sequence.size(), sequence.data());
-            sequence.resize(k - 1);
-            pos = sequence.size();
+            std::copy(line.data() + line.size() - (k - 1), line.data() + line.size(), line.data());
+            line.resize(k - 1);
+            pos = line.size();
         } else {
             pos = 0;
         }
@@ -195,7 +194,7 @@ bool check_correctness_navigational_kmer_query(std::istream& is,
     std::string sequence;
 
     std::cout << "checking correctness of navigational queries for kmers..." << std::endl;
-    while (!is.eof()) {
+    while (appendline(is, line)) {
         std::getline(is, line);
         if (fmt == "fasta") {
             if (line.size() == pos || line[pos] == '>' || line[pos] == ';') {
@@ -279,9 +278,9 @@ bool check_correctness_navigational_kmer_query(std::istream& is,
             ++num_kmers;
         }
         if (sequence.size() > k - 1) {
-            std::copy(sequence.data() + sequence.size() - (k - 1), sequence.data() + sequence.size(), sequence.data());
-            sequence.resize(k - 1);
-            pos = sequence.size();
+            std::copy(line.data() + line.size() - (k - 1), line.data() + line.size(), line.data());
+            line.resize(k - 1);
+            pos = line.size();
         } else {
             pos = 0;
         }
@@ -344,7 +343,6 @@ bool check_correctness_weights(std::istream& is, dictionary const& dict) {
 
     while (!is.eof()) {
         std::getline(is, line);  // header line
-        std::cout << "line is " << line << std::endl;
 
         if (line.empty()) break;