Removed bulges and tips tehmselves from lists of corrections.

AntonBankevich · Nov 24, 2024 · 8701862 · 8701862
1 parent ad659b0
commit 8701862
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Showing 5 changed files with 22 additions and 14 deletions.
diff --git a/src/projects/error_correction/correction_utils.cpp b/src/projects/error_correction/correction_utils.cpp
@@ -76,7 +76,7 @@ namespace dbg {
                 }
             }
         }
-        return std::move(res);
+        return oneline::removeValue(res.begin(), res.end(), path);
     }
 
     GraphPath FindReliableExtension(Vertex &start, size_t len, double min_cov) {
@@ -153,7 +153,7 @@ namespace dbg {
                 }
             }
         }
-        return std::move(res);
+        return oneline::removeValue(res.begin(), res.end(), path);
     }
 
     GraphPath FindLongestCoveredForwardExtension(Edge &start, size_t max_size, double min_rel_cov, double max_err_cov) {
@@ -199,8 +199,9 @@ namespace dbg {
     }
 
     std::vector<GraphPath>
-    SuffixSupportedBulgeAlternatives(const ag::SuffixTracker<DBGTraits> &tracker, Vertex &start, Vertex &end, size_t threshold) {
-//        lock();
+    SuffixSupportedBulgeAlternatives(const ag::SuffixTracker<DBGTraits> &tracker, const GraphPath &bulge, size_t threshold) {
+        Vertex &start = bulge.getStart();
+        Vertex &end = bulge.getFinish();
         std::vector<std::pair<Sequence, int>> candidates;
         for(Edge &first_edge : start) {
             if(first_edge.getFinish() == end) {
@@ -236,7 +237,7 @@ namespace dbg {
             }
             cnt += candidates[i].second;
         }
-        return std::move(res);
+        return oneline::removeValue(res.begin(), res.end(), bulge);
     }
 
     EdgeId SuffixSupportedExtension(const ag::SuffixRecord<DBGTraits> &record, const GraphPath &start, size_t min_good,
@@ -278,7 +279,9 @@ namespace dbg {
     }
 
     std::vector<GraphPath>
-    SuffixSupportedTipAlternatives(const ag::SuffixTracker<DBGTraits> &tracker, Vertex &start, size_t len, double threshold) {
+    SuffixSupportedTipAlternatives(const ag::SuffixTracker<DBGTraits> &tracker, const GraphPath &tip, double threshold) {
+        Vertex &start = tip.getStart();
+        size_t len = tip.truncLen();
         len += std::max<size_t>(30, len / 20);
         std::vector<std::pair<Sequence, int>> candidates;
         for(Edge &first_edge : start) {
@@ -314,6 +317,6 @@ namespace dbg {
             }
             cnt += candidates[i].second;
         }
-        return std::move(res);
+        return oneline::removeValue(res.begin(), res.end(), tip);
     }
 }
diff --git a/src/projects/error_correction/correction_utils.hpp b/src/projects/error_correction/correction_utils.hpp
@@ -12,9 +12,9 @@ namespace dbg {
     GraphPath FindLongestCoveredForwardExtension(Edge &start, size_t max_len, double min_rel_cov, double max_err_cov);
     GraphPath FindLongestCoveredExtension(Edge &start, size_t max_len, double min_rel_cov, double max_err_cov);
 
