variant calling prototype

vgl-hub · Jul 4, 2024 · 12b75da · 12b75da
1 parent 3fd24eb
commit 12b75da
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Showing 6 changed files with 450 additions and 534 deletions.
diff --git a/Makefile b/Makefile
@@ -19,7 +19,7 @@ LDFLAGS := -pthread
 #gfalibs
 GFALIBS_DIR := $(CURDIR)/gfalibs
 
-SOURCES := main input graph-builder kreeq subgraph kreeq-output
+SOURCES := main input graph-builder kreeq subgraph kreeq-output variants
 OBJECTS := $(addprefix $(BINDIR)/, $(SOURCES))
 
 head: $(OBJECTS) gfalibs | $(BUILD)

diff --git a/include/kreeq.h b/include/kreeq.h
@@ -209,7 +209,7 @@ class DBG : public Kmap<DBG, UserInputKreeq, uint64_t, DBGkmer, DBGkmer32> { //
 
     void printVCF();
 
-    bool searchGraph(std::array<uint16_t, 2> mapRange);
+    void searchGraph();
 
     std::pair<DBGkmer*,bool> findDBGkmer(uint8_t *origin);
 
@@ -229,6 +229,8 @@ class DBG : public Kmap<DBG, UserInputKreeq, uint64_t, DBGkmer, DBGkmer32> { //
 
     bool DBGtoVariants(InSegment *inSegment);
 
+    std::pair<bool,std::deque<DBGpath>> searchVariants(std::pair<const uint64_t,DBGkmer32> source, std::array<uint16_t, 2> mapRange, phmap::parallel_flat_hash_map<uint64_t,bool> &targetsMap, ParallelMap32* localGraphCache);
+
     bool variantsToGFA(InSegment *inSegment, Log &threadLog);
 
     void collapseNodes();

diff --git a/include/variants.h b/include/variants.h
@@ -0,0 +1,5 @@
+#ifndef variants_h
+#define variants_h
+
+
+#endif /* variants_h */
diff --git a/src/input.cpp b/src/input.cpp
@@ -167,6 +167,14 @@ void Input::read() {
                 knav.loadGenome(&genome);
             }
             knav.subgraph();
+
+            lg.verbose("Searching graph");
+            knav.searchGraph();
+            lg.verbose("Remove missing edges");
+            knav.removeMissingEdges();
+            lg.verbose("Generating GFA");
+            knav.DBGgraphToGFA();
+
             knav.report(); // output
             knav.cleanup(); // delete tmp files
             break;