-    std::vector<GraphPath> SuffixSupportedBulgeAlternatives(const ag::SuffixTracker<DBGTraits> &tracker, Vertex &start, Vertex &end, size_t threshold);
+    std::vector<GraphPath> SuffixSupportedBulgeAlternatives(const ag::SuffixTracker<DBGTraits> &tracker, const GraphPath &bulge, size_t threshold);
     EdgeId SuffixSupportedExtension(const ag::SuffixRecord<DBGTraits> &record, const GraphPath &start, size_t min_good, size_t max_bad);
     GraphPath FullSuffixSupportedExtension(const ag::SuffixRecord<DBGTraits> &record, GraphPath start, size_t min_good_cov,
                                         size_t max_bad_cov, size_t max_size = size_t(-1));
-    std::vector<GraphPath> SuffixSupportedTipAlternatives(const ag::SuffixTracker<DBGTraits> &record, Vertex &start, size_t len, double threshold);
+    std::vector<GraphPath> SuffixSupportedTipAlternatives(const ag::SuffixTracker<DBGTraits> &record, const GraphPath &tip, double threshold);
 }
diff --git a/src/projects/error_correction/manyk_correction.cpp b/src/projects/error_correction/manyk_correction.cpp
@@ -236,7 +236,7 @@ namespace dbg {
     dbg::GraphPath ManyKCorrector::correctBulgeByBridging(const ManyKCorrector::Bulge &bulge) const {
         VERIFY(bulge.bulge.truncLen() < K);
         std::vector<dbg::GraphPath> alternatives1 =
-                SuffixSupportedBulgeAlternatives(reads.getSuffixes(), bulge.bulge.getStart(), bulge.bulge.getFinish(), 4);
+                SuffixSupportedBulgeAlternatives(reads.getSuffixes(), bulge.bulge, 4);
         std::vector<dbg::GraphPath> alternatives;
         for (dbg::GraphPath &al: alternatives1) {
             if (al.truncLen() + 100 < bulge.bulge.truncLen() && bulge.bulge.truncLen() < al.truncLen() + 100)

diff --git a/src/projects/error_correction/tournament_correction.cpp b/src/projects/error_correction/tournament_correction.cpp
@@ -198,7 +198,7 @@ namespace dbg {
                 dbg::GraphPath tip = badPath.RC();
                 std::vector<dbg::GraphPath> alternatives;
                 if (checkTipSize(tip))
-                    alternatives = SuffixSupportedTipAlternatives(reads_storage.getSuffixes(), tip.getStart(), tip.truncLen(), threshold);
+                    alternatives = SuffixSupportedTipAlternatives(reads_storage.getSuffixes(), tip, threshold);
                 if (alternatives.empty())
                     alternatives = FindPlausibleTipAlternatives(tip, std::max<size_t>(size * 3 / 100, 100), 3);
                 std::string new_message = "";
@@ -216,7 +216,7 @@ namespace dbg {
                 dbg::GraphPath tip = badPath;
                 std::vector<dbg::GraphPath> alternatives;
                 if (checkTipSize(tip))
-                    alternatives = SuffixSupportedTipAlternatives(reads_storage.getSuffixes(), tip.getStart(), tip.truncLen(), threshold);
+                    alternatives = SuffixSupportedTipAlternatives(reads_storage.getSuffixes(), tip, threshold);
                 if (alternatives.empty())
                     alternatives = FindPlausibleTipAlternatives(tip, std::max<size_t>(size * 3 / 100, 100), 3);
                 std::string new_message = "";
@@ -232,7 +232,7 @@ namespace dbg {
                 std::string new_message = "br";
                 if (checkTipSize(badPath))
                     read_alternatives = SuffixSupportedBulgeAlternatives(reads_storage.getSuffixes(),
-                                                                         badPath.getStart(), badPath.getFinish(), threshold);
+                                                                         badPath, threshold);
                 if (read_alternatives.empty()) {
                     new_message = "bp";
                     read_alternatives = FindPlausibleBulgeAlternatives(badPath,
@@ -255,7 +255,7 @@ namespace dbg {
             path_pos = front_pos - 1;
         }
         if (!messages.empty()) {
-            VERIFY(path != corrected_path);
+            VERIFY_MSG(path != corrected_path, join("_", messages));
             path = std::move(corrected_path);
         }
         return join("_", messages);

diff --git a/src/tools/common/oneline_utils.hpp b/src/tools/common/oneline_utils.hpp
@@ -29,6 +29,11 @@ namespace oneline {
         return std::move(result);
     }
 
+    template<class V, class I>
+    std::vector<V> removeValue(I begin, I end, const V &to_remove) {
+        return filter<V, I>(begin, end, [&to_remove](const V &val){return val != to_remove;});
+    }
+
     template<class V, class C>
     C filter(const C&container, const std::function<bool(const V&)> &f) {
         return std::move(filter<V, typename C::const_iterator>(container.begin(), container.getFinish(), f));